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Zinc 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
Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural Basis of A Superoxide Dismutase From A Tardigrade, Ramazzottius Varieornatus Strain Yokozuna-1., PDB code: 7ypr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:31.2
occ:1.00
 OD1 A:ASP124 1.9 24.2 1.0
ND1 A:HIS121 2.2 29.1 1.0
ND1 A:HIS104 2.2 24.4 1.0
ND1 A:HIS112 2.2 30.3 1.0
CG A:ASP124 2.7 32.2 1.0
OD2 A:ASP124 2.9 32.6 1.0
CE1 A:HIS121 3.0 28.8 1.0
CE1 A:HIS112 3.1 38.1 1.0
CE1 A:HIS104 3.2 25.5 1.0
CG A:HIS104 3.2 36.6 1.0
CG A:HIS121 3.2 31.9 1.0
CG A:HIS112 3.3 36.0 1.0
CB A:HIS104 3.5 26.1 1.0
CB A:HIS121 3.6 34.5 1.0
CB A:HIS112 3.6 32.9 1.0
CA A:HIS112 4.0 34.1 1.0
O A:VAL178 4.0 41.4 1.0
NE2 A:HIS121 4.1 31.4 1.0
CB A:ASP124 4.2 29.0 1.0
CD2 A:HIS121 4.3 31.4 1.0
NE2 A:HIS104 4.3 32.8 1.0
NE2 A:HIS112 4.3 35.8 1.0
CD2 A:HIS104 4.3 28.4 1.0
CD2 A:HIS112 4.4 36.4 1.0
CA A:ASN179 4.4 35.7 1.0
CA A:ASP124 4.7 30.8 1.0
N A:HIS121 4.7 32.0 1.0
O A:HOH350 4.7 36.1 1.0
CA A:HIS121 4.8 23.2 1.0
N A:GLY113 4.9 34.1 1.0
N A:ASP124 4.9 23.7 1.0
C A:VAL178 4.9 41.8 1.0
N A:HIS112 4.9 32.0 1.0
C A:HIS112 4.9 41.8 1.0

Zinc binding site 2 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:27.4
occ:1.00
 OD1 B:ASP124 1.9 23.1 1.0
ND1 B:HIS104 2.2 22.2 1.0
ND1 B:HIS121 2.2 25.1 1.0
ND1 B:HIS112 2.3 27.0 1.0
CG B:ASP124 2.7 26.6 1.0
OD2 B:ASP124 2.9 25.6 1.0
CE1 B:HIS121 3.1 28.0 1.0
CE1 B:HIS104 3.1 33.2 1.0
CG B:HIS104 3.2 32.2 1.0
CG B:HIS121 3.2 24.9 1.0
CE1 B:HIS112 3.2 27.9 1.0
CG B:HIS112 3.3 29.4 1.0
CB B:HIS104 3.5 24.5 1.0
CB B:HIS121 3.5 23.5 1.0
CB B:HIS112 3.6 20.6 1.0
CA B:HIS112 3.9 32.4 1.0
CB B:ASP124 4.2 24.7 1.0
NE2 B:HIS121 4.2 29.7 1.0
O B:VAL178 4.2 38.2 1.0
CD2 B:HIS121 4.2 32.2 1.0
NE2 B:HIS104 4.3 33.9 1.0
CD2 B:HIS104 4.3 32.1 1.0
NE2 B:HIS112 4.3 32.4 1.0
CD2 B:HIS112 4.4 31.7 1.0
CA B:ASN179 4.5 30.3 1.0
CA B:ASP124 4.7 24.7 1.0
N B:HIS121 4.7 17.9 1.0
CA B:HIS121 4.8 26.5 1.0
N B:GLY113 4.8 30.1 1.0
N B:ASP124 4.9 26.8 1.0
N B:HIS112 4.9 27.0 1.0
C B:HIS112 4.9 34.7 1.0
O B:HOH336 4.9 33.8 1.0
CA B:HIS104 5.0 27.4 1.0

Zinc binding site 3 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:30.1
occ:1.00
 OD1 C:ASP124 1.9 26.5 1.0
ND1 C:HIS104 2.2 23.8 1.0
ND1 C:HIS121 2.2 32.6 1.0
ND1 C:HIS112 2.3 27.8 1.0
CG C:ASP124 2.7 26.5 1.0
OD2 C:ASP124 2.9 31.2 1.0
CE1 C:HIS121 3.1 29.1 1.0
CE1 C:HIS104 3.1 29.0 1.0
CE1 C:HIS112 3.1 30.3 1.0
CG C:HIS104 3.2 33.2 1.0
CG C:HIS121 3.2 33.2 1.0
CG C:HIS112 3.3 34.3 1.0
CB C:HIS104 3.5 25.2 1.0
CB C:HIS121 3.6 29.1 1.0
CB C:HIS112 3.6 31.4 1.0
CA C:HIS112 4.0 31.7 1.0
O C:VAL178 4.0 35.7 1.0
CB C:ASP124 4.1 24.9 1.0
NE2 C:HIS121 4.2 29.8 1.0
NE2 C:HIS104 4.2 32.3 1.0
CD2 C:HIS104 4.3 29.9 1.0
CD2 C:HIS121 4.3 32.8 1.0
NE2 C:HIS112 4.3 35.4 1.0
CD2 C:HIS112 4.4 31.8 1.0
CA C:ASN179 4.5 29.8 1.0
CA C:ASP124 4.6 26.2 1.0
O C:HOH328 4.7 34.5 1.0
N C:HIS121 4.8 25.9 1.0
N C:ASP124 4.8 23.8 1.0
CA C:HIS121 4.8 27.9 1.0
C C:VAL178 4.8 37.6 1.0
N C:GLY113 4.9 32.3 1.0
N C:HIS112 4.9 33.6 1.0
CA C:HIS104 5.0 34.5 1.0
C C:HIS112 5.0 37.5 1.0

Zinc binding site 4 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:37.5
occ:1.00
 OD1 D:ASP124 2.0 30.6 1.0
ND1 D:HIS104 2.2 27.5 1.0
ND1 D:HIS121 2.2 34.9 1.0
ND1 D:HIS112 2.3 42.2 1.0
CG D:ASP124 2.9 42.5 1.0
OD2 D:ASP124 3.1 37.4 1.0
CE1 D:HIS104 3.1 41.5 1.0
CE1 D:HIS121 3.1 38.9 1.0
CG D:HIS104 3.1 37.5 1.0
CG D:HIS121 3.2 37.1 1.0
CE1 D:HIS112 3.2 44.8 1.0
CG D:HIS112 3.3 43.8 1.0
CB D:HIS104 3.4 31.0 1.0
CB D:HIS121 3.5 34.4 1.0
CB D:HIS112 3.6 34.9 1.0
CA D:HIS112 3.9 43.4 1.0
O D:VAL178 4.2 46.0 1.0
NE2 D:HIS121 4.2 39.1 1.0
NE2 D:HIS104 4.2 40.0 1.0
CB D:ASP124 4.2 33.8 1.0
CD2 D:HIS121 4.3 39.6 1.0
CD2 D:HIS104 4.3 34.7 1.0
O D:VAL178 4.3 45.6 0.0
NE2 D:HIS112 4.3 47.4 1.0
CD2 D:HIS112 4.4 46.6 1.0
CA D:ASN179 4.5 44.3 1.0
CA D:ASP124 4.7 39.2 1.0
N D:HIS121 4.7 38.1 1.0
CA D:HIS121 4.7 42.5 1.0
N D:ASP124 4.8 41.7 1.0
N D:GLY113 4.8 39.2 1.0
O D:HOH332 4.9 42.5 1.0
CD2 D:HIS85 4.9 40.8 1.0
N D:HIS112 4.9 38.3 1.0
C D:HIS112 4.9 43.8 1.0
CA D:HIS104 5.0 40.3 1.0

Zinc binding site 5 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:47.1
occ:1.00
 OD1 E:ASP124 2.0 51.0 1.0
ND1 E:HIS104 2.1 45.5 1.0
ND1 E:HIS121 2.2 50.1 1.0
ND1 E:HIS112 2.3 45.4 1.0
CG E:ASP124 2.8 45.5 1.0
OD2 E:ASP124 2.9 49.4 1.0
CE1 E:HIS104 3.0 51.5 1.0
CG E:HIS104 3.1 52.5 1.0
CG E:HIS121 3.1 51.6 1.0
CE1 E:HIS112 3.1 49.9 1.0
CE1 E:HIS121 3.2 40.8 1.0
CG E:HIS112 3.3 57.3 1.0
CB E:HIS121 3.4 42.4 1.0
CB E:HIS104 3.5 45.9 1.0
CB E:HIS112 3.7 53.6 1.0
CA E:HIS112 4.0 53.4 1.0
O E:VAL178 4.0 52.1 1.0
NE2 E:HIS104 4.1 62.0 1.0
CB E:ASP124 4.2 51.6 1.0
CD2 E:HIS104 4.2 49.5 1.0
NE2 E:HIS121 4.2 50.6 1.0
CD2 E:HIS121 4.2 49.0 1.0
NE2 E:HIS112 4.3 62.9 1.0
CD2 E:HIS112 4.4 58.3 1.0
CA E:ASN179 4.6 53.8 1.0
CA E:ASP124 4.6 47.7 1.0
CA E:HIS121 4.7 48.9 1.0
O E:HOH324 4.7 50.9 1.0
N E:HIS121 4.7 48.3 1.0
N E:ASP124 4.9 48.9 1.0
N E:GLY113 4.9 50.7 1.0
N E:HIS112 4.9 52.3 1.0
C E:ASN179 4.9 60.2 1.0
C E:VAL178 5.0 59.6 1.0
C E:HIS112 5.0 59.1 1.0
O E:ASN179 5.0 51.5 1.0

Zinc binding site 6 out of 6 in 7ypr

Go back to Zinc Binding Sites List in 7ypr
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:49.8
occ:1.00
 OD1 F:ASP124 1.9 50.0 1.0
ND1 F:HIS121 2.2 49.9 1.0
ND1 F:HIS104 2.2 48.5 1.0
ND1 F:HIS112 2.3 58.6 1.0
CG F:ASP124 2.7 61.5 1.0
OD2 F:ASP124 2.8 48.9 1.0
CG F:HIS121 3.1 51.4 1.0
CE1 F:HIS121 3.2 52.6 1.0
CE1 F:HIS104 3.2 50.4 1.0
CG F:HIS104 3.2 41.3 1.0
CG F:HIS112 3.3 59.9 1.0
CE1 F:HIS112 3.3 57.3 1.0
CB F:HIS121 3.4 46.4 1.0
CB F:HIS104 3.5 43.4 1.0
CB F:HIS112 3.5 57.7 1.0
O F:VAL178 3.8 54.7 1.0
CA F:HIS112 4.0 54.7 1.0
CB F:ASP124 4.1 45.0 1.0
NE2 F:HIS121 4.2 57.2 1.0
CD2 F:HIS121 4.2 51.8 1.0
NE2 F:HIS104 4.2 48.9 1.0
CD2 F:HIS104 4.3 54.4 1.0
NE2 F:HIS112 4.4 63.1 1.0
CD2 F:HIS112 4.4 56.6 1.0
CA F:ASN179 4.5 61.9 1.0
N F:HIS121 4.6 50.9 1.0
CA F:ASP124 4.6 50.8 1.0
CA F:HIS121 4.7 59.3 1.0
C F:VAL178 4.7 61.3 1.0
N F:GLY113 4.9 57.2 1.0
N F:ASP124 4.9 41.9 1.0
CD2 F:HIS85 4.9 50.7 1.0
C F:HIS112 5.0 57.8 1.0
N F:HIS112 5.0 63.0 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 12:43:55 2023

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