Nickel in PDB 4ueq: Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
Enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
All present enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;
Protein crystallography data
The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq
was solved by
A.Volbeda,
L.Martin,
P.-P.Liebgott,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
20.00 /
1.70
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.720,
99.800,
190.800,
90.21,
98.61,
90.11
|
|
R / Rfree (%)
|
13.659 /
18.539
|
Other elements in 4ueq:
The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Nickel atom in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
(pdb code 4ueq). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the
Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 1 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ni1551
b:16.6
occ:0.44
|
NI
|
Q:NI1551
|
0.0
|
16.6
|
0.4
|
|
O
|
Q:HOH2066
|
1.4
|
14.8
|
0.1
|
|
SD
|
Q:CYS543
|
1.5
|
13.1
|
0.2
|
|
S
|
Q:H2S1552
|
1.5
|
14.4
|
0.2
|
|
O
|
Q:HOH2068
|
1.9
|
16.2
|
0.4
|
|
NI
|
Q:NI1551
|
1.9
|
14.3
|
0.6
|
|
SG
|
Q:CYS543
|
2.2
|
16.4
|
0.8
|
|
SG
|
Q:CYS72
|
2.3
|
14.8
|
0.4
|
|
SG
|
Q:CYS72
|
2.3
|
16.3
|
0.4
|
|
SG
|
Q:CYS72
|
2.4
|
14.4
|
0.1
|
|
SG
|
Q:CYS75
|
2.5
|
13.7
|
1.0
|
|
SG
|
Q:CYS546
|
2.6
|
15.5
|
1.0
|
|
FE
|
Q:FCO1550
|
2.8
|
12.9
|
1.0
|
|
CB
|
Q:CYS72
|
2.8
|
14.1
|
0.1
|
|
CB
|
Q:CYS72
|
2.9
|
13.9
|
0.4
|
|
CB
|
Q:CYS72
|
2.9
|
13.5
|
0.4
|
|
SG
|
Q:CYS543
|
2.9
|
13.4
|
0.2
|
|
SG
|
Q:CYS74
|
3.1
|
16.0
|
0.6
|
|
CB
|
Q:CYS543
|
3.3
|
11.9
|
0.2
|
|
CB
|
Q:CYS543
|
3.3
|
12.6
|
0.8
|
|
CB
|
Q:CYS546
|
3.5
|
14.1
|
1.0
|
|
N
|
Q:CYS75
|
3.8
|
13.4
|
1.0
|
|
C1
|
Q:FCO1550
|
3.8
|
14.8
|
1.0
|
|
CB
|
Q:CYS75
|
3.8
|
10.2
|
1.0
|
|
C2
|
Q:FCO1550
|
4.1
|
13.0
|
1.0
|
|
CA
|
Q:CYS72
|
4.3
|
13.7
|
1.0
|
|
C3
|
Q:FCO1550
|
4.4
|
11.1
|
1.0
|
|
CA
|
Q:CYS75
|
4.4
|
10.9
|
1.0
|
|
CB
|
Q:CYS74
|
4.4
|
16.2
|
0.2
|
|
CA
|
Q:CYS546
|
4.5
|
12.8
|
1.0
|
|
N
|
Q:CYS546
|
4.5
|
11.5
|
1.0
|
|
CB
|
Q:CYS74
|
4.5
|
17.0
|
0.3
|
|
CA
|
Q:CYS543
|
4.6
|
11.8
|
0.2
|
|
CA
|
Q:CYS543
|
4.6
|
11.8
|
0.8
|
|
N1
|
Q:FCO1550
|
4.7
|
11.2
|
1.0
|
|
CB
|
Q:CYS74
|
4.7
|
17.1
|
0.6
|
|
NH1
|
Q:ARG476
|
4.7
|
15.6
|
1.0
|
|
CG
|
Q:GLU25
|
4.8
|
12.9
|
1.0
|
|
N
|
Q:CYS74
|
4.8
|
14.2
|
1.0
|
|
C
|
Q:CYS74
|
4.8
|
13.7
|
1.0
|
|
C
|
Q:CYS72
|
4.8
|
14.5
|
1.0
|
|
CD
|
Q:ARG476
|
4.9
|
13.2
|
1.0
|
|
CZ
|
Q:ARG476
|
4.9
|
16.6
|
1.0
|
|
OE1
|
Q:GLU25
|
5.0
|
12.1
|
0.8
|
|
CA
|
Q:CYS74
|
5.0
|
15.2
|
1.0
|
|
NE
|
Q:ARG476
|
5.0
|
16.8
|
1.0
|
|
Nickel binding site 2 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 2 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ni1551
b:14.3
occ:0.56
|
NI
|
Q:NI1551
|
0.0
|
14.3
|
0.6
|
|
O
|
Q:HOH2066
|
1.9
|
14.8
|
0.1
|
|
NI
|
Q:NI1551
|
1.9
|
16.6
|
0.4
|
|
N
|
Q:CYS75
|
1.9
|
13.4
|
1.0
|
|
SD
|
Q:CYS543
|
2.1
|
13.1
|
0.2
|
|
S
|
Q:H2S1552
|
2.1
|
14.4
|
0.2
|
|
SG
|
Q:CYS75
|
2.2
|
13.7
|
1.0
|
|
SG
|
Q:CYS74
|
2.3
|
16.0
|
0.6
|
|
SG
|
Q:CYS72
|
2.4
|
14.4
|
0.1
|
|
SG
|
Q:CYS72
|
2.5
|
16.3
|
0.4
|
|
O
|
Q:HOH2068
|
2.5
|
16.2
|
0.4
|
|
CB
|
Q:CYS75
|
2.6
|
10.2
|
1.0
|
|
CA
|
Q:CYS75
|
2.7
|
10.9
|
1.0
|
|
C
|
Q:CYS74
|
3.0
|
13.7
|
1.0
|
|
SG
|
Q:CYS72
|
3.0
|
14.8
|
0.4
|
|
CB
|
Q:CYS74
|
3.1
|
16.2
|
0.2
|
|
CB
|
Q:CYS74
|
3.3
|
17.0
|
0.3
|
|
CB
|
Q:CYS74
|
3.4
|
17.1
|
0.6
|
|
CA
|
Q:CYS74
|
3.4
|
15.2
|
1.0
|
|
FE
|
Q:FCO1550
|
3.6
|
12.9
|
1.0
|
|
CB
|
Q:CYS72
|
3.6
|
13.9
|
0.4
|
|
SG
|
Q:CYS543
|
3.6
|
13.4
|
0.2
|
|
CB
|
Q:CYS72
|
3.6
|
13.5
|
0.4
|
|
CB
|
Q:CYS72
|
3.6
|
14.1
|
0.1
|
|
N
|
Q:CYS74
|
3.6
|
14.2
|
1.0
|
|
SG
|
Q:CYS543
|
3.6
|
16.4
|
0.8
|
|
C
|
Q:CYS75
|
3.6
|
12.4
|
1.0
|
|
NH1
|
Q:ARG476
|
3.8
|
15.6
|
1.0
|
|
C2
|
Q:FCO1550
|
4.1
|
13.0
|
1.0
|
|
O
|
Q:CYS74
|
4.1
|
15.6
|
1.0
|
|
SG
|
Q:CYS546
|
4.1
|
15.5
|
1.0
|
|
O
|
Q:CYS75
|
4.1
|
14.3
|
1.0
|
|
CZ
|
Q:ARG476
|
4.3
|
16.6
|
1.0
|
|
SG
|
Q:CYS74
|
4.3
|
16.8
|
0.2
|
|
N
|
Q:THR76
|
4.4
|
11.8
|
1.0
|
|
CB
|
Q:CYS543
|
4.7
|
12.6
|
0.8
|
|
C
|
Q:CYS72
|
4.7
|
14.5
|
1.0
|
|
CB
|
Q:CYS543
|
4.7
|
11.9
|
0.2
|
|
C
|
Q:GLY73
|
4.7
|
13.4
|
1.0
|
|
SG
|
Q:CYS74
|
4.7
|
18.4
|
0.3
|
|
NH2
|
Q:ARG476
|
4.7
|
15.3
|
1.0
|
|
N2
|
Q:FCO1550
|
4.8
|
10.8
|
1.0
|
|
CA
|
Q:CYS72
|
4.8
|
13.7
|
1.0
|
|
OD2
|
Q:ASP114
|
4.8
|
16.2
|
1.0
|
|
O
|
Q:CYS72
|
4.8
|
16.0
|
1.0
|
|
N
|
Q:GLY73
|
4.9
|
13.0
|
1.0
|
|
NE
|
Q:ARG476
|
4.9
|
16.8
|
1.0
|
|
C1
|
Q:FCO1550
|
5.0
|
14.8
|
1.0
|
|
Nickel binding site 3 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 3 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Ni1551
b:18.5
occ:0.44
|
NI
|
R:NI1551
|
0.0
|
18.5
|
0.4
|
|
O
|
R:HOH2060
|
1.4
|
13.2
|
0.1
|
|
SD
|
R:CYS543
|
1.5
|
13.0
|
0.2
|
|
S
|
R:H2S1552
|
1.5
|
12.9
|
0.2
|
|
NI
|
R:NI1551
|
1.9
|
15.5
|
0.6
|
|
O
|
R:HOH2062
|
1.9
|
14.9
|
0.4
|
|
SG
|
R:CYS543
|
2.2
|
17.9
|
0.8
|
|
SG
|
R:CYS72
|
2.2
|
18.4
|
0.4
|
|
SG
|
R:CYS72
|
2.3
|
19.0
|
0.4
|
|
SG
|
R:CYS72
|
2.3
|
16.9
|
0.1
|
|
SG
|
R:CYS75
|
2.5
|
14.9
|
1.0
|
|
SG
|
R:CYS546
|
2.6
|
14.9
|
1.0
|
|
FE
|
R:FCO1550
|
2.8
|
12.5
|
1.0
|
|
CB
|
R:CYS72
|
2.8
|
16.1
|
0.1
|
|
CB
|
R:CYS72
|
2.8
|
16.1
|
0.4
|
|
CB
|
R:CYS72
|
2.9
|
17.0
|
0.4
|
|
SG
|
R:CYS543
|
3.0
|
15.4
|
0.2
|
|
SG
|
R:CYS74
|
3.1
|
16.1
|
0.6
|
|
CB
|
R:CYS543
|
3.3
|
13.3
|
0.2
|
|
CB
|
R:CYS543
|
3.4
|
15.5
|
0.8
|
|
CB
|
R:CYS546
|
3.5
|
15.3
|
1.0
|
|
N
|
R:CYS75
|
3.8
|
15.6
|
1.0
|
|
CB
|
R:CYS75
|
3.8
|
13.8
|
1.0
|
|
C1
|
R:FCO1550
|
3.8
|
12.1
|
1.0
|
|
C2
|
R:FCO1550
|
4.1
|
8.1
|
1.0
|
|
CA
|
R:CYS72
|
4.3
|
16.1
|
1.0
|
|
C3
|
R:FCO1550
|
4.3
|
13.0
|
1.0
|
|
CA
|
R:CYS75
|
4.4
|
14.8
|
1.0
|
|
CB
|
R:CYS74
|
4.4
|
15.7
|
0.2
|
|
CB
|
R:CYS74
|
4.5
|
17.4
|
0.3
|
|
CA
|
R:CYS546
|
4.5
|
12.6
|
1.0
|
|
N
|
R:CYS546
|
4.5
|
12.0
|
1.0
|
|
CB
|
R:CYS74
|
4.6
|
16.5
|
0.6
|
|
CA
|
R:CYS543
|
4.7
|
11.8
|
0.8
|
|
CA
|
R:CYS543
|
4.7
|
11.8
|
0.2
|
|
NH1
|
R:ARG476
|
4.7
|
15.4
|
1.0
|
|
N1
|
R:FCO1550
|
4.7
|
11.4
|
1.0
|
|
N
|
R:CYS74
|
4.8
|
15.3
|
1.0
|
|
C
|
R:CYS72
|
4.8
|
17.8
|
1.0
|
|
C
|
R:CYS74
|
4.8
|
15.9
|
1.0
|
|
CD
|
R:ARG476
|
4.9
|
11.3
|
1.0
|
|
CG
|
R:GLU25
|
4.9
|
15.5
|
1.0
|
|
OE1
|
R:GLU25
|
4.9
|
14.7
|
0.8
|
|
CZ
|
R:ARG476
|
4.9
|
15.1
|
1.0
|
|
NE
|
R:ARG476
|
4.9
|
14.4
|
1.0
|
|
CA
|
R:CYS74
|
4.9
|
15.8
|
1.0
|
|
Nickel binding site 4 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 4 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Ni1551
b:15.5
occ:0.56
|
NI
|
R:NI1551
|
0.0
|
15.5
|
0.6
|
|
O
|
R:HOH2060
|
1.9
|
13.2
|
0.1
|
|
NI
|
R:NI1551
|
1.9
|
18.5
|
0.4
|
|
N
|
R:CYS75
|
1.9
|
15.6
|
1.0
|
|
SD
|
R:CYS543
|
2.0
|
13.0
|
0.2
|
|
S
|
R:H2S1552
|
2.0
|
12.9
|
0.2
|
|
SG
|
R:CYS74
|
2.2
|
16.1
|
0.6
|
|
SG
|
R:CYS75
|
2.3
|
14.9
|
1.0
|
|
O
|
R:HOH2062
|
2.5
|
14.9
|
0.4
|
|
SG
|
R:CYS72
|
2.5
|
16.9
|
0.1
|
|
SG
|
R:CYS72
|
2.6
|
18.4
|
0.4
|
|
CB
|
R:CYS75
|
2.6
|
13.8
|
1.0
|
|
CA
|
R:CYS75
|
2.7
|
14.8
|
1.0
|
|
C
|
R:CYS74
|
3.0
|
15.9
|
1.0
|
|
SG
|
R:CYS72
|
3.0
|
19.0
|
0.4
|
|
CB
|
R:CYS74
|
3.1
|
15.7
|
0.2
|
|
CB
|
R:CYS74
|
3.2
|
17.4
|
0.3
|
|
CB
|
R:CYS74
|
3.3
|
16.5
|
0.6
|
|
CA
|
R:CYS74
|
3.4
|
15.8
|
1.0
|
|
FE
|
R:FCO1550
|
3.6
|
12.5
|
1.0
|
|
SG
|
R:CYS543
|
3.6
|
15.4
|
0.2
|
|
N
|
R:CYS74
|
3.6
|
15.3
|
1.0
|
|
CB
|
R:CYS72
|
3.6
|
16.1
|
0.4
|
|
SG
|
R:CYS543
|
3.6
|
17.9
|
0.8
|
|
CB
|
R:CYS72
|
3.6
|
16.1
|
0.1
|
|
CB
|
R:CYS72
|
3.6
|
17.0
|
0.4
|
|
C
|
R:CYS75
|
3.7
|
16.0
|
1.0
|
|
NH1
|
R:ARG476
|
3.7
|
15.4
|
1.0
|
|
C2
|
R:FCO1550
|
4.1
|
8.1
|
1.0
|
|
O
|
R:CYS74
|
4.1
|
16.0
|
1.0
|
|
SG
|
R:CYS546
|
4.1
|
14.9
|
1.0
|
|
O
|
R:CYS75
|
4.1
|
17.4
|
1.0
|
|
CZ
|
R:ARG476
|
4.2
|
15.1
|
1.0
|
|
SG
|
R:CYS74
|
4.3
|
15.1
|
0.2
|
|
N
|
R:THR76
|
4.4
|
14.4
|
1.0
|
|
NH2
|
R:ARG476
|
4.7
|
15.9
|
1.0
|
|
CB
|
R:CYS543
|
4.7
|
15.5
|
0.8
|
|
SG
|
R:CYS74
|
4.7
|
19.7
|
0.3
|
|
C
|
R:CYS72
|
4.7
|
17.8
|
1.0
|
|
CB
|
R:CYS543
|
4.7
|
13.3
|
0.2
|
|
C
|
R:GLY73
|
4.7
|
16.4
|
1.0
|
|
NE
|
R:ARG476
|
4.7
|
14.4
|
1.0
|
|
N2
|
R:FCO1550
|
4.7
|
10.6
|
1.0
|
|
OD2
|
R:ASP114
|
4.8
|
15.9
|
1.0
|
|
CA
|
R:CYS72
|
4.8
|
16.1
|
1.0
|
|
N
|
R:GLY73
|
4.9
|
15.8
|
1.0
|
|
O
|
R:CYS72
|
4.9
|
18.3
|
1.0
|
|
C1
|
R:FCO1550
|
5.0
|
12.1
|
1.0
|
|
Nickel binding site 5 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 5 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ni1551
b:21.4
occ:0.44
|
NI
|
S:NI1551
|
0.0
|
21.4
|
0.4
|
|
O
|
S:HOH2040
|
1.3
|
16.4
|
0.1
|
|
SD
|
S:CYS543
|
1.4
|
17.3
|
0.2
|
|
S
|
S:H2S1552
|
1.4
|
16.4
|
0.2
|
|
O
|
S:HOH2042
|
1.9
|
19.6
|
0.4
|
|
NI
|
S:NI1551
|
1.9
|
17.1
|
0.6
|
|
SG
|
S:CYS543
|
2.2
|
19.0
|
0.8
|
|
SG
|
S:CYS72
|
2.3
|
19.6
|
0.4
|
|
SG
|
S:CYS72
|
2.3
|
19.2
|
0.4
|
|
SG
|
S:CYS72
|
2.3
|
17.5
|
0.1
|
|
SG
|
S:CYS75
|
2.6
|
17.6
|
1.0
|
|
SG
|
S:CYS546
|
2.6
|
17.1
|
1.0
|
|
FE
|
S:FCO1550
|
2.7
|
16.6
|
1.0
|
|
CB
|
S:CYS72
|
2.9
|
16.2
|
0.1
|
|
CB
|
S:CYS72
|
2.9
|
16.5
|
0.4
|
|
CB
|
S:CYS72
|
2.9
|
17.0
|
0.4
|
|
SG
|
S:CYS543
|
3.0
|
17.6
|
0.2
|
|
SG
|
S:CYS74
|
3.2
|
20.7
|
0.6
|
|
CB
|
S:CYS543
|
3.3
|
15.4
|
0.2
|
|
CB
|
S:CYS543
|
3.3
|
14.7
|
0.8
|
|
CB
|
S:CYS546
|
3.5
|
16.4
|
1.0
|
|
C1
|
S:FCO1550
|
3.8
|
16.0
|
1.0
|
|
N
|
S:CYS75
|
3.8
|
16.2
|
1.0
|
|
CB
|
S:CYS75
|
3.8
|
16.4
|
1.0
|
|
C2
|
S:FCO1550
|
4.0
|
16.2
|
1.0
|
|
C3
|
S:FCO1550
|
4.3
|
17.1
|
1.0
|
|
CA
|
S:CYS75
|
4.3
|
16.1
|
1.0
|
|
CA
|
S:CYS72
|
4.4
|
16.0
|
1.0
|
|
CB
|
S:CYS74
|
4.4
|
18.2
|
0.2
|
|
CB
|
S:CYS74
|
4.5
|
18.4
|
0.3
|
|
CA
|
S:CYS546
|
4.5
|
15.4
|
1.0
|
|
N
|
S:CYS546
|
4.5
|
14.8
|
1.0
|
|
NH1
|
S:ARG476
|
4.6
|
17.8
|
1.0
|
|
N1
|
S:FCO1550
|
4.7
|
16.3
|
1.0
|
|
CA
|
S:CYS543
|
4.7
|
14.5
|
0.2
|
|
CA
|
S:CYS543
|
4.7
|
14.5
|
0.8
|
|
CB
|
S:CYS74
|
4.7
|
20.3
|
0.6
|
|
N
|
S:CYS74
|
4.8
|
16.6
|
1.0
|
|
C
|
S:CYS74
|
4.8
|
16.9
|
1.0
|
|
CD
|
S:ARG476
|
4.8
|
15.3
|
1.0
|
|
CG
|
S:GLU25
|
4.8
|
16.3
|
1.0
|
|
C
|
S:CYS72
|
4.9
|
17.3
|
1.0
|
|
CZ
|
S:ARG476
|
4.9
|
17.4
|
1.0
|
|
OE1
|
S:GLU25
|
5.0
|
18.4
|
0.8
|
|
NE
|
S:ARG476
|
5.0
|
16.4
|
1.0
|
|
CA
|
S:CYS74
|
5.0
|
17.5
|
1.0
|
|
Nickel binding site 6 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 6 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ni1551
b:17.1
occ:0.56
|
NI
|
S:NI1551
|
0.0
|
17.1
|
0.6
|
|
N
|
S:CYS75
|
1.9
|
16.2
|
1.0
|
|
O
|
S:HOH2040
|
1.9
|
16.4
|
0.1
|
|
NI
|
S:NI1551
|
1.9
|
21.4
|
0.4
|
|
SD
|
S:CYS543
|
2.1
|
17.3
|
0.2
|
|
S
|
S:H2S1552
|
2.1
|
16.4
|
0.2
|
|
SG
|
S:CYS75
|
2.3
|
17.6
|
1.0
|
|
SG
|
S:CYS74
|
2.3
|
20.7
|
0.6
|
|
SG
|
S:CYS72
|
2.4
|
17.5
|
0.1
|
|
O
|
S:HOH2042
|
2.6
|
19.6
|
0.4
|
|
SG
|
S:CYS72
|
2.6
|
19.2
|
0.4
|
|
CB
|
S:CYS75
|
2.6
|
16.4
|
1.0
|
|
CA
|
S:CYS75
|
2.7
|
16.1
|
1.0
|
|
C
|
S:CYS74
|
3.0
|
16.9
|
1.0
|
|
SG
|
S:CYS72
|
3.0
|
19.6
|
0.4
|
|
CB
|
S:CYS74
|
3.1
|
18.2
|
0.2
|
|
CB
|
S:CYS74
|
3.2
|
18.4
|
0.3
|
|
CB
|
S:CYS74
|
3.4
|
20.3
|
0.6
|
|
CA
|
S:CYS74
|
3.4
|
17.5
|
1.0
|
|
FE
|
S:FCO1550
|
3.5
|
16.6
|
1.0
|
|
N
|
S:CYS74
|
3.6
|
16.6
|
1.0
|
|
C
|
S:CYS75
|
3.6
|
16.3
|
1.0
|
|
CB
|
S:CYS72
|
3.6
|
16.5
|
0.4
|
|
CB
|
S:CYS72
|
3.6
|
16.2
|
0.1
|
|
CB
|
S:CYS72
|
3.7
|
17.0
|
0.4
|
|
NH1
|
S:ARG476
|
3.7
|
17.8
|
1.0
|
|
SG
|
S:CYS543
|
3.7
|
17.6
|
0.2
|
|
SG
|
S:CYS543
|
3.7
|
19.0
|
0.8
|
|
O
|
S:CYS74
|
4.0
|
17.1
|
1.0
|
|
C2
|
S:FCO1550
|
4.1
|
16.2
|
1.0
|
|
O
|
S:CYS75
|
4.1
|
15.5
|
1.0
|
|
SG
|
S:CYS546
|
4.2
|
17.1
|
1.0
|
|
CZ
|
S:ARG476
|
4.3
|
17.4
|
1.0
|
|
N
|
S:THR76
|
4.3
|
14.1
|
1.0
|
|
SG
|
S:CYS74
|
4.4
|
19.8
|
0.2
|
|
C
|
S:CYS72
|
4.7
|
17.3
|
1.0
|
|
OD2
|
S:ASP114
|
4.7
|
22.7
|
1.0
|
|
SG
|
S:CYS74
|
4.7
|
17.4
|
0.3
|
|
CB
|
S:CYS543
|
4.7
|
14.7
|
0.8
|
|
C
|
S:GLY73
|
4.7
|
16.8
|
1.0
|
|
N2
|
S:FCO1550
|
4.7
|
14.8
|
1.0
|
|
CB
|
S:CYS543
|
4.8
|
15.4
|
0.2
|
|
NH2
|
S:ARG476
|
4.8
|
16.7
|
1.0
|
|
CA
|
S:CYS72
|
4.8
|
16.0
|
1.0
|
|
NE
|
S:ARG476
|
4.9
|
16.4
|
1.0
|
|
N
|
S:GLY73
|
4.9
|
18.9
|
1.0
|
|
O
|
S:CYS72
|
4.9
|
17.9
|
1.0
|
|
C1
|
S:FCO1550
|
5.0
|
16.0
|
1.0
|
|
C3
|
S:FCO1550
|
5.0
|
17.1
|
1.0
|
|
Nickel binding site 7 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 7 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Ni1551
b:16.2
occ:0.44
|
NI
|
T:NI1551
|
0.0
|
16.2
|
0.4
|
|
O
|
T:HOH2076
|
1.3
|
13.4
|
0.1
|
|
SD
|
T:CYS543
|
1.4
|
13.6
|
0.2
|
|
S
|
T:H2S1552
|
1.4
|
13.8
|
0.2
|
|
NI
|
T:NI1551
|
1.8
|
13.4
|
0.6
|
|
O
|
T:HOH2078
|
1.9
|
15.8
|
0.4
|
|
SG
|
T:CYS543
|
2.2
|
18.6
|
0.8
|
|
SG
|
T:CYS72
|
2.2
|
16.1
|
0.4
|
|
SG
|
T:CYS72
|
2.3
|
16.5
|
0.4
|
|
SG
|
T:CYS72
|
2.4
|
15.3
|
0.1
|
|
SG
|
T:CYS75
|
2.4
|
13.5
|
1.0
|
|
SG
|
T:CYS546
|
2.7
|
15.2
|
1.0
|
|
FE
|
T:FCO1550
|
2.8
|
12.8
|
1.0
|
|
SG
|
T:CYS543
|
2.9
|
14.8
|
0.2
|
|
CB
|
T:CYS72
|
2.9
|
14.2
|
0.1
|
|
CB
|
T:CYS72
|
2.9
|
13.8
|
0.4
|
|
CB
|
T:CYS72
|
2.9
|
14.0
|
0.4
|
|
SG
|
T:CYS74
|
3.0
|
14.7
|
0.6
|
|
CB
|
T:CYS543
|
3.3
|
13.3
|
0.2
|
|
CB
|
T:CYS543
|
3.3
|
14.3
|
0.8
|
|
CB
|
T:CYS546
|
3.6
|
12.2
|
1.0
|
|
CB
|
T:CYS75
|
3.7
|
11.5
|
1.0
|
|
N
|
T:CYS75
|
3.7
|
12.1
|
1.0
|
|
C1
|
T:FCO1550
|
3.8
|
12.8
|
1.0
|
|
C2
|
T:FCO1550
|
4.0
|
14.8
|
1.0
|
|
CA
|
T:CYS75
|
4.3
|
11.7
|
1.0
|
|
CB
|
T:CYS74
|
4.3
|
15.2
|
0.2
|
|
C3
|
T:FCO1550
|
4.4
|
10.7
|
1.0
|
|
CA
|
T:CYS72
|
4.4
|
14.5
|
1.0
|
|
CB
|
T:CYS74
|
4.5
|
15.4
|
0.3
|
|
CA
|
T:CYS546
|
4.6
|
11.8
|
1.0
|
|
CB
|
T:CYS74
|
4.6
|
15.7
|
0.6
|
|
N
|
T:CYS546
|
4.6
|
10.3
|
1.0
|
|
NH1
|
T:ARG476
|
4.6
|
17.1
|
1.0
|
|
N1
|
T:FCO1550
|
4.7
|
11.1
|
1.0
|
|
CA
|
T:CYS543
|
4.7
|
13.3
|
0.8
|
|
CA
|
T:CYS543
|
4.7
|
13.3
|
0.2
|
|
N
|
T:CYS74
|
4.7
|
12.6
|
1.0
|
|
C
|
T:CYS74
|
4.8
|
12.5
|
1.0
|
|
CG
|
T:GLU25
|
4.8
|
11.0
|
1.0
|
|
CD
|
T:ARG476
|
4.8
|
10.6
|
1.0
|
|
C
|
T:CYS72
|
4.9
|
14.4
|
1.0
|
|
CZ
|
T:ARG476
|
4.9
|
15.4
|
1.0
|
|
CA
|
T:CYS74
|
4.9
|
13.7
|
1.0
|
|
NE
|
T:ARG476
|
4.9
|
12.8
|
1.0
|
|
C
|
T:CYS75
|
5.0
|
12.4
|
1.0
|
|
Nickel binding site 8 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 8 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Ni1551
b:13.4
occ:0.56
|
NI
|
T:NI1551
|
0.0
|
13.4
|
0.6
|
|
NI
|
T:NI1551
|
1.8
|
16.2
|
0.4
|
|
O
|
T:HOH2076
|
1.9
|
13.4
|
0.1
|
|
N
|
T:CYS75
|
1.9
|
12.1
|
1.0
|
|
SD
|
T:CYS543
|
2.1
|
13.6
|
0.2
|
|
S
|
T:H2S1552
|
2.1
|
13.8
|
0.2
|
|
SG
|
T:CYS74
|
2.2
|
14.7
|
0.6
|
|
SG
|
T:CYS75
|
2.3
|
13.5
|
1.0
|
|
SG
|
T:CYS72
|
2.5
|
16.1
|
0.4
|
|
O
|
T:HOH2078
|
2.6
|
15.8
|
0.4
|
|
SG
|
T:CYS72
|
2.6
|
15.3
|
0.1
|
|
CB
|
T:CYS75
|
2.6
|
11.5
|
1.0
|
|
CA
|
T:CYS75
|
2.7
|
11.7
|
1.0
|
|
C
|
T:CYS74
|
3.0
|
12.5
|
1.0
|
|
SG
|
T:CYS72
|
3.0
|
16.5
|
0.4
|
|
CB
|
T:CYS74
|
3.1
|
15.2
|
0.2
|
|
CB
|
T:CYS74
|
3.2
|
15.4
|
0.3
|
|
CB
|
T:CYS74
|
3.3
|
15.7
|
0.6
|
|
CA
|
T:CYS74
|
3.4
|
13.7
|
1.0
|
|
N
|
T:CYS74
|
3.6
|
12.6
|
1.0
|
|
SG
|
T:CYS543
|
3.6
|
14.8
|
0.2
|
|
FE
|
T:FCO1550
|
3.6
|
12.8
|
1.0
|
|
CB
|
T:CYS72
|
3.6
|
13.8
|
0.4
|
|
CB
|
T:CYS72
|
3.6
|
14.0
|
0.4
|
|
CB
|
T:CYS72
|
3.6
|
14.2
|
0.1
|
|
SG
|
T:CYS543
|
3.6
|
18.6
|
0.8
|
|
C
|
T:CYS75
|
3.6
|
12.4
|
1.0
|
|
NH1
|
T:ARG476
|
3.8
|
17.1
|
1.0
|
|
O
|
T:CYS74
|
4.1
|
13.1
|
1.0
|
|
C2
|
T:FCO1550
|
4.1
|
14.8
|
1.0
|
|
SG
|
T:CYS546
|
4.1
|
15.2
|
1.0
|
|
O
|
T:CYS75
|
4.1
|
13.3
|
1.0
|
|
SG
|
T:CYS74
|
4.3
|
17.8
|
0.2
|
|
CZ
|
T:ARG476
|
4.3
|
15.4
|
1.0
|
|
N
|
T:THR76
|
4.4
|
12.6
|
1.0
|
|
C
|
T:GLY73
|
4.7
|
12.3
|
1.0
|
|
C
|
T:CYS72
|
4.7
|
14.4
|
1.0
|
|
CB
|
T:CYS543
|
4.7
|
14.3
|
0.8
|
|
SG
|
T:CYS74
|
4.7
|
15.5
|
0.3
|
|
CB
|
T:CYS543
|
4.7
|
13.3
|
0.2
|
|
OD2
|
T:ASP114
|
4.8
|
17.9
|
1.0
|
|
NH2
|
T:ARG476
|
4.8
|
18.6
|
1.0
|
|
CA
|
T:CYS72
|
4.8
|
14.5
|
1.0
|
|
N2
|
T:FCO1550
|
4.8
|
11.9
|
1.0
|
|
N
|
T:GLY73
|
4.8
|
13.2
|
1.0
|
|
O
|
T:CYS72
|
4.8
|
16.0
|
1.0
|
|
NE
|
T:ARG476
|
4.8
|
12.8
|
1.0
|
|
C1
|
T:FCO1550
|
5.0
|
12.8
|
1.0
|
|
Nickel binding site 9 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 9 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ni1551
b:19.5
occ:0.44
|
NI
|
U:NI1551
|
0.0
|
19.5
|
0.4
|
|
O
|
U:HOH2071
|
1.4
|
13.2
|
0.1
|
|
SD
|
U:CYS543
|
1.5
|
13.1
|
0.2
|
|
S
|
U:H2S1552
|
1.5
|
12.4
|
0.2
|
|
NI
|
U:NI1551
|
1.9
|
15.6
|
0.6
|
|
O
|
U:HOH2073
|
1.9
|
14.2
|
0.4
|
|
SG
|
U:CYS543
|
2.2
|
17.9
|
0.8
|
|
SG
|
U:CYS72
|
2.2
|
20.5
|
0.4
|
|
SG
|
U:CYS72
|
2.3
|
22.0
|
0.4
|
|
SG
|
U:CYS72
|
2.4
|
16.9
|
0.1
|
|
SG
|
U:CYS75
|
2.5
|
14.6
|
1.0
|
|
SG
|
U:CYS546
|
2.6
|
14.8
|
1.0
|
|
FE
|
U:FCO1550
|
2.8
|
12.7
|
1.0
|
|
CB
|
U:CYS72
|
2.8
|
16.2
|
0.1
|
|
CB
|
U:CYS72
|
2.8
|
16.9
|
0.4
|
|
CB
|
U:CYS72
|
2.9
|
17.7
|
0.4
|
|
SG
|
U:CYS543
|
2.9
|
15.1
|
0.2
|
|
SG
|
U:CYS74
|
3.0
|
15.7
|
0.6
|
|
CB
|
U:CYS543
|
3.3
|
13.1
|
0.2
|
|
CB
|
U:CYS543
|
3.4
|
14.3
|
0.8
|
|
CB
|
U:CYS546
|
3.6
|
14.0
|
1.0
|
|
N
|
U:CYS75
|
3.8
|
15.4
|
1.0
|
|
CB
|
U:CYS75
|
3.8
|
13.4
|
1.0
|
|
C1
|
U:FCO1550
|
3.8
|
11.7
|
1.0
|
|
C2
|
U:FCO1550
|
4.1
|
11.6
|
1.0
|
|
CA
|
U:CYS72
|
4.3
|
16.0
|
1.0
|
|
CA
|
U:CYS75
|
4.3
|
14.8
|
1.0
|
|
C3
|
U:FCO1550
|
4.4
|
13.5
|
1.0
|
|
CB
|
U:CYS74
|
4.4
|
17.0
|
0.2
|
|
CB
|
U:CYS74
|
4.5
|
17.5
|
0.3
|
|
N
|
U:CYS546
|
4.5
|
11.8
|
1.0
|
|
CA
|
U:CYS546
|
4.5
|
12.0
|
1.0
|
|
CB
|
U:CYS74
|
4.6
|
17.5
|
0.6
|
|
NH1
|
U:ARG476
|
4.6
|
15.1
|
1.0
|
|
CA
|
U:CYS543
|
4.7
|
12.0
|
0.8
|
|
CA
|
U:CYS543
|
4.7
|
12.0
|
0.2
|
|
N1
|
U:FCO1550
|
4.7
|
12.4
|
1.0
|
|
N
|
U:CYS74
|
4.8
|
16.3
|
1.0
|
|
C
|
U:CYS74
|
4.8
|
15.9
|
1.0
|
|
C
|
U:CYS72
|
4.8
|
18.2
|
1.0
|
|
CG
|
U:GLU25
|
4.9
|
15.0
|
1.0
|
|
CD
|
U:ARG476
|
4.9
|
11.8
|
1.0
|
|
CZ
|
U:ARG476
|
4.9
|
13.9
|
1.0
|
|
CA
|
U:CYS74
|
4.9
|
16.9
|
1.0
|
|
NE
|
U:ARG476
|
5.0
|
12.6
|
1.0
|
|
C
|
U:CYS75
|
5.0
|
16.1
|
1.0
|
|
Nickel binding site 10 out
of 12 in 4ueq
Go back to
Nickel Binding Sites List in 4ueq
Nickel binding site 10 out
of 12 in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ni1551
b:15.6
occ:0.56
|
NI
|
U:NI1551
|
0.0
|
15.6
|
0.6
|
|
NI
|
U:NI1551
|
1.9
|
19.5
|
0.4
|
|
O
|
U:HOH2071
|
1.9
|
13.2
|
0.1
|
|
N
|
U:CYS75
|
1.9
|
15.4
|
1.0
|
|
SD
|
U:CYS543
|
2.1
|
13.1
|
0.2
|
|
S
|
U:H2S1552
|
2.1
|
12.4
|
0.2
|
|
SG
|
U:CYS74
|
2.2
|
15.7
|
0.6
|
|
SG
|
U:CYS75
|
2.2
|
14.6
|
1.0
|
|
SG
|
U:CYS72
|
2.5
|
20.5
|
0.4
|
|
SG
|
U:CYS72
|
2.5
|
16.9
|
0.1
|
|
O
|
U:HOH2073
|
2.6
|
14.2
|
0.4
|
|
CB
|
U:CYS75
|
2.6
|
13.4
|
1.0
|
|
CA
|
U:CYS75
|
2.7
|
14.8
|
1.0
|
|
C
|
U:CYS74
|
3.0
|
15.9
|
1.0
|
|
SG
|
U:CYS72
|
3.0
|
22.0
|
0.4
|
|
CB
|
U:CYS74
|
3.1
|
17.0
|
0.2
|
|
CB
|
U:CYS74
|
3.2
|
17.5
|
0.3
|
|
CB
|
U:CYS74
|
3.3
|
17.5
|
0.6
|
|
CA
|
U:CYS74
|
3.4
|
16.9
|
1.0
|
|
N
|
U:CYS74
|
3.6
|
16.3
|
1.0
|
|
CB
|
U:CYS72
|
3.6
|
16.9
|
0.4
|
|
FE
|
U:FCO1550
|
3.6
|
12.7
|
1.0
|
|
CB
|
U:CYS72
|
3.6
|
16.2
|
0.1
|
|
CB
|
U:CYS72
|
3.6
|
17.7
|
0.4
|
|
C
|
U:CYS75
|
3.6
|
16.1
|
1.0
|
|
SG
|
U:CYS543
|
3.6
|
15.1
|
0.2
|
|
SG
|
U:CYS543
|
3.7
|
17.9
|
0.8
|
|
NH1
|
U:ARG476
|
3.8
|
15.1
|
1.0
|
|
O
|
U:CYS74
|
4.1
|
16.2
|
1.0
|
|
C2
|
U:FCO1550
|
4.1
|
11.6
|
1.0
|
|
SG
|
U:CYS546
|
4.1
|
14.8
|
1.0
|
|
O
|
U:CYS75
|
4.1
|
17.6
|
1.0
|
|
CZ
|
U:ARG476
|
4.3
|
13.9
|
1.0
|
|
N
|
U:THR76
|
4.4
|
14.2
|
1.0
|
|
SG
|
U:CYS74
|
4.4
|
16.4
|
0.2
|
|
C
|
U:CYS72
|
4.6
|
18.2
|
1.0
|
|
SG
|
U:CYS74
|
4.7
|
18.5
|
0.3
|
|
C
|
U:GLY73
|
4.7
|
17.0
|
1.0
|
|
CB
|
U:CYS543
|
4.7
|
14.3
|
0.8
|
|
CB
|
U:CYS543
|
4.7
|
13.1
|
0.2
|
|
NH2
|
U:ARG476
|
4.8
|
15.2
|
1.0
|
|
CA
|
U:CYS72
|
4.8
|
16.0
|
1.0
|
|
N2
|
U:FCO1550
|
4.8
|
13.9
|
1.0
|
|
OD2
|
U:ASP114
|
4.8
|
15.7
|
1.0
|
|
N
|
U:GLY73
|
4.8
|
18.2
|
1.0
|
|
NE
|
U:ARG476
|
4.9
|
12.6
|
1.0
|
|
O
|
U:CYS72
|
4.9
|
18.7
|
1.0
|
|
C1
|
U:FCO1550
|
5.0
|
11.7
|
1.0
|
|
Reference:
A.Volbeda,
L.Martin,
P.-P.Liebgott,
A.L.De Lacey,
J.C.Fontecilla-Camps.
[Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H
Page generated: Wed Oct 9 19:13:21 2024
|
