Copper in PDB 2zkx: Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
Enzymatic activity of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
All present enzymatic activity of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121:
1.15.1.1;
Protein crystallography data
The structure of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121, PDB code: 2zkx
was solved by
S.Yoshikawa,
M.Kukimoto-Niino,
K.Ito,
L.Chen,
Z.Q.Fu,
J.Chrzas,
B.C.Wang,
M.Shirouzu,
M.Urushitani,
R.Takahashi,
S.Yokoyama,
Riken Structuralgenomics/Proteomics Initiative (Rsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.55 /
2.72
|
Space group
|
I 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.105,
113.080,
146.375,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
24.6
|
Other elements in 2zkx:
The structure of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
(pdb code 2zkx). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121, PDB code: 2zkx:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 2zkx
Go back to
Copper Binding Sites List in 2zkx
Copper binding site 1 out
of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu301
b:45.7
occ:1.00
|
ND1
|
A:HIS46
|
1.9
|
38.6
|
1.0
|
NE2
|
A:HIS120
|
2.0
|
34.9
|
1.0
|
NE2
|
A:HIS48
|
2.2
|
22.7
|
1.0
|
CE1
|
A:HIS46
|
2.7
|
35.7
|
1.0
|
CD2
|
A:HIS120
|
3.0
|
30.8
|
1.0
|
CG
|
A:HIS46
|
3.0
|
37.5
|
1.0
|
CE1
|
A:HIS48
|
3.0
|
18.6
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
33.4
|
1.0
|
NE2
|
A:HIS63
|
3.0
|
33.7
|
1.0
|
CD2
|
A:HIS48
|
3.3
|
25.0
|
1.0
|
CD2
|
A:HIS63
|
3.5
|
33.3
|
1.0
|
CB
|
A:HIS46
|
3.5
|
29.6
|
1.0
|
NE2
|
A:HIS46
|
3.9
|
37.1
|
1.0
|
CE1
|
A:HIS63
|
4.0
|
30.8
|
1.0
|
CD2
|
A:HIS46
|
4.0
|
39.0
|
1.0
|
ND1
|
A:HIS120
|
4.1
|
29.5
|
1.0
|
CG
|
A:HIS120
|
4.1
|
32.3
|
1.0
|
CB
|
A:VAL118
|
4.2
|
26.1
|
1.0
|
ND1
|
A:HIS48
|
4.2
|
26.6
|
1.0
|
N
|
A:HIS46
|
4.2
|
23.1
|
1.0
|
CG1
|
A:VAL118
|
4.3
|
19.4
|
1.0
|
CA
|
A:HIS46
|
4.3
|
28.0
|
1.0
|
CG
|
A:HIS48
|
4.4
|
26.8
|
1.0
|
CG
|
A:HIS63
|
4.5
|
29.2
|
1.0
|
C
|
A:HIS46
|
4.7
|
27.6
|
1.0
|
ND1
|
A:HIS63
|
4.7
|
34.0
|
1.0
|
O
|
A:VAL118
|
4.8
|
29.1
|
1.0
|
O
|
A:HIS46
|
4.9
|
27.4
|
1.0
|
CG2
|
A:VAL118
|
4.9
|
28.9
|
1.0
|
|
Copper binding site 2 out
of 4 in 2zkx
Go back to
Copper Binding Sites List in 2zkx
Copper binding site 2 out
of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu302
b:49.5
occ:1.00
|
NE2
|
B:HIS120
|
2.1
|
39.8
|
1.0
|
NE2
|
B:HIS48
|
2.2
|
28.0
|
1.0
|
ND1
|
B:HIS46
|
2.5
|
28.6
|
1.0
|
NE2
|
B:HIS63
|
2.8
|
27.1
|
1.0
|
CE1
|
B:HIS48
|
2.9
|
23.9
|
1.0
|
CE1
|
B:HIS120
|
3.0
|
36.1
|
1.0
|
CD2
|
B:HIS120
|
3.1
|
37.3
|
1.0
|
CG
|
B:HIS46
|
3.3
|
27.7
|
1.0
|
CD2
|
B:HIS48
|
3.3
|
27.5
|
1.0
|
CD2
|
B:HIS63
|
3.3
|
25.5
|
1.0
|
CB
|
B:HIS46
|
3.4
|
21.4
|
1.0
|
CE1
|
B:HIS46
|
3.5
|
27.0
|
1.0
|
CE1
|
B:HIS63
|
3.7
|
32.8
|
1.0
|
ND1
|
B:HIS48
|
4.0
|
18.9
|
1.0
|
ND1
|
B:HIS120
|
4.1
|
36.0
|
1.0
|
CG
|
B:HIS120
|
4.2
|
28.2
|
1.0
|
CG
|
B:HIS48
|
4.3
|
26.9
|
1.0
|
CG
|
B:HIS63
|
4.4
|
24.9
|
1.0
|
CA
|
B:HIS46
|
4.4
|
20.7
|
1.0
|
CB
|
B:VAL118
|
4.5
|
20.2
|
1.0
|
CD2
|
B:HIS46
|
4.5
|
31.4
|
1.0
|
N
|
B:HIS46
|
4.5
|
24.7
|
1.0
|
NE2
|
B:HIS46
|
4.6
|
30.5
|
1.0
|
ND1
|
B:HIS63
|
4.6
|
22.4
|
1.0
|
CG1
|
B:VAL118
|
4.7
|
15.9
|
1.0
|
C
|
B:HIS46
|
4.8
|
25.8
|
1.0
|
O
|
B:HIS46
|
4.9
|
24.3
|
1.0
|
O
|
B:VAL118
|
4.9
|
24.3
|
1.0
|
|
Copper binding site 3 out
of 4 in 2zkx
Go back to
Copper Binding Sites List in 2zkx
Copper binding site 3 out
of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu303
b:41.0
occ:1.00
|
NE2
|
C:HIS120
|
1.9
|
22.5
|
1.0
|
ND1
|
C:HIS46
|
2.0
|
33.6
|
1.0
|
NE2
|
C:HIS48
|
2.0
|
23.8
|
1.0
|
CE1
|
C:HIS120
|
2.6
|
14.5
|
1.0
|
CE1
|
C:HIS46
|
2.9
|
35.0
|
1.0
|
CE1
|
C:HIS48
|
3.0
|
27.9
|
1.0
|
CD2
|
C:HIS48
|
3.0
|
35.4
|
1.0
|
NE2
|
C:HIS63
|
3.0
|
25.5
|
1.0
|
CG
|
C:HIS46
|
3.1
|
25.8
|
1.0
|
CD2
|
C:HIS120
|
3.1
|
27.5
|
1.0
|
CD2
|
C:HIS63
|
3.4
|
26.9
|
1.0
|
CB
|
C:HIS46
|
3.5
|
24.7
|
1.0
|
ND1
|
C:HIS120
|
3.8
|
19.7
|
1.0
|
CE1
|
C:HIS63
|
4.0
|
23.1
|
1.0
|
NE2
|
C:HIS46
|
4.1
|
35.1
|
1.0
|
CB
|
C:VAL118
|
4.1
|
22.0
|
1.0
|
ND1
|
C:HIS48
|
4.1
|
20.8
|
1.0
|
CG
|
C:HIS120
|
4.1
|
24.6
|
1.0
|
CG
|
C:HIS48
|
4.1
|
15.6
|
1.0
|
CD2
|
C:HIS46
|
4.2
|
27.7
|
1.0
|
N
|
C:HIS46
|
4.3
|
30.4
|
1.0
|
CA
|
C:HIS46
|
4.3
|
31.1
|
1.0
|
O
|
C:HIS46
|
4.3
|
29.9
|
1.0
|
O
|
C:VAL118
|
4.4
|
27.3
|
1.0
|
CG
|
C:HIS63
|
4.4
|
21.1
|
1.0
|
CG1
|
C:VAL118
|
4.4
|
17.3
|
1.0
|
C
|
C:HIS46
|
4.6
|
29.1
|
1.0
|
ND1
|
C:HIS63
|
4.7
|
20.8
|
1.0
|
CG2
|
C:VAL118
|
4.7
|
20.5
|
1.0
|
C
|
C:VAL118
|
4.9
|
16.4
|
1.0
|
|
Copper binding site 4 out
of 4 in 2zkx
Go back to
Copper Binding Sites List in 2zkx
Copper binding site 4 out
of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu304
b:63.7
occ:1.00
|
NE2
|
D:HIS120
|
2.0
|
48.7
|
1.0
|
ND1
|
D:HIS46
|
2.3
|
52.0
|
1.0
|
CE1
|
D:HIS46
|
2.3
|
52.6
|
1.0
|
NE2
|
D:HIS48
|
2.3
|
31.9
|
1.0
|
CE1
|
D:HIS120
|
2.9
|
44.5
|
1.0
|
NE2
|
D:HIS63
|
2.9
|
74.0
|
1.0
|
CD2
|
D:HIS120
|
3.0
|
46.8
|
1.0
|
CE1
|
D:HIS48
|
3.1
|
26.5
|
1.0
|
CD2
|
D:HIS63
|
3.3
|
68.8
|
1.0
|
CD2
|
D:HIS48
|
3.4
|
36.7
|
1.0
|
NE2
|
D:HIS46
|
3.6
|
39.3
|
1.0
|
CG
|
D:HIS46
|
3.6
|
51.3
|
1.0
|
ND1
|
D:HIS120
|
3.9
|
46.3
|
1.0
|
CE1
|
D:HIS63
|
4.0
|
70.7
|
1.0
|
CG
|
D:HIS120
|
4.1
|
48.0
|
1.0
|
CD2
|
D:HIS46
|
4.2
|
45.1
|
1.0
|
ND1
|
D:HIS48
|
4.3
|
34.0
|
1.0
|
CG
|
D:HIS48
|
4.5
|
33.8
|
1.0
|
CG
|
D:HIS63
|
4.5
|
63.8
|
1.0
|
CB
|
D:HIS46
|
4.6
|
52.0
|
1.0
|
CG1
|
D:VAL118
|
4.6
|
43.4
|
1.0
|
CB
|
D:VAL118
|
4.6
|
38.8
|
1.0
|
ND1
|
D:HIS63
|
4.8
|
63.8
|
1.0
|
N
|
D:HIS46
|
4.8
|
38.8
|
1.0
|
O
|
D:HIS46
|
4.9
|
56.3
|
1.0
|
|
Reference:
S.Yoshikawa,
M.Kukimoto-Niino,
K.Ito,
L.Chen,
Z.Q.Fu,
J.Chrzas,
B.C.Wang,
M.Shirouzu,
M.Urushitani,
R.Takahashi,
S.Yokoyama.
Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 To Be Published.
Page generated: Wed Jul 31 00:29:03 2024
|