Nickel in PDB 1t6u: Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
Enzymatic activity of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
All present enzymatic activity of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure:
1.15.1.1;
Protein crystallography data
The structure of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure, PDB code: 1t6u
was solved by
D.P.Barondeau,
C.J.Kassmann,
C.K.Bruns,
J.A.Tainer,
E.D.Getzoff,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
1.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.147,
111.680,
106.834,
90.00,
94.51,
90.00
|
|
R / Rfree (%)
|
15.8 /
20.1
|
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Nickel atom in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
(pdb code 1t6u). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the
Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure, PDB code: 1t6u:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 1 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni201
b:9.3
occ:1.00
|
N
|
A:HIS1
|
1.9
|
11.0
|
0.4
|
|
N
|
A:HIS1
|
1.9
|
10.6
|
0.6
|
|
N
|
A:CYS2
|
1.9
|
10.4
|
1.0
|
|
SG
|
A:CYS2
|
2.2
|
13.2
|
1.0
|
|
SG
|
A:CYS6
|
2.2
|
11.9
|
1.0
|
|
ND1
|
A:HIS1
|
2.3
|
14.6
|
0.6
|
|
C
|
A:HIS1
|
2.8
|
11.1
|
1.0
|
|
CA
|
A:HIS1
|
2.8
|
11.4
|
0.6
|
|
CA
|
A:HIS1
|
2.8
|
10.4
|
0.4
|
|
CA
|
A:CYS2
|
2.9
|
10.5
|
1.0
|
|
CB
|
A:CYS2
|
3.0
|
11.3
|
1.0
|
|
CE1
|
A:HIS1
|
3.2
|
16.9
|
0.6
|
|
CG
|
A:HIS1
|
3.3
|
13.3
|
0.6
|
|
CB
|
A:CYS6
|
3.4
|
11.2
|
1.0
|
|
CB
|
A:HIS1
|
3.6
|
10.9
|
0.6
|
|
N
|
A:ASP3
|
3.7
|
9.9
|
1.0
|
|
CG
|
A:HIS1
|
3.8
|
10.0
|
0.4
|
|
C
|
A:CYS2
|
3.8
|
9.3
|
1.0
|
|
O
|
A:HOH2746
|
3.8
|
17.2
|
1.0
|
|
CB
|
A:HIS1
|
3.8
|
9.2
|
0.4
|
|
N
|
A:CYS6
|
3.9
|
13.1
|
1.0
|
|
O
|
A:HIS1
|
4.0
|
12.7
|
1.0
|
|
ND1
|
A:HIS1
|
4.0
|
11.7
|
0.4
|
|
O
|
A:HOH2671
|
4.1
|
21.9
|
1.0
|
|
CA
|
A:CYS6
|
4.2
|
11.9
|
1.0
|
|
O
|
A:VAL8
|
4.2
|
11.4
|
1.0
|
|
CD2
|
A:HIS1
|
4.3
|
11.8
|
0.4
|
|
NE2
|
A:HIS1
|
4.4
|
12.6
|
0.6
|
|
CD2
|
A:HIS1
|
4.5
|
13.0
|
0.6
|
|
CE1
|
A:HIS1
|
4.6
|
10.5
|
0.4
|
|
NE2
|
A:HIS1
|
4.7
|
11.7
|
0.4
|
|
O
|
A:CYS2
|
4.8
|
11.5
|
1.0
|
|
N
|
A:LEU4
|
4.9
|
12.6
|
1.0
|
|
C
|
A:CYS6
|
4.9
|
11.8
|
1.0
|
|
N
|
A:GLY7
|
4.9
|
13.1
|
1.0
|
|
CB
|
D:SER20
|
4.9
|
13.6
|
1.0
|
|
N
|
A:VAL8
|
5.0
|
10.9
|
1.0
|
|
Nickel binding site 2 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 2 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni202
b:9.7
occ:1.00
|
N
|
B:CYS2
|
1.9
|
12.3
|
1.0
|
|
N
|
B:HIS1
|
2.0
|
11.7
|
0.5
|
|
N
|
B:HIS1
|
2.0
|
12.9
|
0.6
|
|
SG
|
B:CYS2
|
2.2
|
13.1
|
1.0
|
|
SG
|
B:CYS6
|
2.2
|
12.7
|
1.0
|
|
ND1
|
B:HIS1
|
2.4
|
13.1
|
0.6
|
|
C
|
B:HIS1
|
2.8
|
13.7
|
1.0
|
|
CA
|
B:HIS1
|
2.8
|
12.4
|
0.6
|
|
CA
|
B:HIS1
|
2.9
|
11.8
|
0.5
|
|
CA
|
B:CYS2
|
2.9
|
11.6
|
1.0
|
|
CB
|
B:CYS2
|
3.0
|
12.1
|
1.0
|
|
CE1
|
B:HIS1
|
3.3
|
13.7
|
0.6
|
|
CB
|
B:CYS6
|
3.4
|
13.2
|
1.0
|
|
CG
|
B:HIS1
|
3.4
|
12.5
|
0.6
|
|
O
|
B:HOH2745
|
3.6
|
16.1
|
1.0
|
|
CB
|
B:HIS1
|
3.6
|
11.2
|
0.6
|
|
N
|
B:ASP3
|
3.7
|
11.2
|
1.0
|
|
C
|
B:CYS2
|
3.7
|
11.4
|
1.0
|
|
CG
|
B:HIS1
|
3.8
|
11.1
|
0.5
|
|
CB
|
B:HIS1
|
3.9
|
11.6
|
0.5
|
|
N
|
B:CYS6
|
3.9
|
13.8
|
1.0
|
|
O
|
B:HIS1
|
3.9
|
11.7
|
1.0
|
|
O
|
B:HOH1541
|
4.0
|
26.3
|
1.0
|
|
ND1
|
B:HIS1
|
4.0
|
14.3
|
0.5
|
|
O
|
B:VAL8
|
4.2
|
13.6
|
1.0
|
|
CD2
|
B:HIS1
|
4.2
|
13.3
|
0.5
|
|
CA
|
B:CYS6
|
4.3
|
12.8
|
1.0
|
|
NE2
|
B:HIS1
|
4.5
|
15.9
|
0.6
|
|
CD2
|
B:HIS1
|
4.5
|
14.6
|
0.6
|
|
CE1
|
B:HIS1
|
4.6
|
15.7
|
0.5
|
|
NE2
|
B:HIS1
|
4.7
|
16.1
|
0.5
|
|
O
|
B:CYS2
|
4.8
|
12.6
|
1.0
|
|
N
|
B:LEU4
|
4.9
|
10.8
|
1.0
|
|
C
|
B:CYS6
|
4.9
|
11.9
|
1.0
|
|
N
|
B:GLY7
|
4.9
|
12.3
|
1.0
|
|
N
|
B:VAL8
|
5.0
|
11.1
|
1.0
|
|
Nickel binding site 3 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 3 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni203
b:8.6
occ:1.00
|
N
|
C:HIS1
|
1.8
|
9.0
|
0.5
|
|
N
|
C:CYS2
|
1.9
|
10.2
|
1.0
|
|
N
|
C:HIS1
|
2.0
|
11.1
|
0.5
|
|
SG
|
C:CYS2
|
2.2
|
12.7
|
1.0
|
|
SG
|
C:CYS6
|
2.2
|
11.8
|
1.0
|
|
ND1
|
C:HIS1
|
2.3
|
14.5
|
0.5
|
|
C
|
C:HIS1
|
2.8
|
10.7
|
1.0
|
|
CA
|
C:HIS1
|
2.8
|
10.5
|
0.5
|
|
CA
|
C:HIS1
|
2.8
|
11.1
|
0.5
|
|
CA
|
C:CYS2
|
2.9
|
9.9
|
1.0
|
|
CB
|
C:CYS2
|
2.9
|
12.3
|
1.0
|
|
CE1
|
C:HIS1
|
3.2
|
15.3
|
0.5
|
|
CG
|
C:HIS1
|
3.3
|
10.9
|
0.5
|
|
CB
|
C:CYS6
|
3.4
|
10.2
|
1.0
|
|
CB
|
C:HIS1
|
3.6
|
11.6
|
0.5
|
|
CG
|
C:HIS1
|
3.7
|
10.4
|
0.5
|
|
N
|
C:ASP3
|
3.7
|
11.3
|
1.0
|
|
C
|
C:CYS2
|
3.7
|
9.9
|
1.0
|
|
CB
|
C:HIS1
|
3.8
|
11.3
|
0.5
|
|
O
|
C:HOH2778
|
3.8
|
9.1
|
1.0
|
|
CD2
|
C:HIS1
|
3.9
|
11.6
|
0.5
|
|
O
|
C:HIS1
|
3.9
|
11.9
|
1.0
|
|
N
|
C:CYS6
|
4.0
|
11.5
|
1.0
|
|
O
|
C:HOH1589
|
4.1
|
16.8
|
1.0
|
|
O
|
C:VAL8
|
4.2
|
11.8
|
1.0
|
|
CA
|
C:CYS6
|
4.3
|
11.0
|
1.0
|
|
ND1
|
C:HIS1
|
4.3
|
15.2
|
0.5
|
|
NE2
|
C:HIS1
|
4.3
|
14.9
|
0.5
|
|
CD2
|
C:HIS1
|
4.4
|
13.0
|
0.5
|
|
NE2
|
C:HIS1
|
4.6
|
13.7
|
0.5
|
|
CE1
|
C:HIS1
|
4.7
|
15.8
|
0.5
|
|
O
|
C:CYS2
|
4.8
|
11.9
|
1.0
|
|
N
|
C:GLY7
|
4.9
|
12.3
|
1.0
|
|
N
|
C:LEU4
|
4.9
|
10.4
|
1.0
|
|
C
|
C:CYS6
|
4.9
|
12.7
|
1.0
|
|
CB
|
E:SER20
|
4.9
|
12.5
|
1.0
|
|
N
|
C:VAL8
|
5.0
|
11.2
|
1.0
|
|
Nickel binding site 4 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 4 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni204
b:7.5
occ:1.00
|
N
|
D:CYS2
|
1.9
|
7.9
|
1.0
|
|
N
|
D:HIS1
|
1.9
|
8.2
|
0.5
|
|
N
|
D:HIS1
|
2.0
|
8.2
|
0.5
|
|
SG
|
D:CYS2
|
2.1
|
12.2
|
1.0
|
|
SG
|
D:CYS6
|
2.2
|
9.9
|
1.0
|
|
ND1
|
D:HIS1
|
2.4
|
11.0
|
0.5
|
|
C
|
D:HIS1
|
2.8
|
9.6
|
1.0
|
|
CA
|
D:HIS1
|
2.8
|
7.7
|
0.5
|
|
CA
|
D:HIS1
|
2.8
|
6.9
|
0.5
|
|
CA
|
D:CYS2
|
2.9
|
8.5
|
1.0
|
|
CB
|
D:CYS2
|
2.9
|
9.9
|
1.0
|
|
CE1
|
D:HIS1
|
3.3
|
13.2
|
0.5
|
|
CB
|
D:CYS6
|
3.4
|
10.9
|
1.0
|
|
CG
|
D:HIS1
|
3.4
|
10.2
|
0.5
|
|
CB
|
D:HIS1
|
3.6
|
9.9
|
0.5
|
|
O
|
D:HOH2929
|
3.7
|
11.5
|
1.0
|
|
N
|
D:ASP3
|
3.7
|
8.9
|
1.0
|
|
C
|
D:CYS2
|
3.7
|
8.4
|
1.0
|
|
CG
|
D:HIS1
|
3.8
|
9.2
|
0.5
|
|
CB
|
D:HIS1
|
3.9
|
9.2
|
0.5
|
|
CD2
|
D:HIS1
|
3.9
|
12.4
|
0.5
|
|
N
|
D:CYS6
|
3.9
|
10.5
|
1.0
|
|
O
|
D:HIS1
|
4.0
|
9.9
|
1.0
|
|
O
|
D:HOH1001
|
4.2
|
17.2
|
1.0
|
|
CA
|
D:CYS6
|
4.2
|
11.1
|
1.0
|
|
O
|
D:VAL8
|
4.2
|
10.6
|
1.0
|
|
ND1
|
D:HIS1
|
4.3
|
13.2
|
0.5
|
|
NE2
|
D:HIS1
|
4.5
|
13.7
|
0.5
|
|
CD2
|
D:HIS1
|
4.5
|
12.1
|
0.5
|
|
NE2
|
D:HIS1
|
4.5
|
13.6
|
0.5
|
|
CE1
|
D:HIS1
|
4.8
|
14.3
|
0.5
|
|
O
|
D:CYS2
|
4.8
|
9.7
|
1.0
|
|
CB
|
A:SER20
|
4.8
|
12.7
|
1.0
|
|
N
|
D:LEU4
|
4.9
|
8.8
|
1.0
|
|
C
|
D:CYS6
|
4.9
|
11.1
|
1.0
|
|
N
|
D:GLY7
|
4.9
|
10.9
|
1.0
|
|
N
|
D:VAL8
|
5.0
|
9.8
|
1.0
|
|
Nickel binding site 5 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 5 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni205
b:7.4
occ:1.00
|
N
|
E:HIS1
|
1.9
|
9.9
|
0.5
|
|
N
|
E:CYS2
|
1.9
|
8.4
|
1.0
|
|
N
|
E:HIS1
|
2.0
|
8.4
|
0.5
|
|
SG
|
E:CYS2
|
2.2
|
11.4
|
1.0
|
|
SG
|
E:CYS6
|
2.2
|
9.7
|
1.0
|
|
ND1
|
E:HIS1
|
2.4
|
10.9
|
0.5
|
|
C
|
E:HIS1
|
2.8
|
9.3
|
1.0
|
|
CA
|
E:HIS1
|
2.8
|
8.7
|
0.5
|
|
CA
|
E:HIS1
|
2.8
|
9.4
|
0.5
|
|
CA
|
E:CYS2
|
3.0
|
8.5
|
1.0
|
|
CB
|
E:CYS2
|
3.0
|
9.7
|
1.0
|
|
CE1
|
E:HIS1
|
3.3
|
12.0
|
0.5
|
|
CB
|
E:CYS6
|
3.4
|
10.1
|
1.0
|
|
CG
|
E:HIS1
|
3.4
|
9.4
|
0.5
|
|
CB
|
E:HIS1
|
3.6
|
8.8
|
0.5
|
|
N
|
E:ASP3
|
3.7
|
8.3
|
1.0
|
|
CG
|
E:HIS1
|
3.7
|
9.9
|
0.5
|
|
C
|
E:CYS2
|
3.8
|
8.9
|
1.0
|
|
O
|
E:HOH2930
|
3.8
|
12.7
|
1.0
|
|
CB
|
E:HIS1
|
3.8
|
9.2
|
0.5
|
|
N
|
E:CYS6
|
4.0
|
9.8
|
1.0
|
|
O
|
E:HIS1
|
4.0
|
9.8
|
1.0
|
|
ND1
|
E:HIS1
|
4.0
|
12.2
|
0.5
|
|
O
|
E:HOH1709
|
4.1
|
20.0
|
1.0
|
|
CD2
|
E:HIS1
|
4.2
|
10.9
|
0.5
|
|
CA
|
E:CYS6
|
4.2
|
10.9
|
1.0
|
|
O
|
E:VAL8
|
4.3
|
11.3
|
1.0
|
|
NE2
|
E:HIS1
|
4.5
|
11.5
|
0.5
|
|
CE1
|
E:HIS1
|
4.5
|
10.6
|
0.5
|
|
CD2
|
E:HIS1
|
4.6
|
10.5
|
0.5
|
|
NE2
|
E:HIS1
|
4.6
|
11.6
|
0.5
|
|
O
|
E:CYS2
|
4.8
|
10.5
|
1.0
|
|
N
|
E:GLY7
|
4.8
|
10.8
|
1.0
|
|
C
|
E:CYS6
|
4.9
|
11.1
|
1.0
|
|
N
|
E:LEU4
|
4.9
|
9.4
|
1.0
|
|
N
|
E:VAL8
|
5.0
|
9.5
|
1.0
|
|
CB
|
C:SER20
|
5.0
|
12.8
|
1.0
|
|
Nickel binding site 6 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 6 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni206
b:9.9
occ:1.00
|
N
|
F:HIS1
|
1.9
|
11.8
|
0.6
|
|
N
|
F:CYS2
|
1.9
|
11.7
|
1.0
|
|
N
|
F:HIS1
|
2.1
|
11.8
|
0.4
|
|
SG
|
F:CYS2
|
2.1
|
14.4
|
1.0
|
|
SG
|
F:CYS6
|
2.2
|
13.9
|
1.0
|
|
ND1
|
F:HIS1
|
2.3
|
18.1
|
0.4
|
|
C
|
F:HIS1
|
2.8
|
11.7
|
1.0
|
|
CA
|
F:HIS1
|
2.9
|
11.3
|
0.6
|
|
CA
|
F:HIS1
|
2.9
|
11.5
|
0.4
|
|
CA
|
F:CYS2
|
2.9
|
11.8
|
1.0
|
|
CB
|
F:CYS2
|
2.9
|
13.2
|
1.0
|
|
CE1
|
F:HIS1
|
3.2
|
16.4
|
0.4
|
|
CG
|
F:HIS1
|
3.3
|
12.1
|
0.4
|
|
CB
|
F:CYS6
|
3.4
|
12.1
|
1.0
|
|
CB
|
F:HIS1
|
3.6
|
11.6
|
0.4
|
|
O
|
F:HOH2822
|
3.7
|
23.9
|
1.0
|
|
C
|
F:CYS2
|
3.7
|
9.8
|
1.0
|
|
N
|
F:ASP3
|
3.7
|
9.8
|
1.0
|
|
CG
|
F:HIS1
|
3.8
|
11.9
|
0.6
|
|
CB
|
F:HIS1
|
3.8
|
11.6
|
0.6
|
|
N
|
F:CYS6
|
4.0
|
14.2
|
1.0
|
|
O
|
F:HIS1
|
4.0
|
11.9
|
1.0
|
|
O
|
F:HOH2823
|
4.0
|
26.6
|
1.0
|
|
ND1
|
F:HIS1
|
4.0
|
14.9
|
0.6
|
|
O
|
F:VAL8
|
4.2
|
14.5
|
1.0
|
|
CA
|
F:CYS6
|
4.2
|
13.4
|
1.0
|
|
CD2
|
F:HIS1
|
4.3
|
13.9
|
0.6
|
|
NE2
|
F:HIS1
|
4.4
|
13.1
|
0.4
|
|
CD2
|
F:HIS1
|
4.4
|
13.0
|
0.4
|
|
CE1
|
F:HIS1
|
4.6
|
13.3
|
0.6
|
|
O
|
F:CYS2
|
4.8
|
12.3
|
1.0
|
|
NE2
|
F:HIS1
|
4.8
|
15.5
|
0.6
|
|
N
|
F:LEU4
|
4.9
|
11.2
|
1.0
|
|
C
|
F:CYS6
|
4.9
|
15.5
|
1.0
|
|
N
|
F:GLY7
|
5.0
|
18.0
|
1.0
|
|
CB
|
B:SER20
|
5.0
|
16.3
|
1.0
|
|
Nickel binding site 7 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 7 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ni207
b:7.4
occ:1.00
|
N
|
G:HIS1
|
1.9
|
6.5
|
0.4
|
|
N
|
G:CYS2
|
1.9
|
9.4
|
1.0
|
|
N
|
G:HIS1
|
2.0
|
10.2
|
0.6
|
|
SG
|
G:CYS2
|
2.2
|
11.0
|
1.0
|
|
SG
|
G:CYS6
|
2.2
|
11.2
|
1.0
|
|
ND1
|
G:HIS1
|
2.3
|
13.1
|
0.6
|
|
C
|
G:HIS1
|
2.8
|
9.7
|
1.0
|
|
CA
|
G:HIS1
|
2.8
|
8.3
|
0.4
|
|
CA
|
G:HIS1
|
2.8
|
9.3
|
0.6
|
|
CA
|
G:CYS2
|
2.9
|
8.3
|
1.0
|
|
CB
|
G:CYS2
|
3.0
|
11.0
|
1.0
|
|
CE1
|
G:HIS1
|
3.2
|
11.9
|
0.6
|
|
CG
|
G:HIS1
|
3.3
|
11.4
|
0.6
|
|
CB
|
G:CYS6
|
3.4
|
11.0
|
1.0
|
|
CB
|
G:HIS1
|
3.6
|
10.0
|
0.6
|
|
O
|
G:HOH2843
|
3.6
|
15.7
|
1.0
|
|
N
|
G:ASP3
|
3.7
|
9.2
|
1.0
|
|
C
|
G:CYS2
|
3.7
|
8.4
|
1.0
|
|
CG
|
G:HIS1
|
3.8
|
9.6
|
0.4
|
|
CB
|
G:HIS1
|
3.8
|
9.7
|
0.4
|
|
O
|
G:HIS1
|
4.0
|
10.9
|
1.0
|
|
N
|
G:CYS6
|
4.0
|
12.3
|
1.0
|
|
O
|
G:HOH2259
|
4.1
|
23.8
|
1.0
|
|
ND1
|
G:HIS1
|
4.1
|
13.4
|
0.4
|
|
CD2
|
G:HIS1
|
4.2
|
13.1
|
0.4
|
|
O
|
G:VAL8
|
4.2
|
10.9
|
1.0
|
|
CA
|
G:CYS6
|
4.3
|
10.4
|
1.0
|
|
NE2
|
G:HIS1
|
4.3
|
14.5
|
0.6
|
|
CD2
|
G:HIS1
|
4.4
|
12.6
|
0.6
|
|
CE1
|
G:HIS1
|
4.7
|
11.1
|
0.4
|
|
NE2
|
G:HIS1
|
4.7
|
11.9
|
0.4
|
|
O
|
G:CYS2
|
4.8
|
10.0
|
1.0
|
|
N
|
G:LEU4
|
4.9
|
9.2
|
1.0
|
|
N
|
G:GLY7
|
4.9
|
10.2
|
1.0
|
|
C
|
G:CYS6
|
4.9
|
9.7
|
1.0
|
|
N
|
G:VAL8
|
5.0
|
10.0
|
1.0
|
|
CB
|
J:SER20
|
5.0
|
12.9
|
1.0
|
|
CA
|
G:ASP3
|
5.0
|
8.8
|
1.0
|
|
Nickel binding site 8 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 8 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni208
b:8.5
occ:1.00
|
N
|
H:HIS1
|
1.8
|
12.0
|
0.5
|
|
N
|
H:CYS2
|
1.9
|
10.3
|
1.0
|
|
N
|
H:HIS1
|
2.0
|
11.7
|
0.5
|
|
SG
|
H:CYS6
|
2.1
|
11.1
|
1.0
|
|
SG
|
H:CYS2
|
2.2
|
12.2
|
1.0
|
|
ND1
|
H:HIS1
|
2.4
|
12.9
|
0.5
|
|
CA
|
H:HIS1
|
2.8
|
10.5
|
0.5
|
|
C
|
H:HIS1
|
2.8
|
11.1
|
1.0
|
|
CA
|
H:HIS1
|
2.9
|
11.1
|
0.5
|
|
CA
|
H:CYS2
|
2.9
|
10.5
|
1.0
|
|
CB
|
H:CYS2
|
3.0
|
10.8
|
1.0
|
|
CB
|
H:CYS6
|
3.3
|
12.0
|
1.0
|
|
CE1
|
H:HIS1
|
3.3
|
13.5
|
0.5
|
|
CG
|
H:HIS1
|
3.4
|
12.7
|
0.5
|
|
CB
|
H:HIS1
|
3.6
|
11.8
|
0.5
|
|
O
|
H:HOH2867
|
3.7
|
16.2
|
1.0
|
|
CG
|
H:HIS1
|
3.7
|
12.8
|
0.5
|
|
N
|
H:ASP3
|
3.7
|
8.7
|
1.0
|
|
C
|
H:CYS2
|
3.7
|
9.0
|
1.0
|
|
CB
|
H:HIS1
|
3.8
|
13.1
|
0.5
|
|
CD2
|
H:HIS1
|
3.8
|
14.1
|
0.5
|
|
N
|
H:CYS6
|
4.0
|
13.5
|
1.0
|
|
O
|
H:HIS1
|
4.0
|
11.3
|
1.0
|
|
O
|
H:VAL8
|
4.2
|
12.0
|
1.0
|
|
O
|
H:HOH2428
|
4.2
|
34.6
|
1.0
|
|
ND1
|
H:HIS1
|
4.2
|
16.3
|
0.5
|
|
CA
|
H:CYS6
|
4.2
|
12.2
|
1.0
|
|
NE2
|
H:HIS1
|
4.4
|
14.5
|
0.5
|
|
NE2
|
H:HIS1
|
4.5
|
15.0
|
0.5
|
|
CD2
|
H:HIS1
|
4.5
|
14.8
|
0.5
|
|
CE1
|
H:HIS1
|
4.7
|
15.7
|
0.5
|
|
O
|
H:CYS2
|
4.8
|
10.3
|
1.0
|
|
N
|
H:LEU4
|
4.9
|
10.2
|
1.0
|
|
N
|
H:GLY7
|
4.9
|
12.6
|
1.0
|
|
C
|
H:CYS6
|
4.9
|
11.1
|
1.0
|
|
Nickel binding site 9 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 9 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ni209
b:7.5
occ:1.00
|
N
|
I:HIS1
|
1.9
|
9.0
|
0.5
|
|
N
|
I:HIS1
|
1.9
|
10.2
|
0.5
|
|
N
|
I:CYS2
|
1.9
|
8.1
|
1.0
|
|
SG
|
I:CYS2
|
2.2
|
11.4
|
1.0
|
|
SG
|
I:CYS6
|
2.2
|
10.3
|
1.0
|
|
ND1
|
I:HIS1
|
2.3
|
12.7
|
0.5
|
|
C
|
I:HIS1
|
2.8
|
8.7
|
1.0
|
|
CA
|
I:HIS1
|
2.8
|
10.3
|
0.5
|
|
CA
|
I:HIS1
|
2.9
|
10.1
|
0.5
|
|
CA
|
I:CYS2
|
2.9
|
9.6
|
1.0
|
|
CB
|
I:CYS2
|
2.9
|
9.4
|
1.0
|
|
CE1
|
I:HIS1
|
3.2
|
13.6
|
0.5
|
|
CG
|
I:HIS1
|
3.3
|
10.4
|
0.5
|
|
CB
|
I:CYS6
|
3.4
|
10.7
|
1.0
|
|
CB
|
I:HIS1
|
3.6
|
9.0
|
0.5
|
|
N
|
I:ASP3
|
3.7
|
8.9
|
1.0
|
|
C
|
I:CYS2
|
3.7
|
8.2
|
1.0
|
|
O
|
I:HOH2894
|
3.8
|
14.4
|
1.0
|
|
CG
|
I:HIS1
|
3.8
|
9.6
|
0.5
|
|
CB
|
I:HIS1
|
3.9
|
9.8
|
0.5
|
|
O
|
I:HIS1
|
3.9
|
10.3
|
1.0
|
|
N
|
I:CYS6
|
4.0
|
10.4
|
1.0
|
|
O
|
I:HOH2308
|
4.1
|
20.8
|
1.0
|
|
ND1
|
I:HIS1
|
4.2
|
12.3
|
0.5
|
|
CD2
|
I:HIS1
|
4.2
|
10.6
|
0.5
|
|
CA
|
I:CYS6
|
4.2
|
10.4
|
1.0
|
|
O
|
I:VAL8
|
4.3
|
10.2
|
1.0
|
|
NE2
|
I:HIS1
|
4.4
|
12.5
|
0.5
|
|
CD2
|
I:HIS1
|
4.4
|
11.7
|
0.5
|
|
CE1
|
I:HIS1
|
4.7
|
11.4
|
0.5
|
|
NE2
|
I:HIS1
|
4.7
|
12.1
|
0.5
|
|
O
|
I:CYS2
|
4.8
|
11.3
|
1.0
|
|
N
|
I:GLY7
|
4.9
|
10.7
|
1.0
|
|
C
|
I:CYS6
|
4.9
|
10.8
|
1.0
|
|
N
|
I:LEU4
|
4.9
|
9.0
|
1.0
|
|
CB
|
K:SER20
|
4.9
|
13.7
|
1.0
|
|
N
|
I:VAL8
|
5.0
|
10.1
|
1.0
|
|
CA
|
I:ASP3
|
5.0
|
8.8
|
1.0
|
|
Nickel binding site 10 out
of 12 in 1t6u
Go back to
Nickel Binding Sites List in 1t6u
Nickel binding site 10 out
of 12 in the Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Nickel Superoxide Dismutase (Nisod) Native 1.30 A Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ni210
b:9.4
occ:1.00
|
N
|
J:CYS2
|
1.9
|
9.6
|
1.0
|
|
N
|
J:HIS1
|
1.9
|
9.8
|
0.5
|
|
SG
|
J:CYS2
|
2.2
|
13.3
|
1.0
|
|
SG
|
J:CYS6
|
2.2
|
12.1
|
1.0
|
|
N
|
J:HIS1
|
2.2
|
13.0
|
0.5
|
|
ND1
|
J:HIS1
|
2.4
|
15.2
|
0.5
|
|
C
|
J:HIS1
|
2.8
|
10.5
|
1.0
|
|
CA
|
J:HIS1
|
2.9
|
11.1
|
0.5
|
|
CA
|
J:CYS2
|
2.9
|
10.5
|
1.0
|
|
CA
|
J:HIS1
|
3.0
|
11.4
|
0.5
|
|
CB
|
J:CYS2
|
3.0
|
11.4
|
1.0
|
|
CE1
|
J:HIS1
|
3.2
|
12.9
|
0.5
|
|
CB
|
J:CYS6
|
3.3
|
12.5
|
1.0
|
|
CG
|
J:HIS1
|
3.4
|
12.3
|
0.5
|
|
O
|
J:HOH2932
|
3.6
|
19.0
|
1.0
|
|
C
|
J:CYS2
|
3.7
|
10.4
|
1.0
|
|
CB
|
J:HIS1
|
3.7
|
12.5
|
0.5
|
|
N
|
J:ASP3
|
3.7
|
10.5
|
1.0
|
|
CG
|
J:HIS1
|
3.8
|
12.2
|
0.5
|
|
CB
|
J:HIS1
|
3.8
|
12.4
|
0.5
|
|
N
|
J:CYS6
|
4.0
|
13.1
|
1.0
|
|
O
|
J:HIS1
|
4.0
|
11.1
|
1.0
|
|
O
|
J:HOH1385
|
4.1
|
22.2
|
1.0
|
|
ND1
|
J:HIS1
|
4.1
|
14.8
|
0.5
|
|
O
|
J:VAL8
|
4.2
|
12.0
|
1.0
|
|
CA
|
J:CYS6
|
4.2
|
13.0
|
1.0
|
|
CD2
|
J:HIS1
|
4.2
|
14.3
|
0.5
|
|
NE2
|
J:HIS1
|
4.4
|
12.4
|
0.5
|
|
CD2
|
J:HIS1
|
4.5
|
13.3
|
0.5
|
|
CE1
|
J:HIS1
|
4.7
|
13.3
|
0.5
|
|
NE2
|
J:HIS1
|
4.7
|
13.6
|
0.5
|
|
O
|
J:CYS2
|
4.8
|
12.9
|
1.0
|
|
N
|
J:GLY7
|
4.9
|
14.4
|
1.0
|
|
N
|
J:LEU4
|
4.9
|
10.7
|
1.0
|
|
C
|
J:CYS6
|
4.9
|
12.7
|
1.0
|
|
CB
|
G:SER20
|
4.9
|
14.8
|
1.0
|
|
N
|
J:VAL8
|
5.0
|
13.2
|
1.0
|
|
Reference:
D.P.Barondeau,
C.J.Kassmann,
C.K.Bruns,
J.A.Tainer,
E.D.Getzoff.
Nickel Superoxide Dismutase Structure and Mechanism. Biochemistry V. 43 8038 2004.
ISSN: ISSN 0006-2960
PubMed: 15209499
DOI: 10.1021/BI0496081
Page generated: Wed Oct 9 16:28:07 2024
|
