Nickel in PDB 4kl8: High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
Enzymatic activity of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
All present enzymatic activity of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air:
1.12.99.6;
Protein crystallography data
The structure of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kl8
was solved by
A.Volbeda,
C.Cavazza,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
25.00 /
1.52
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.200,
108.720,
136.620,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
12.2 /
17.1
|
Other elements in 4kl8:
The structure of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
(pdb code 4kl8). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the
High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kl8:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
Nickel binding site 1 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 1 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni502
b:12.2
occ:0.48
|
NI
|
L:NI502
|
0.0
|
12.2
|
0.5
|
|
NI
|
L:NI502
|
0.9
|
11.3
|
0.3
|
|
OD
|
L:UOX492
|
1.4
|
8.4
|
0.2
|
|
O
|
L:HOH608
|
1.7
|
12.1
|
0.3
|
|
OD1
|
L:UOX492
|
1.9
|
11.5
|
0.5
|
|
SE
|
L:UOX492
|
2.0
|
9.4
|
0.2
|
|
SG
|
L:CYS70
|
2.0
|
9.7
|
0.4
|
|
OD2
|
L:UOX492
|
2.0
|
11.5
|
0.5
|
|
SG
|
L:CYS70
|
2.1
|
9.7
|
0.5
|
|
SG
|
L:CYS73
|
2.3
|
9.0
|
0.5
|
|
SG
|
L:CYS70
|
2.5
|
8.7
|
0.1
|
|
SE
|
L:UOX492
|
2.5
|
12.5
|
0.3
|
|
SG
|
L:CYS73
|
2.6
|
6.9
|
0.4
|
|
SG
|
L:CYS73
|
2.6
|
5.8
|
0.1
|
|
SEG
|
L:UOX492
|
2.7
|
10.5
|
0.5
|
|
FE
|
L:FCO501
|
2.9
|
8.3
|
0.7
|
|
NI
|
L:NI502
|
3.0
|
11.5
|
0.2
|
|
SG
|
L:CYS495
|
3.1
|
6.8
|
0.2
|
|
FE
|
L:FCO501
|
3.1
|
7.7
|
0.3
|
|
SG
|
L:CYS495
|
3.1
|
6.6
|
0.3
|
|
CB
|
L:CYS70
|
3.2
|
7.6
|
0.5
|
|
CB
|
L:CYS70
|
3.2
|
7.5
|
0.1
|
|
CB
|
L:CYS70
|
3.2
|
6.6
|
0.4
|
|
SG
|
L:CYS495
|
3.2
|
6.8
|
0.5
|
|
CB
|
L:CYS73
|
3.3
|
7.0
|
0.5
|
|
CB
|
L:CYS73
|
3.3
|
6.6
|
0.4
|
|
CB
|
L:CYS73
|
3.4
|
6.0
|
0.1
|
|
N
|
L:CYS73
|
3.4
|
5.8
|
1.0
|
|
CB
|
L:UOX492
|
3.6
|
9.4
|
0.3
|
|
CB
|
L:UOX492
|
3.6
|
10.0
|
0.5
|
|
O
|
L:HOH609
|
3.6
|
12.3
|
0.5
|
|
CB
|
L:UOX492
|
3.7
|
8.9
|
0.2
|
|
C2
|
L:FCO501
|
3.8
|
7.9
|
0.3
|
|
CB
|
L:VAL72
|
3.8
|
7.0
|
1.0
|
|
C2
|
L:FCO501
|
3.8
|
7.9
|
0.7
|
|
CA
|
L:CYS73
|
4.0
|
5.8
|
1.0
|
|
C1
|
L:FCO501
|
4.1
|
9.3
|
0.7
|
|
C1
|
L:FCO501
|
4.1
|
8.7
|
0.3
|
|
NH1
|
L:ARG425
|
4.2
|
6.8
|
1.0
|
|
C
|
L:VAL72
|
4.2
|
6.0
|
1.0
|
|
CA
|
L:VAL72
|
4.4
|
6.7
|
1.0
|
|
N
|
L:VAL72
|
4.4
|
4.7
|
1.0
|
|
CG1
|
L:VAL72
|
4.4
|
8.3
|
1.0
|
|
C3
|
L:FCO501
|
4.5
|
7.4
|
0.7
|
|
CA
|
L:CYS70
|
4.5
|
5.8
|
0.4
|
|
CA
|
L:CYS70
|
4.5
|
5.9
|
0.5
|
|
N2
|
L:FCO501
|
4.6
|
6.5
|
0.3
|
|
CA
|
L:CYS70
|
4.6
|
6.5
|
0.1
|
|
CB
|
L:CYS495
|
4.6
|
5.5
|
0.2
|
|
CB
|
L:CYS495
|
4.6
|
5.9
|
0.5
|
|
CB
|
L:CYS495
|
4.6
|
5.7
|
0.3
|
|
N2
|
L:FCO501
|
4.6
|
6.0
|
0.7
|
|
C3
|
L:FCO501
|
4.7
|
7.9
|
0.3
|
|
CZ
|
L:ARG425
|
4.7
|
6.9
|
1.0
|
|
CG2
|
L:VAL72
|
4.7
|
7.2
|
1.0
|
|
CD
|
L:ARG425
|
4.7
|
5.5
|
1.0
|
|
NE
|
L:ARG425
|
4.8
|
6.3
|
1.0
|
|
C
|
L:CYS70
|
4.9
|
5.8
|
1.0
|
|
C
|
L:CYS73
|
4.9
|
6.1
|
1.0
|
|
CA
|
L:UOX492
|
4.9
|
7.6
|
0.2
|
|
CA
|
L:UOX492
|
4.9
|
7.6
|
0.3
|
|
CA
|
L:UOX492
|
4.9
|
7.6
|
0.5
|
|
N1
|
L:FCO501
|
5.0
|
6.9
|
0.3
|
|
Nickel binding site 2 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 2 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni502
b:11.5
occ:0.19
|
NI
|
L:NI502
|
0.0
|
11.5
|
0.2
|
|
O
|
L:HOH609
|
1.4
|
12.3
|
0.5
|
|
SE
|
L:UOX492
|
1.7
|
12.5
|
0.3
|
|
SG
|
L:CYS495
|
2.2
|
6.8
|
0.2
|
|
N
|
L:CYS495
|
2.2
|
6.0
|
1.0
|
|
SG
|
L:CYS495
|
2.3
|
6.6
|
0.3
|
|
SG
|
L:CYS495
|
2.3
|
6.8
|
0.5
|
|
SE
|
L:UOX492
|
2.3
|
9.4
|
0.2
|
|
NI
|
L:NI502
|
2.5
|
11.3
|
0.3
|
|
CB
|
L:CYS495
|
2.7
|
5.9
|
0.5
|
|
CB
|
L:CYS495
|
2.7
|
5.5
|
0.2
|
|
CB
|
L:CYS495
|
2.7
|
5.7
|
0.3
|
|
CB
|
L:UOX492
|
2.8
|
10.0
|
0.5
|
|
CA
|
L:CYS495
|
2.9
|
4.8
|
1.0
|
|
CB
|
L:UOX492
|
3.0
|
9.4
|
0.3
|
|
CB
|
L:UOX492
|
3.0
|
8.9
|
0.2
|
|
NI
|
L:NI502
|
3.0
|
12.2
|
0.5
|
|
OD
|
L:UOX492
|
3.1
|
8.4
|
0.2
|
|
CB
|
L:CYS70
|
3.2
|
7.5
|
0.1
|
|
SG
|
L:CYS70
|
3.2
|
9.7
|
0.4
|
|
OD2
|
L:UOX492
|
3.2
|
11.5
|
0.5
|
|
C
|
L:GLY494
|
3.3
|
5.7
|
1.0
|
|
CB
|
L:CYS70
|
3.3
|
7.6
|
0.5
|
|
SG
|
L:CYS70
|
3.3
|
9.7
|
0.5
|
|
CB
|
L:CYS70
|
3.3
|
6.6
|
0.4
|
|
SEG
|
L:UOX492
|
3.6
|
10.5
|
0.5
|
|
O
|
L:UOX492
|
3.7
|
7.0
|
0.5
|
|
O
|
L:UOX492
|
3.7
|
7.0
|
0.3
|
|
O
|
L:UOX492
|
3.7
|
7.0
|
0.2
|
|
OD1
|
L:UOX492
|
3.7
|
11.5
|
0.5
|
|
CA
|
L:GLY494
|
3.7
|
5.9
|
1.0
|
|
C
|
L:UOX492
|
3.7
|
7.2
|
0.3
|
|
C
|
L:UOX492
|
3.7
|
7.2
|
0.2
|
|
C
|
L:UOX492
|
3.7
|
7.2
|
0.5
|
|
N
|
L:GLY494
|
3.7
|
4.4
|
1.0
|
|
OE1
|
L:GLU23
|
3.7
|
11.3
|
1.0
|
|
SG
|
L:CYS70
|
3.7
|
8.7
|
0.1
|
|
CA
|
L:UOX492
|
3.8
|
7.6
|
0.2
|
|
CA
|
L:UOX492
|
3.8
|
7.6
|
0.3
|
|
CA
|
L:UOX492
|
3.8
|
7.6
|
0.5
|
|
O
|
L:HOH608
|
3.9
|
12.1
|
0.3
|
|
FE
|
L:FCO501
|
3.9
|
8.3
|
0.7
|
|
FE
|
L:FCO501
|
4.0
|
7.7
|
0.3
|
|
C1
|
L:FCO501
|
4.2
|
9.3
|
0.7
|
|
C1
|
L:FCO501
|
4.2
|
8.7
|
0.3
|
|
C
|
L:CYS495
|
4.2
|
5.4
|
1.0
|
|
SG
|
L:CYS73
|
4.3
|
9.0
|
0.5
|
|
N
|
L:LEU493
|
4.3
|
6.6
|
1.0
|
|
O
|
L:GLY494
|
4.3
|
6.0
|
1.0
|
|
O
|
L:ILE69
|
4.4
|
6.6
|
1.0
|
|
CD
|
L:GLU23
|
4.4
|
10.8
|
1.0
|
|
SG
|
L:CYS73
|
4.4
|
6.9
|
0.4
|
|
SG
|
L:CYS73
|
4.5
|
5.8
|
0.1
|
|
CA
|
L:CYS70
|
4.5
|
5.8
|
0.4
|
|
N
|
L:ALA496
|
4.5
|
4.9
|
1.0
|
|
CA
|
L:CYS70
|
4.5
|
5.9
|
0.5
|
|
C
|
L:LEU493
|
4.5
|
6.2
|
1.0
|
|
CA
|
L:CYS70
|
4.5
|
6.5
|
0.1
|
|
N1
|
L:FCO501
|
4.7
|
6.9
|
0.3
|
|
N1
|
L:FCO501
|
4.7
|
6.4
|
0.7
|
|
CG2
|
L:ILE69
|
4.8
|
6.1
|
1.0
|
|
CG
|
L:GLU23
|
4.9
|
9.2
|
1.0
|
|
C3
|
L:FCO501
|
5.0
|
7.4
|
0.7
|
|
Nickel binding site 3 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 3 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni502
b:11.3
occ:0.33
|
NI
|
L:NI502
|
0.0
|
11.3
|
0.3
|
|
NI
|
L:NI502
|
0.9
|
12.2
|
0.5
|
|
OD
|
L:UOX492
|
1.2
|
8.4
|
0.2
|
|
O
|
L:HOH608
|
2.0
|
12.1
|
0.3
|
|
SE
|
L:UOX492
|
2.0
|
9.4
|
0.2
|
|
OD1
|
L:UOX492
|
2.0
|
11.5
|
0.5
|
|
SG
|
L:CYS73
|
2.1
|
9.0
|
0.5
|
|
SG
|
L:CYS495
|
2.2
|
6.8
|
0.2
|
|
SG
|
L:CYS495
|
2.2
|
6.6
|
0.3
|
|
SG
|
L:CYS70
|
2.3
|
9.7
|
0.4
|
|
SG
|
L:CYS495
|
2.3
|
6.8
|
0.5
|
|
FE
|
L:FCO501
|
2.3
|
8.3
|
0.7
|
|
SE
|
L:UOX492
|
2.4
|
12.5
|
0.3
|
|
SG
|
L:CYS73
|
2.4
|
6.9
|
0.4
|
|
SG
|
L:CYS70
|
2.4
|
8.7
|
0.1
|
|
SG
|
L:CYS73
|
2.4
|
5.8
|
0.1
|
|
NI
|
L:NI502
|
2.5
|
11.5
|
0.2
|
|
SG
|
L:CYS70
|
2.5
|
9.7
|
0.5
|
|
FE
|
L:FCO501
|
2.5
|
7.7
|
0.3
|
|
OD2
|
L:UOX492
|
2.5
|
11.5
|
0.5
|
|
SEG
|
L:UOX492
|
2.9
|
10.5
|
0.5
|
|
CB
|
L:CYS70
|
3.0
|
6.6
|
0.4
|
|
CB
|
L:CYS70
|
3.0
|
7.6
|
0.5
|
|
CB
|
L:CYS70
|
3.0
|
7.5
|
0.1
|
|
CB
|
L:UOX492
|
3.3
|
10.0
|
0.5
|
|
O
|
L:HOH609
|
3.3
|
12.3
|
0.5
|
|
CB
|
L:UOX492
|
3.3
|
9.4
|
0.3
|
|
CB
|
L:UOX492
|
3.4
|
8.9
|
0.2
|
|
C1
|
L:FCO501
|
3.5
|
9.3
|
0.7
|
|
C1
|
L:FCO501
|
3.5
|
8.7
|
0.3
|
|
CB
|
L:CYS73
|
3.6
|
6.6
|
0.4
|
|
CB
|
L:CYS73
|
3.6
|
7.0
|
0.5
|
|
C2
|
L:FCO501
|
3.6
|
7.9
|
0.3
|
|
CB
|
L:CYS73
|
3.6
|
6.0
|
0.1
|
|
C2
|
L:FCO501
|
3.6
|
7.9
|
0.7
|
|
CB
|
L:CYS495
|
3.7
|
5.5
|
0.2
|
|
CB
|
L:CYS495
|
3.7
|
5.9
|
0.5
|
|
CB
|
L:CYS495
|
3.7
|
5.7
|
0.3
|
|
C3
|
L:FCO501
|
3.8
|
7.4
|
0.7
|
|
C3
|
L:FCO501
|
4.0
|
7.9
|
0.3
|
|
N
|
L:CYS73
|
4.1
|
5.8
|
1.0
|
|
CA
|
L:CYS73
|
4.4
|
5.8
|
1.0
|
|
N1
|
L:FCO501
|
4.4
|
6.9
|
0.3
|
|
N1
|
L:FCO501
|
4.5
|
6.4
|
0.7
|
|
CA
|
L:CYS70
|
4.5
|
5.8
|
0.4
|
|
CA
|
L:CYS70
|
4.5
|
5.9
|
0.5
|
|
N
|
L:CYS495
|
4.5
|
6.0
|
1.0
|
|
N2
|
L:FCO501
|
4.5
|
6.5
|
0.3
|
|
CA
|
L:CYS70
|
4.5
|
6.5
|
0.1
|
|
N2
|
L:FCO501
|
4.6
|
6.0
|
0.7
|
|
CA
|
L:CYS495
|
4.7
|
4.8
|
1.0
|
|
CB
|
L:VAL72
|
4.7
|
7.0
|
1.0
|
|
NH1
|
L:ARG425
|
4.7
|
6.8
|
1.0
|
|
CA
|
L:UOX492
|
4.7
|
7.6
|
0.2
|
|
CA
|
L:UOX492
|
4.7
|
7.6
|
0.3
|
|
CA
|
L:UOX492
|
4.7
|
7.6
|
0.5
|
|
CD
|
L:ARG425
|
4.8
|
5.5
|
1.0
|
|
NE2
|
L:HIS77
|
4.9
|
5.3
|
1.0
|
|
O3
|
L:FCO501
|
4.9
|
11.2
|
0.7
|
|
C
|
L:VAL72
|
5.0
|
6.0
|
1.0
|
|
Nickel binding site 4 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 4 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ni502
b:14.3
occ:0.48
|
NI
|
M:NI502
|
0.0
|
14.3
|
0.5
|
|
NI
|
M:NI502
|
0.9
|
14.0
|
0.3
|
|
O
|
M:HOH620
|
1.6
|
13.3
|
0.3
|
|
OD
|
M:UOX492
|
1.7
|
9.9
|
0.2
|
|
OD1
|
M:UOX492
|
1.9
|
13.7
|
0.5
|
|
SG
|
M:CYS70
|
2.0
|
11.4
|
0.4
|
|
SE
|
M:UOX492
|
2.0
|
13.0
|
0.2
|
|
OD2
|
M:UOX492
|
2.1
|
13.6
|
0.5
|
|
SG
|
M:CYS70
|
2.1
|
12.8
|
0.5
|
|
SG
|
M:CYS73
|
2.2
|
10.7
|
0.5
|
|
SG
|
M:CYS70
|
2.5
|
9.9
|
0.1
|
|
SG
|
M:CYS73
|
2.5
|
11.3
|
0.4
|
|
SG
|
M:CYS73
|
2.5
|
9.0
|
0.1
|
|
SE
|
M:UOX492
|
2.5
|
14.5
|
0.3
|
|
SEG
|
M:UOX492
|
2.7
|
13.0
|
0.5
|
|
FE
|
M:FCO501
|
2.9
|
10.5
|
0.7
|
|
NI
|
M:NI502
|
3.0
|
14.3
|
0.2
|
|
SG
|
M:CYS495
|
3.1
|
9.4
|
0.2
|
|
FE
|
M:FCO501
|
3.1
|
9.7
|
0.3
|
|
SG
|
M:CYS495
|
3.1
|
9.0
|
0.5
|
|
CB
|
M:CYS70
|
3.1
|
8.9
|
0.1
|
|
CB
|
M:CYS70
|
3.1
|
9.2
|
0.5
|
|
SG
|
M:CYS495
|
3.2
|
8.7
|
0.3
|
|
CB
|
M:CYS70
|
3.2
|
8.6
|
0.4
|
|
CB
|
M:CYS73
|
3.3
|
8.7
|
0.4
|
|
CB
|
M:CYS73
|
3.3
|
8.2
|
0.5
|
|
CB
|
M:CYS73
|
3.3
|
8.0
|
0.1
|
|
N
|
M:CYS73
|
3.5
|
8.0
|
1.0
|
|
CB
|
M:UOX492
|
3.6
|
11.1
|
0.3
|
|
CB
|
M:UOX492
|
3.6
|
10.6
|
0.5
|
|
O
|
M:HOH621
|
3.6
|
13.9
|
0.5
|
|
CB
|
M:UOX492
|
3.7
|
10.8
|
0.2
|
|
C2
|
M:FCO501
|
3.7
|
7.4
|
0.7
|
|
C2
|
M:FCO501
|
3.8
|
8.5
|
0.3
|
|
CB
|
M:VAL72
|
3.8
|
7.3
|
1.0
|
|
CA
|
M:CYS73
|
4.0
|
8.1
|
1.0
|
|
C1
|
M:FCO501
|
4.0
|
11.9
|
0.7
|
|
C1
|
M:FCO501
|
4.1
|
10.7
|
0.3
|
|
NH1
|
M:ARG425
|
4.2
|
10.9
|
1.0
|
|
C
|
M:VAL72
|
4.3
|
7.5
|
1.0
|
|
C3
|
M:FCO501
|
4.4
|
10.9
|
0.7
|
|
CA
|
M:VAL72
|
4.4
|
7.1
|
1.0
|
|
N
|
M:VAL72
|
4.5
|
7.8
|
1.0
|
|
CG1
|
M:VAL72
|
4.5
|
8.8
|
1.0
|
|
CA
|
M:CYS70
|
4.5
|
8.7
|
0.4
|
|
CB
|
M:CYS495
|
4.5
|
7.9
|
0.2
|
|
CB
|
M:CYS495
|
4.5
|
8.0
|
0.3
|
|
CA
|
M:CYS70
|
4.5
|
8.9
|
0.5
|
|
N2
|
M:FCO501
|
4.5
|
8.7
|
0.3
|
|
CB
|
M:CYS495
|
4.5
|
8.1
|
0.5
|
|
CA
|
M:CYS70
|
4.5
|
8.5
|
0.1
|
|
N2
|
M:FCO501
|
4.6
|
7.4
|
0.7
|
|
C3
|
M:FCO501
|
4.7
|
11.5
|
0.3
|
|
CZ
|
M:ARG425
|
4.7
|
9.7
|
1.0
|
|
CD
|
M:ARG425
|
4.7
|
9.1
|
1.0
|
|
CG2
|
M:VAL72
|
4.8
|
9.6
|
1.0
|
|
C
|
M:CYS70
|
4.9
|
7.7
|
1.0
|
|
NE
|
M:ARG425
|
4.9
|
10.6
|
1.0
|
|
C
|
M:CYS73
|
4.9
|
7.5
|
1.0
|
|
N1
|
M:FCO501
|
5.0
|
10.3
|
0.3
|
|
CA
|
M:UOX492
|
5.0
|
9.8
|
0.5
|
|
CA
|
M:UOX492
|
5.0
|
9.8
|
0.2
|
|
CA
|
M:UOX492
|
5.0
|
9.8
|
0.3
|
|
N1
|
M:FCO501
|
5.0
|
9.4
|
0.7
|
|
Nickel binding site 5 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 5 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ni502
b:14.3
occ:0.19
|
NI
|
M:NI502
|
0.0
|
14.3
|
0.2
|
|
O
|
M:HOH621
|
1.4
|
13.9
|
0.5
|
|
SE
|
M:UOX492
|
1.8
|
14.5
|
0.3
|
|
SG
|
M:CYS495
|
2.2
|
9.4
|
0.2
|
|
N
|
M:CYS495
|
2.2
|
7.5
|
1.0
|
|
SG
|
M:CYS495
|
2.3
|
9.0
|
0.5
|
|
SG
|
M:CYS495
|
2.3
|
8.7
|
0.3
|
|
SE
|
M:UOX492
|
2.3
|
13.0
|
0.2
|
|
NI
|
M:NI502
|
2.4
|
14.0
|
0.3
|
|
CB
|
M:CYS495
|
2.6
|
7.9
|
0.2
|
|
CB
|
M:CYS495
|
2.6
|
8.0
|
0.3
|
|
CB
|
M:CYS495
|
2.6
|
8.1
|
0.5
|
|
CB
|
M:UOX492
|
2.9
|
10.6
|
0.5
|
|
CA
|
M:CYS495
|
2.9
|
7.4
|
1.0
|
|
NI
|
M:NI502
|
3.0
|
14.3
|
0.5
|
|
CB
|
M:UOX492
|
3.0
|
11.1
|
0.3
|
|
OD
|
M:UOX492
|
3.1
|
9.9
|
0.2
|
|
CB
|
M:UOX492
|
3.1
|
10.8
|
0.2
|
|
CB
|
M:CYS70
|
3.1
|
8.9
|
0.1
|
|
SG
|
M:CYS70
|
3.1
|
11.4
|
0.4
|
|
CB
|
M:CYS70
|
3.2
|
9.2
|
0.5
|
|
CB
|
M:CYS70
|
3.3
|
8.6
|
0.4
|
|
C
|
M:GLY494
|
3.3
|
7.7
|
1.0
|
|
SG
|
M:CYS70
|
3.3
|
12.8
|
0.5
|
|
OD2
|
M:UOX492
|
3.3
|
13.6
|
0.5
|
|
OD1
|
M:UOX492
|
3.6
|
13.7
|
0.5
|
|
SG
|
M:CYS70
|
3.7
|
9.9
|
0.1
|
|
CA
|
M:GLY494
|
3.7
|
6.7
|
1.0
|
|
O
|
M:UOX492
|
3.7
|
9.2
|
0.2
|
|
O
|
M:UOX492
|
3.7
|
9.2
|
0.3
|
|
O
|
M:UOX492
|
3.7
|
9.2
|
0.5
|
|
SEG
|
M:UOX492
|
3.7
|
13.0
|
0.5
|
|
OE1
|
M:GLU23
|
3.7
|
16.7
|
1.0
|
|
C
|
M:UOX492
|
3.8
|
10.2
|
0.3
|
|
C
|
M:UOX492
|
3.8
|
10.2
|
0.2
|
|
C
|
M:UOX492
|
3.8
|
10.2
|
0.5
|
|
N
|
M:GLY494
|
3.8
|
7.4
|
1.0
|
|
FE
|
M:FCO501
|
3.8
|
10.5
|
0.7
|
|
O
|
M:HOH620
|
3.9
|
13.3
|
0.3
|
|
CA
|
M:UOX492
|
3.9
|
9.8
|
0.5
|
|
CA
|
M:UOX492
|
3.9
|
9.8
|
0.2
|
|
CA
|
M:UOX492
|
3.9
|
9.8
|
0.3
|
|
FE
|
M:FCO501
|
4.0
|
9.7
|
0.3
|
|
C1
|
M:FCO501
|
4.1
|
11.9
|
0.7
|
|
C1
|
M:FCO501
|
4.2
|
10.7
|
0.3
|
|
SG
|
M:CYS73
|
4.2
|
10.7
|
0.5
|
|
C
|
M:CYS495
|
4.2
|
7.1
|
1.0
|
|
O
|
M:GLY494
|
4.3
|
8.2
|
1.0
|
|
SG
|
M:CYS73
|
4.4
|
11.3
|
0.4
|
|
O
|
M:ILE69
|
4.4
|
7.6
|
1.0
|
|
CD
|
M:GLU23
|
4.4
|
13.5
|
1.0
|
|
SG
|
M:CYS73
|
4.4
|
9.0
|
0.1
|
|
N
|
M:LEU493
|
4.4
|
9.0
|
1.0
|
|
CA
|
M:CYS70
|
4.4
|
8.7
|
0.4
|
|
CA
|
M:CYS70
|
4.5
|
8.9
|
0.5
|
|
CA
|
M:CYS70
|
4.5
|
8.5
|
0.1
|
|
N
|
M:ALA496
|
4.5
|
7.0
|
1.0
|
|
C
|
M:LEU493
|
4.6
|
7.9
|
1.0
|
|
N1
|
M:FCO501
|
4.7
|
10.3
|
0.3
|
|
N1
|
M:FCO501
|
4.7
|
9.4
|
0.7
|
|
CG2
|
M:ILE69
|
4.7
|
8.7
|
1.0
|
|
CG
|
M:GLU23
|
4.9
|
11.3
|
1.0
|
|
C3
|
M:FCO501
|
4.9
|
10.9
|
0.7
|
|
C
|
M:ILE69
|
5.0
|
8.1
|
1.0
|
|
Nickel binding site 6 out
of 6 in 4kl8
Go back to
Nickel Binding Sites List in 4kl8
Nickel binding site 6 out
of 6 in the High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ni502
b:14.0
occ:0.33
|
NI
|
M:NI502
|
0.0
|
14.0
|
0.3
|
|
NI
|
M:NI502
|
0.9
|
14.3
|
0.5
|
|
OD
|
M:UOX492
|
1.5
|
9.9
|
0.2
|
|
OD1
|
M:UOX492
|
2.0
|
13.7
|
0.5
|
|
O
|
M:HOH620
|
2.0
|
13.3
|
0.3
|
|
SE
|
M:UOX492
|
2.0
|
13.0
|
0.2
|
|
SG
|
M:CYS73
|
2.1
|
10.7
|
0.5
|
|
SG
|
M:CYS495
|
2.2
|
9.4
|
0.2
|
|
SG
|
M:CYS70
|
2.3
|
11.4
|
0.4
|
|
SG
|
M:CYS495
|
2.3
|
9.0
|
0.5
|
|
SG
|
M:CYS495
|
2.3
|
8.7
|
0.3
|
|
FE
|
M:FCO501
|
2.3
|
10.5
|
0.7
|
|
SG
|
M:CYS73
|
2.4
|
11.3
|
0.4
|
|
SE
|
M:UOX492
|
2.4
|
14.5
|
0.3
|
|
SG
|
M:CYS70
|
2.4
|
9.9
|
0.1
|
|
SG
|
M:CYS73
|
2.4
|
9.0
|
0.1
|
|
NI
|
M:NI502
|
2.4
|
14.3
|
0.2
|
|
SG
|
M:CYS70
|
2.4
|
12.8
|
0.5
|
|
OD2
|
M:UOX492
|
2.5
|
13.6
|
0.5
|
|
FE
|
M:FCO501
|
2.6
|
9.7
|
0.3
|
|
SEG
|
M:UOX492
|
3.0
|
13.0
|
0.5
|
|
CB
|
M:CYS70
|
3.0
|
8.9
|
0.1
|
|
CB
|
M:CYS70
|
3.0
|
9.2
|
0.5
|
|
CB
|
M:CYS70
|
3.0
|
8.6
|
0.4
|
|
O
|
M:HOH621
|
3.3
|
13.9
|
0.5
|
|
CB
|
M:UOX492
|
3.3
|
10.6
|
0.5
|
|
CB
|
M:UOX492
|
3.3
|
11.1
|
0.3
|
|
CB
|
M:UOX492
|
3.4
|
10.8
|
0.2
|
|
C1
|
M:FCO501
|
3.5
|
11.9
|
0.7
|
|
C1
|
M:FCO501
|
3.5
|
10.7
|
0.3
|
|
CB
|
M:CYS73
|
3.6
|
8.7
|
0.4
|
|
CB
|
M:CYS73
|
3.6
|
8.2
|
0.5
|
|
CB
|
M:CYS73
|
3.6
|
8.0
|
0.1
|
|
C2
|
M:FCO501
|
3.6
|
7.4
|
0.7
|
|
C2
|
M:FCO501
|
3.6
|
8.5
|
0.3
|
|
CB
|
M:CYS495
|
3.7
|
7.9
|
0.2
|
|
CB
|
M:CYS495
|
3.7
|
8.0
|
0.3
|
|
CB
|
M:CYS495
|
3.7
|
8.1
|
0.5
|
|
C3
|
M:FCO501
|
3.8
|
10.9
|
0.7
|
|
N
|
M:CYS73
|
4.1
|
8.0
|
1.0
|
|
C3
|
M:FCO501
|
4.1
|
11.5
|
0.3
|
|
N1
|
M:FCO501
|
4.4
|
10.3
|
0.3
|
|
CA
|
M:CYS73
|
4.4
|
8.1
|
1.0
|
|
N1
|
M:FCO501
|
4.4
|
9.4
|
0.7
|
|
CA
|
M:CYS70
|
4.5
|
8.7
|
0.4
|
|
CA
|
M:CYS70
|
4.5
|
8.9
|
0.5
|
|
N
|
M:CYS495
|
4.5
|
7.5
|
1.0
|
|
CA
|
M:CYS70
|
4.5
|
8.5
|
0.1
|
|
N2
|
M:FCO501
|
4.5
|
8.7
|
0.3
|
|
N2
|
M:FCO501
|
4.6
|
7.4
|
0.7
|
|
CA
|
M:CYS495
|
4.6
|
7.4
|
1.0
|
|
CB
|
M:VAL72
|
4.7
|
7.3
|
1.0
|
|
CA
|
M:UOX492
|
4.7
|
9.8
|
0.5
|
|
CA
|
M:UOX492
|
4.7
|
9.8
|
0.2
|
|
CA
|
M:UOX492
|
4.7
|
9.8
|
0.3
|
|
NH1
|
M:ARG425
|
4.7
|
10.9
|
1.0
|
|
CD
|
M:ARG425
|
4.8
|
9.1
|
1.0
|
|
NE2
|
M:HIS77
|
4.9
|
8.6
|
1.0
|
|
O3
|
M:FCO501
|
4.9
|
12.5
|
0.7
|
|
Reference:
A.Volbeda,
P.Amara,
M.Iannello,
A.L.De Lacey,
C.Cavazza,
J.C.Fontecilla-Camps.
Structural Foundations For the O2 Resistance of Desulfomicrobium Baculatum [Nifese]-Hydrogenase. Chem.Commun.(Camb.) V. 49 7061 2013.
ISSN: ISSN 1359-7345
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Wed Oct 9 18:18:31 2024
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