Atomistry » Zinc » PDB 7ypa-7z1z » 7ypr
Atomistry »
  Zinc »
    PDB 7ypa-7z1z »
      7ypr »

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

Last articles

Ca in 5XT4
Ca in 5XTL
Ca in 5XSM
Ca in 5XT0
Ca in 5XSB
Ca in 5XSA
Ca in 5XQO
Ca in 5XS6
Ca in 5XRY
Ca in 5XRV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy