Calcium in PDB 7ypp: 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;

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

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
Copper	(Cu)	6 atoms

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

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca503 b:31.2 occ:1.00 O A:THR143 2.4 21.5 1.0 O E:THR143 2.4 29.6 1.0 O A:HOH659 2.5 44.8 1.0 O A:HOH627 2.6 36.0 1.0 O E:HOH645 2.6 30.7 1.0 O E:HOH613 2.7 23.9 1.0 O E:HOH669 2.9 38.8 1.0 C A:THR143 3.6 23.1 1.0 C E:THR143 3.7 31.1 1.0 CA A:VAL144 4.4 26.0 1.0 N A:VAL144 4.4 23.6 1.0 O A:VAL144 4.5 24.7 1.0 CA A:THR143 4.5 24.3 1.0 CA E:VAL144 4.6 29.2 1.0 N E:VAL144 4.6 30.8 1.0 CA E:THR143 4.6 29.5 1.0 CB E:THR143 4.7 29.5 1.0 CB A:THR143 4.7 24.3 1.0 O E:ASP65 4.7 30.2 1.0 O E:VAL144 4.8 33.7 1.0 OD1 E:ASP65 4.8 41.5 1.0 C A:VAL144 4.8 26.6 1.0 OD1 A:ASP65 4.8 32.7 1.0 CA E:ASP65 4.8 30.2 1.0 CA A:ASP65 4.9 30.6 1.0 O A:HOH622 4.9 27.9 1.0 O A:ASP65 4.9 28.4 1.0 O A:HOH644 4.9 58.4 1.0 O E:HOH639 4.9 29.0 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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 D:Ca503 b:32.6 occ:1.00 O F:HOH641 2.3 35.5 1.0 O D:HOH651 2.4 34.0 1.0 O F:HOH618 2.4 28.4 1.0 O F:HOH626 2.5 30.9 1.0 O F:THR143 2.5 24.6 1.0 O D:THR143 2.5 23.4 1.0 O F:HOH627 2.6 26.7 1.0 C F:THR143 3.7 26.5 1.0 C D:THR143 3.7 25.2 1.0 CA D:VAL144 4.5 27.8 1.0 N D:VAL144 4.6 26.1 1.0 CA F:VAL144 4.6 29.9 1.0 N F:VAL144 4.6 28.1 1.0 O D:VAL144 4.6 28.5 1.0 O D:ASP65 4.6 29.0 1.0 CA F:THR143 4.6 25.4 1.0 CA D:THR143 4.6 27.2 1.0 O F:ASP65 4.6 27.8 1.0 CB F:THR143 4.7 25.0 1.0 O F:VAL144 4.7 32.8 1.0 CB D:THR143 4.8 28.3 1.0 CA D:ASP65 4.8 33.5 1.0 OD1 D:ASP65 4.8 35.8 1.0 CA F:ASP65 4.9 29.6 1.0 C D:VAL144 4.9 29.1 1.0 O D:HOH619 4.9 23.4 1.0 C F:VAL144 5.0 32.1 1.0 C D:ASP65 5.0 32.2 1.0 O F:HOH623 5.0 29.0 1.0

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