Zinc 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:

Calcium (Ca) 2 atoms
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 7ypp). 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: 7ypp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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:Zn502

b:32.4
occ:1.00
 OD1 A:ASP124 1.9 26.5 1.0
ND1 A:HIS121 1.9 25.0 1.0
ND1 A:HIS112 2.1 27.7 1.0
ND1 A:HIS104 2.1 23.0 1.0
CG A:ASP124 2.7 26.3 1.0
CE1 A:HIS121 2.8 25.5 1.0
OD2 A:ASP124 2.8 26.0 1.0
CE1 A:HIS112 3.0 29.9 1.0
CG A:HIS121 3.0 23.6 1.0
CE1 A:HIS104 3.0 25.5 1.0
CG A:HIS104 3.1 23.5 1.0
CG A:HIS112 3.2 28.6 1.0
CB A:HIS104 3.4 22.0 1.0
CB A:HIS121 3.5 23.3 1.0
CB A:HIS112 3.6 28.4 1.0
CA A:HIS112 3.9 28.3 1.0
NE2 A:HIS121 4.0 25.4 1.0
CD2 A:HIS121 4.1 25.1 1.0
O A:VAL178 4.1 31.2 1.0
CB A:ASP124 4.1 25.6 1.0
NE2 A:HIS112 4.1 28.4 1.0
NE2 A:HIS104 4.2 25.7 1.0
CD2 A:HIS112 4.2 28.6 1.0
CD2 A:HIS104 4.3 23.4 1.0
N A:HIS121 4.6 25.7 1.0
CA A:ASP124 4.6 24.7 1.0
CA A:ASN179 4.6 31.4 1.0
CA A:HIS121 4.7 25.1 1.0
O A:HOH646 4.7 42.2 1.0
N A:GLY113 4.8 29.6 1.0
N A:ASP124 4.8 22.9 1.0
N A:HIS112 4.9 26.2 1.0
C A:HIS112 4.9 29.8 1.0
CA A:HIS104 5.0 24.8 1.0
C A:VAL178 5.0 31.9 1.0

Zinc binding site 2 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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
C:Zn502

b:37.4
occ:1.00
 OD1 C:ASP124 1.9 29.6 1.0
ND1 C:HIS121 2.0 21.0 1.0
ND1 C:HIS112 2.0 30.7 1.0
ND1 C:HIS104 2.1 32.2 1.0
CG C:ASP124 2.7 30.6 1.0
OD2 C:ASP124 2.8 31.1 1.0
CE1 C:HIS121 2.8 19.7 1.0
CE1 C:HIS112 2.9 28.0 1.0
CE1 C:HIS104 3.0 32.5 1.0
CG C:HIS104 3.1 31.6 1.0
CG C:HIS121 3.1 20.7 1.0
CG C:HIS112 3.1 29.5 1.0
CB C:HIS104 3.5 28.6 1.0
CB C:HIS121 3.6 22.6 1.0
CB C:HIS112 3.6 28.1 1.0
CA C:HIS112 3.9 29.0 1.0
NE2 C:HIS121 4.0 20.8 1.0
NE2 C:HIS112 4.0 29.7 1.0
O C:VAL178 4.1 36.9 1.0
CB C:ASP124 4.1 28.0 1.0
NE2 C:HIS104 4.1 31.5 1.0
CD2 C:HIS121 4.2 21.2 1.0
CD2 C:HIS112 4.2 28.1 1.0
CD2 C:HIS104 4.2 29.1 1.0
CA C:ASN179 4.6 34.8 1.0
CA C:ASP124 4.6 28.2 1.0
N C:HIS121 4.7 24.8 1.0
CA C:HIS121 4.8 24.1 1.0
N C:GLY113 4.8 29.4 1.0
N C:ASP124 4.9 26.0 1.0
C C:HIS112 4.9 29.9 1.0
N C:HIS112 4.9 30.2 1.0
C C:VAL178 5.0 39.5 1.0
O C:HOH650 5.0 34.5 1.0
CA C:HIS104 5.0 29.6 1.0

Zinc binding site 3 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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
D:Zn502

b:33.7
occ:1.00
 ND1 D:HIS121 1.9 29.4 1.0
OD1 D:ASP124 1.9 29.4 1.0
ND1 D:HIS104 2.1 26.3 1.0
ND1 D:HIS112 2.1 29.4 1.0
CG D:ASP124 2.7 27.4 1.0
CE1 D:HIS121 2.8 28.3 1.0
OD2 D:ASP124 2.9 25.4 1.0
CE1 D:HIS112 3.0 28.7 1.0
CE1 D:HIS104 3.0 24.8 1.0
CG D:HIS121 3.0 27.1 1.0
CG D:HIS104 3.1 26.4 1.0
CG D:HIS112 3.2 30.7 1.0
CB D:HIS104 3.4 26.6 1.0
CB D:HIS121 3.5 23.9 1.0
CB D:HIS112 3.6 28.3 1.0
NE2 D:HIS121 3.9 28.1 1.0
CA D:HIS112 4.0 29.2 1.0
CD2 D:HIS121 4.1 28.6 1.0
O D:VAL178 4.1 40.0 1.0
NE2 D:HIS104 4.1 27.0 1.0
CB D:ASP124 4.1 28.1 1.0
NE2 D:HIS112 4.2 29.4 1.0
CD2 D:HIS104 4.2 25.6 1.0
CD2 D:HIS112 4.3 29.2 1.0
CA D:ASN179 4.6 35.2 1.0
N D:HIS121 4.6 25.7 1.0
CA D:ASP124 4.7 27.5 1.0
CA D:HIS121 4.7 25.2 1.0
N D:GLY113 4.9 31.1 1.0
N D:ASP124 4.9 25.7 1.0
N D:HIS112 4.9 28.6 1.0
CA D:HIS104 4.9 25.8 1.0
C D:HIS112 5.0 32.8 1.0
C D:VAL178 5.0 34.8 1.0

Zinc binding site 4 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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
E:Zn502

b:37.4
occ:1.00
 OD1 E:ASP124 2.0 27.3 1.0
ND1 E:HIS121 2.0 26.4 1.0
ND1 E:HIS104 2.0 29.7 1.0
ND1 E:HIS112 2.0 25.6 1.0
CG E:ASP124 2.7 26.4 1.0
CE1 E:HIS121 2.8 24.5 1.0
CE1 E:HIS112 2.9 24.7 1.0
OD2 E:ASP124 2.9 28.9 1.0
CE1 E:HIS104 3.0 30.6 1.0
CG E:HIS104 3.1 29.3 1.0
CG E:HIS121 3.1 26.4 1.0
CG E:HIS112 3.1 25.7 1.0
CB E:HIS104 3.4 27.4 1.0
CB E:HIS112 3.6 26.7 1.0
CB E:HIS121 3.6 24.2 1.0
CA E:HIS112 4.0 29.2 1.0
NE2 E:HIS121 4.0 26.9 1.0
O E:VAL178 4.0 39.1 1.0
NE2 E:HIS112 4.1 25.4 1.0
NE2 E:HIS104 4.1 30.2 1.0
CD2 E:HIS121 4.1 26.2 1.0
CB E:ASP124 4.2 25.4 1.0
CD2 E:HIS104 4.2 27.8 1.0
CD2 E:HIS112 4.2 27.2 1.0
CA E:ASN179 4.6 32.6 1.0
CA E:ASP124 4.7 26.5 1.0
N E:HIS121 4.7 25.2 1.0
CA E:HIS121 4.8 24.6 1.0
N E:GLY113 4.9 30.4 1.0
N E:ASP124 4.9 25.8 1.0
C E:VAL178 4.9 36.3 1.0
N E:HIS112 4.9 29.8 1.0
C E:HIS112 5.0 30.8 1.0
CA E:HIS104 5.0 28.2 1.0
O E:HOH665 5.0 35.7 1.0

Zinc binding site 5 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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
B:Zn502

b:35.3
occ:1.00
 OD1 B:ASP124 1.9 26.3 1.0
ND1 B:HIS121 2.0 26.8 1.0
ND1 B:HIS112 2.0 29.7 1.0
ND1 B:HIS104 2.1 32.0 1.0
CG B:ASP124 2.7 26.6 1.0
CE1 B:HIS121 2.8 27.7 1.0
OD2 B:ASP124 2.9 27.1 1.0
CE1 B:HIS112 2.9 29.1 1.0
CE1 B:HIS104 3.0 31.1 1.0
CG B:HIS121 3.1 25.7 1.0
CG B:HIS104 3.1 34.6 1.0
CG B:HIS112 3.1 31.4 1.0
CB B:HIS104 3.5 29.8 1.0
CB B:HIS112 3.5 30.3 1.0
CB B:HIS121 3.6 25.7 1.0
CA B:HIS112 3.9 31.2 1.0
NE2 B:HIS121 4.0 26.0 1.0
NE2 B:HIS112 4.1 32.0 1.0
O B:VAL178 4.1 37.9 1.0
CB B:ASP124 4.1 26.1 1.0
CD2 B:HIS121 4.1 26.3 1.0
NE2 B:HIS104 4.1 33.3 1.0
CD2 B:HIS112 4.2 31.6 1.0
CD2 B:HIS104 4.2 33.1 1.0
CA B:ASN179 4.6 33.6 1.0
CA B:ASP124 4.7 26.7 1.0
N B:HIS121 4.7 26.1 1.0
CA B:HIS121 4.8 25.2 1.0
N B:GLY113 4.8 28.9 1.0
N B:ASP124 4.9 26.1 1.0
O B:HOH639 4.9 28.9 1.0
N B:HIS112 4.9 29.6 1.0
C B:HIS112 4.9 30.1 1.0
C B:VAL178 5.0 36.4 1.0
CA B:HIS104 5.0 30.5 1.0

Zinc binding site 6 out of 6 in 7ypp

Go back to Zinc Binding Sites List in 7ypp
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:Zn502

b:39.1
occ:1.00
 OD1 F:ASP124 2.0 25.6 1.0
ND1 F:HIS121 2.0 28.0 1.0
ND1 F:HIS104 2.0 29.8 1.0
ND1 F:HIS112 2.1 30.6 1.0
CG F:ASP124 2.7 23.9 1.0
CE1 F:HIS121 2.8 24.5 1.0
OD2 F:ASP124 2.9 23.7 1.0
CE1 F:HIS112 2.9 28.0 1.0
CE1 F:HIS104 3.0 30.9 1.0
CG F:HIS104 3.1 30.2 1.0
CG F:HIS121 3.1 27.7 1.0
CG F:HIS112 3.2 30.1 1.0
CB F:HIS104 3.4 29.4 1.0
CB F:HIS121 3.6 24.4 1.0
CB F:HIS112 3.6 28.0 1.0
CA F:HIS112 4.0 31.3 1.0
NE2 F:HIS121 4.0 25.9 1.0
O F:VAL178 4.1 37.6 1.0
NE2 F:HIS112 4.1 30.2 1.0
NE2 F:HIS104 4.1 28.6 1.0
CD2 F:HIS121 4.1 26.6 1.0
CB F:ASP124 4.2 23.9 1.0
CD2 F:HIS104 4.2 29.3 1.0
CD2 F:HIS112 4.2 30.3 1.0
CA F:ASN179 4.6 31.2 1.0
CA F:ASP124 4.7 26.4 1.0
N F:HIS121 4.7 26.4 1.0
CA F:HIS121 4.8 25.6 1.0
O F:HOH648 4.9 25.1 1.0
N F:GLY113 4.9 29.3 1.0
N F:ASP124 4.9 24.6 1.0
CA F:HIS104 4.9 28.6 1.0
C F:VAL178 5.0 37.8 1.0
N F:HIS112 5.0 30.6 1.0
C F:HIS112 5.0 34.3 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 Oct 30 15:57:32 2024

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