Copper in PDB 7ypp: Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Enzymatic activity of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
All present enzymatic activity of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.:
1.15.1.1;
Protein crystallography data
The structure of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1., PDB code: 7ypp
was solved by
K.-S.Sim,
Y.Fukuda,
T.Inoue,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.30 /
2.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.102,
68.049,
68.135,
94.9,
108.39,
114.4
|
R / Rfree (%)
|
19.8 /
23.4
|
Other elements in 7ypp:
The structure of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
(pdb code 7ypp). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1., PDB code: 7ypp:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 7ypp
Go back to
Copper Binding Sites List in 7ypp
Copper binding site 1 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:49.7
occ:1.00
|
ND1
|
A:HIS85
|
2.0
|
29.9
|
1.0
|
NE2
|
A:HIS104
|
2.1
|
25.7
|
1.0
|
NE2
|
A:HIS162
|
2.2
|
32.4
|
1.0
|
CE1
|
A:HIS85
|
2.9
|
28.1
|
1.0
|
CE1
|
A:HIS104
|
2.9
|
25.5
|
1.0
|
CG
|
A:HIS85
|
3.0
|
31.9
|
1.0
|
O
|
A:HOH610
|
3.0
|
35.0
|
1.0
|
CD2
|
A:HIS162
|
3.1
|
32.0
|
1.0
|
CD2
|
A:HIS104
|
3.1
|
23.4
|
1.0
|
CE1
|
A:HIS162
|
3.1
|
30.3
|
1.0
|
CB
|
A:HIS85
|
3.3
|
26.5
|
1.0
|
NE2
|
A:HIS85
|
4.0
|
28.6
|
1.0
|
ND1
|
A:HIS104
|
4.0
|
23.0
|
1.0
|
CD2
|
A:HIS85
|
4.0
|
27.8
|
1.0
|
O
|
A:ASN179
|
4.1
|
36.8
|
1.0
|
CG
|
A:HIS104
|
4.1
|
23.5
|
1.0
|
CG
|
A:HIS162
|
4.1
|
30.1
|
1.0
|
ND1
|
A:HIS162
|
4.1
|
33.4
|
1.0
|
CB
|
A:ASN179
|
4.5
|
30.3
|
1.0
|
O
|
A:HOH672
|
4.6
|
38.1
|
1.0
|
O
|
A:HOH625
|
4.8
|
40.1
|
1.0
|
CA
|
A:HIS85
|
4.8
|
25.9
|
1.0
|
|
Copper binding site 2 out
of 6 in 7ypp
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Copper Binding Sites List in 7ypp
Copper binding site 2 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu501
b:55.9
occ:1.00
|
ND1
|
C:HIS85
|
2.0
|
30.9
|
1.0
|
NE2
|
C:HIS104
|
2.1
|
31.5
|
1.0
|
NE2
|
C:HIS162
|
2.2
|
31.8
|
1.0
|
CE1
|
C:HIS85
|
2.9
|
28.0
|
1.0
|
CE1
|
C:HIS104
|
3.0
|
32.5
|
1.0
|
CG
|
C:HIS85
|
3.0
|
27.6
|
1.0
|
CD2
|
C:HIS162
|
3.1
|
29.8
|
1.0
|
CD2
|
C:HIS104
|
3.1
|
29.1
|
1.0
|
CE1
|
C:HIS162
|
3.2
|
27.6
|
1.0
|
CB
|
C:HIS85
|
3.4
|
24.7
|
1.0
|
O
|
C:HOH671
|
3.4
|
56.5
|
1.0
|
NE2
|
C:HIS85
|
4.0
|
28.7
|
1.0
|
ND1
|
C:HIS104
|
4.1
|
32.2
|
1.0
|
CD2
|
C:HIS85
|
4.1
|
26.7
|
1.0
|
O
|
C:ASN179
|
4.1
|
31.4
|
1.0
|
CG
|
C:HIS104
|
4.2
|
31.6
|
1.0
|
CG
|
C:HIS162
|
4.2
|
28.5
|
1.0
|
ND1
|
C:HIS162
|
4.2
|
28.4
|
1.0
|
CB
|
C:ASN179
|
4.5
|
32.9
|
1.0
|
CA
|
C:HIS85
|
4.8
|
24.9
|
1.0
|
|
Copper binding site 3 out
of 6 in 7ypp
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Copper Binding Sites List in 7ypp
Copper binding site 3 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cu501
b:53.4
occ:1.00
|
NE2
|
D:HIS104
|
2.0
|
27.0
|
1.0
|
ND1
|
D:HIS85
|
2.1
|
33.7
|
1.0
|
NE2
|
D:HIS162
|
2.2
|
32.9
|
1.0
|
CE1
|
D:HIS104
|
2.9
|
24.8
|
1.0
|
CE1
|
D:HIS85
|
2.9
|
31.3
|
1.0
|
CD2
|
D:HIS104
|
3.0
|
25.6
|
1.0
|
CG
|
D:HIS85
|
3.1
|
32.6
|
1.0
|
CD2
|
D:HIS162
|
3.1
|
28.0
|
1.0
|
CE1
|
D:HIS162
|
3.1
|
29.2
|
1.0
|
O
|
D:HOH659
|
3.2
|
46.8
|
1.0
|
CB
|
D:HIS85
|
3.4
|
28.8
|
1.0
|
ND1
|
D:HIS104
|
4.0
|
26.3
|
1.0
|
O
|
D:ASN179
|
4.0
|
33.7
|
1.0
|
NE2
|
D:HIS85
|
4.0
|
34.1
|
1.0
|
CG
|
D:HIS104
|
4.1
|
26.4
|
1.0
|
CD2
|
D:HIS85
|
4.1
|
31.5
|
1.0
|
ND1
|
D:HIS162
|
4.2
|
29.8
|
1.0
|
CG
|
D:HIS162
|
4.2
|
29.3
|
1.0
|
CB
|
D:ASN179
|
4.4
|
35.4
|
1.0
|
CA
|
D:HIS85
|
4.9
|
29.0
|
1.0
|
C
|
D:ASN179
|
5.0
|
33.0
|
1.0
|
|
Copper binding site 4 out
of 6 in 7ypp
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Copper Binding Sites List in 7ypp
Copper binding site 4 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cu501
b:58.2
occ:1.00
|
ND1
|
E:HIS85
|
2.0
|
29.7
|
1.0
|
NE2
|
E:HIS162
|
2.1
|
31.8
|
1.0
|
NE2
|
E:HIS104
|
2.2
|
30.2
|
1.0
|
O
|
E:HOH673
|
2.7
|
44.5
|
1.0
|
CD2
|
E:HIS162
|
3.0
|
28.3
|
1.0
|
CE1
|
E:HIS85
|
3.0
|
30.2
|
1.0
|
CG
|
E:HIS85
|
3.0
|
27.0
|
1.0
|
CE1
|
E:HIS162
|
3.1
|
32.3
|
1.0
|
CE1
|
E:HIS104
|
3.1
|
30.6
|
1.0
|
CD2
|
E:HIS104
|
3.2
|
27.8
|
1.0
|
O
|
E:HOH620
|
3.3
|
44.0
|
1.0
|
CB
|
E:HIS85
|
3.4
|
23.6
|
1.0
|
CG
|
E:HIS162
|
4.1
|
28.2
|
1.0
|
ND1
|
E:HIS162
|
4.1
|
30.0
|
1.0
|
NE2
|
E:HIS85
|
4.1
|
34.8
|
1.0
|
CD2
|
E:HIS85
|
4.1
|
28.5
|
1.0
|
ND1
|
E:HIS104
|
4.2
|
29.7
|
1.0
|
O
|
E:ASN179
|
4.2
|
33.4
|
1.0
|
CG
|
E:HIS104
|
4.3
|
29.3
|
1.0
|
CB
|
E:ASN179
|
4.6
|
34.0
|
1.0
|
O
|
E:HOH658
|
4.6
|
51.6
|
1.0
|
O
|
E:HOH618
|
4.7
|
36.7
|
1.0
|
CA
|
E:HIS85
|
4.8
|
24.6
|
1.0
|
|
Copper binding site 5 out
of 6 in 7ypp
Go back to
Copper Binding Sites List in 7ypp
Copper binding site 5 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu501
b:51.7
occ:1.00
|
ND1
|
B:HIS85
|
1.9
|
30.2
|
1.0
|
NE2
|
B:HIS162
|
2.1
|
34.5
|
1.0
|
NE2
|
B:HIS104
|
2.2
|
33.3
|
1.0
|
O
|
B:HOH651
|
2.6
|
39.4
|
1.0
|
CE1
|
B:HIS85
|
2.8
|
29.9
|
1.0
|
CG
|
B:HIS85
|
3.0
|
27.2
|
1.0
|
CD2
|
B:HIS162
|
3.0
|
32.9
|
1.0
|
CE1
|
B:HIS104
|
3.0
|
31.1
|
1.0
|
CE1
|
B:HIS162
|
3.1
|
30.9
|
1.0
|
CD2
|
B:HIS104
|
3.2
|
33.1
|
1.0
|
CB
|
B:HIS85
|
3.3
|
24.3
|
1.0
|
O
|
B:HOH601
|
3.4
|
42.1
|
1.0
|
NE2
|
B:HIS85
|
4.0
|
30.7
|
1.0
|
CD2
|
B:HIS85
|
4.0
|
28.0
|
1.0
|
CG
|
B:HIS162
|
4.0
|
29.0
|
1.0
|
ND1
|
B:HIS162
|
4.0
|
31.2
|
1.0
|
ND1
|
B:HIS104
|
4.1
|
32.0
|
1.0
|
O
|
B:ASN179
|
4.2
|
31.2
|
1.0
|
CG
|
B:HIS104
|
4.2
|
34.6
|
1.0
|
CB
|
B:ASN179
|
4.6
|
33.5
|
1.0
|
O
|
B:HOH627
|
4.6
|
49.9
|
1.0
|
CA
|
B:HIS85
|
4.8
|
25.7
|
1.0
|
|
Copper binding site 6 out
of 6 in 7ypp
Go back to
Copper Binding Sites List in 7ypp
Copper binding site 6 out
of 6 in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1.
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cu501
b:60.4
occ:1.00
|
ND1
|
F:HIS85
|
2.0
|
27.1
|
1.0
|
NE2
|
F:HIS162
|
2.1
|
42.6
|
1.0
|
NE2
|
F:HIS104
|
2.3
|
28.6
|
1.0
|
CD2
|
F:HIS162
|
2.9
|
36.5
|
1.0
|
CE1
|
F:HIS85
|
2.9
|
28.0
|
1.0
|
CE1
|
F:HIS162
|
3.0
|
40.2
|
1.0
|
CG
|
F:HIS85
|
3.0
|
25.2
|
1.0
|
CE1
|
F:HIS104
|
3.1
|
30.9
|
1.0
|
CD2
|
F:HIS104
|
3.3
|
29.3
|
1.0
|
CB
|
F:HIS85
|
3.4
|
24.4
|
1.0
|
O
|
F:HOH615
|
3.6
|
41.3
|
1.0
|
O
|
F:HOH668
|
3.7
|
52.9
|
1.0
|
CG
|
F:HIS162
|
4.0
|
35.8
|
1.0
|
ND1
|
F:HIS162
|
4.0
|
40.1
|
1.0
|
NE2
|
F:HIS85
|
4.1
|
27.3
|
1.0
|
CD2
|
F:HIS85
|
4.1
|
26.2
|
1.0
|
O
|
F:ASN179
|
4.2
|
30.9
|
1.0
|
ND1
|
F:HIS104
|
4.2
|
29.8
|
1.0
|
CG
|
F:HIS104
|
4.3
|
30.2
|
1.0
|
O
|
F:HOH647
|
4.4
|
51.4
|
1.0
|
CB
|
F:ASN179
|
4.6
|
33.6
|
1.0
|
CA
|
F:HIS85
|
4.9
|
24.8
|
1.0
|
|
Reference:
K.S.Sim,
T.Inoue.
Structure of A Superoxide Dismutase From A Tardigrade: Ramazzottius Varieornatus Strain Yokozuna-1. Acta Crystallogr.,Sect.F V. 79 169 2023.
ISSN: ESSN 2053-230X
PubMed: 37358501
DOI: 10.1107/S2053230X2300523X
Page generated: Wed Jul 31 09:24:14 2024
|