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Copper in PDB 7ypr: 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: 7ypr 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) 45.87 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 105.825, 105.825, 76.956, 90, 90, 120
R / Rfree (%) 18 / 22.8

Other elements in 7ypr:

The structure of Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1. also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 6 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 7ypr). 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: 7ypr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7ypr

Go back to Copper Binding Sites List in 7ypr
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:Cu202

b:39.2
occ:1.00
 NE2 A:HIS104 2.0 32.8 1.0
NE2 A:HIS162 2.0 34.4 1.0
ND1 A:HIS85 2.1 35.4 1.0
CE1 A:HIS104 2.8 25.5 1.0
O A:HOH301 2.9 42.3 1.0
CD2 A:HIS162 2.9 31.9 1.0
CG A:HIS85 3.0 29.4 1.0
CD2 A:HIS104 3.0 28.4 1.0
CE1 A:HIS162 3.1 29.2 1.0
CE1 A:HIS85 3.1 38.7 1.0
CB A:HIS85 3.3 30.7 1.0
ND1 A:HIS104 3.9 24.4 1.0
CG A:HIS104 4.1 36.6 1.0
CG A:HIS162 4.1 31.2 1.0
ND1 A:HIS162 4.1 27.5 1.0
CD2 A:HIS85 4.1 32.3 1.0
NE2 A:HIS85 4.1 32.9 1.0
O A:ASN179 4.4 34.9 1.0
CB A:ASN179 4.5 35.8 1.0
NH1 A:ARG185 4.5 35.8 0.5
O A:HOH365 4.6 42.6 1.0
CA A:HIS85 4.8 26.8 1.0

Copper binding site 2 out of 6 in 7ypr

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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
B:Cu202

b:49.1
occ:1.00
 NE2 B:HIS162 2.0 45.3 1.0
ND1 B:HIS85 2.2 35.7 1.0
NE2 B:HIS104 2.4 33.9 1.0
O B:HOH325 2.6 44.4 0.9
NE2 B:HIS87 2.7 37.5 1.0
CD2 B:HIS162 2.9 28.7 1.0
CG B:HIS85 3.0 31.9 1.0
CE1 B:HIS162 3.0 31.2 1.0
CB B:HIS85 3.1 28.0 1.0
CD2 B:HIS104 3.1 32.1 1.0
CE1 B:HIS85 3.3 37.1 1.0
CE1 B:HIS104 3.4 33.2 1.0
CD2 B:HIS87 3.5 39.5 1.0
CE1 B:HIS87 3.8 42.1 1.0
CG B:HIS162 4.1 33.4 1.0
ND1 B:HIS162 4.1 38.9 1.0
O B:HOH338 4.1 42.2 1.0
CD2 B:HIS85 4.2 31.5 1.0
CG B:HIS104 4.3 32.2 1.0
NE2 B:HIS85 4.3 38.2 1.0
ND1 B:HIS104 4.3 22.2 1.0
CA B:HIS85 4.4 30.8 1.0
CG1 B:VAL160 4.5 31.3 1.0
CB B:VAL160 4.6 28.6 1.0
N B:HIS85 4.7 25.5 1.0
CG B:HIS87 4.7 41.0 1.0
ND1 B:HIS87 4.8 44.8 1.0
C B:HIS85 5.0 30.3 1.0
O B:ASN179 5.0 30.4 1.0
O B:HIS85 5.0 28.9 1.0

Copper binding site 3 out of 6 in 7ypr

Go back to Copper Binding Sites List in 7ypr
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
C:Cu202

b:42.9
occ:1.00
 NE2 C:HIS104 2.0 32.3 1.0
NE2 C:HIS162 2.0 37.6 1.0
ND1 C:HIS85 2.1 28.7 1.0
CD2 C:HIS162 2.9 32.0 1.0
CE1 C:HIS104 2.9 29.0 1.0
CG C:HIS85 3.0 31.3 1.0
CD2 C:HIS104 3.0 29.9 1.0
O C:HOH366 3.0 49.1 1.0
CE1 C:HIS85 3.1 34.9 1.0
CE1 C:HIS162 3.1 35.2 1.0
CB C:HIS85 3.2 25.0 1.0
ND1 C:HIS104 4.0 23.8 1.0
CG C:HIS162 4.0 30.6 1.0
CG C:HIS104 4.1 33.2 1.0
ND1 C:HIS162 4.1 39.3 1.0
CD2 C:HIS85 4.1 33.5 1.0
NE2 C:HIS85 4.2 34.3 1.0
O C:ASN179 4.4 32.2 1.0
O C:HOH342 4.6 42.5 1.0
CB C:ASN179 4.7 30.4 1.0
CA C:HIS85 4.7 25.9 1.0
CG1 C:VAL160 4.9 31.8 1.0

Copper binding site 4 out of 6 in 7ypr

Go back to Copper Binding Sites List in 7ypr
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
D:Cu202

b:53.9
occ:1.00
 NE2 D:HIS162 2.1 43.5 1.0
ND1 D:HIS85 2.1 47.7 1.0
NE2 D:HIS104 2.2 40.0 1.0
NE2 D:HIS87 2.7 61.4 1.0
CD2 D:HIS162 2.8 39.7 1.0
CG D:HIS85 2.8 38.9 1.0
CB D:HIS85 3.0 35.7 1.0
CD2 D:HIS104 3.1 34.7 1.0
CE1 D:HIS162 3.1 39.8 1.0
CE1 D:HIS85 3.1 45.3 1.0
CE1 D:HIS104 3.2 41.5 1.0
CE1 D:HIS87 3.5 45.9 1.0
CD2 D:HIS87 3.8 54.5 1.0
O D:HOH304 3.9 30.0 1.0
CD2 D:HIS85 4.0 40.8 1.0
CG D:HIS162 4.0 38.6 1.0
ND1 D:HIS162 4.1 41.2 1.0
NE2 D:HIS85 4.1 48.8 1.0
ND1 D:HIS104 4.2 27.5 1.0
CG D:HIS104 4.2 37.5 1.0
CA D:HIS85 4.5 38.7 1.0
ND1 D:HIS87 4.6 44.8 1.0
O D:ASN179 4.8 43.2 1.0
CG D:HIS87 4.8 48.9 1.0
N D:HIS85 4.8 32.7 1.0
CG1 D:VAL160 5.0 35.1 1.0

Copper binding site 5 out of 6 in 7ypr

Go back to Copper Binding Sites List in 7ypr
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
E:Cu202

b:65.4
occ:1.00
 NE2 E:HIS162 1.9 56.8 1.0
ND1 E:HIS85 2.1 53.7 1.0
CD2 E:HIS162 2.6 44.6 1.0
NE2 E:HIS104 2.7 62.0 1.0
NE2 E:HIS87 2.8 53.3 0.6
CG E:HIS85 2.9 49.5 1.0
CE1 E:HIS162 3.1 55.1 1.0
O E:HOH322 3.1 52.1 1.0
CE1 E:HIS85 3.1 50.4 1.0
CB E:HIS85 3.2 49.6 1.0
CD2 E:HIS104 3.4 49.5 1.0
CD2 E:HIS87 3.6 50.9 0.6
CE1 E:HIS104 3.7 51.5 1.0
CE1 E:HIS87 3.8 55.5 0.6
CG E:HIS162 3.8 51.3 1.0
ND1 E:HIS162 4.0 46.7 1.0
CD2 E:HIS85 4.1 53.1 1.0
NE2 E:HIS85 4.2 56.3 1.0
CG1 E:VAL160 4.3 48.1 1.0
CA E:HIS85 4.5 49.8 1.0
CG E:HIS104 4.6 52.5 1.0
CB E:VAL160 4.6 49.6 1.0
N E:HIS85 4.7 48.3 1.0
ND1 E:HIS104 4.7 45.5 1.0
CG E:HIS87 4.8 51.2 0.6
ND1 E:HIS87 4.8 51.2 0.6
O E:ASN179 5.0 51.5 1.0

Copper binding site 6 out of 6 in 7ypr

Go back to Copper Binding Sites List in 7ypr
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:Cu202

b:46.9
occ:0.77
 NE2 F:HIS162 1.9 52.9 1.0
NE2 F:HIS104 2.0 48.9 1.0
ND1 F:HIS85 2.2 52.3 1.0
CE1 F:HIS162 2.8 53.5 1.0
CE1 F:HIS104 2.9 50.4 1.0
CD2 F:HIS162 2.9 47.9 1.0
CD2 F:HIS104 3.1 54.4 1.0
CG F:HIS85 3.1 50.8 1.0
CE1 F:HIS85 3.2 50.2 1.0
O F:HOH303 3.4 57.8 1.0
CB F:HIS85 3.4 43.7 1.0
ND1 F:HIS162 3.9 46.9 1.0
CG F:HIS162 3.9 50.0 1.0
ND1 F:HIS104 4.0 48.5 1.0
O F:HOH326 4.1 55.9 1.0
CG F:HIS104 4.1 41.3 1.0
CD2 F:HIS85 4.2 50.7 1.0
NE2 F:HIS85 4.2 52.9 1.0
O F:ASN179 4.4 60.6 1.0
CB F:ASN179 4.4 58.6 1.0
CA F:HIS85 4.8 46.1 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 09:24:20 2024

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