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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:

Zinc (Zn) 6 atoms
Calcium (Ca) 2 atoms

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 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 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

Go back to 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

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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: Thu Dec 28 03:50:41 2023

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