Calcium in PDB 7apy: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A:
1.7.2.4;

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A, PDB code: 7apy was solved by L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.84 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.964, 76.627, 108.563, 90, 93.41, 90
R / Rfree (%)	16.6 / 22.5

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Copper	(Cu)	12 atoms
Chlorine	(Cl)	3 atoms
Potassium	(K)	2 atoms

The binding sites of Calcium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A (pdb code 7apy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A, PDB code: 7apy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:17.8 occ:0.58 OE2 A:GLU259 2.3 31.8 1.0 OD1 A:ASN324 2.3 36.9 1.0 OD1 A:ASP273 2.4 31.1 1.0 OD2 A:ASP273 2.4 30.8 1.0 O A:HOH824 2.4 32.3 1.0 O A:MET267 2.4 43.2 1.0 O A:TYR256 2.4 29.9 1.0 CG A:ASP273 2.7 33.2 1.0 OE1 A:GLU259 2.8 34.9 1.0 CD A:GLU259 2.9 40.8 1.0 CG A:ASN324 3.3 23.6 1.0 C A:TYR256 3.5 32.9 1.0 C A:MET267 3.5 47.3 1.0 ND2 A:ASN324 3.9 19.8 1.0 CB A:ASP273 4.3 27.9 1.0 CA A:MET268 4.3 41.9 1.0 CA A:TYR256 4.3 30.8 1.0 N A:ASN257 4.3 29.2 1.0 N A:MET268 4.3 36.0 1.0 CA A:ASN257 4.4 28.6 1.0 CG A:GLU259 4.4 39.2 1.0 OG A:SER258 4.4 38.8 1.0 N A:ASN324 4.4 21.2 1.0 CA A:ASN324 4.4 21.5 1.0 N A:SER258 4.5 30.1 1.0 CB A:ASN324 4.5 20.7 1.0 CA A:MET267 4.5 45.8 1.0 O A:ASN270 4.6 29.5 1.0 CB A:ASN270 4.8 35.2 1.0 C A:MET268 4.8 45.6 1.0 N A:ASN270 4.8 36.9 1.0 C A:ASN257 4.9 23.3 1.0 N A:ARG269 4.9 44.0 1.0 CB A:TYR256 5.0 32.9 1.0

Calcium binding site 2 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, D576A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:30.8 occ:0.96 O B:TYR256 2.4 24.0 1.0 OD2 B:ASP273 2.4 33.9 1.0 O B:MET267 2.4 31.1 1.0 O B:HOH830 2.4 33.0 1.0 OD1 B:ASN324 2.5 30.2 1.0 OE2 B:GLU259 2.5 30.8 1.0 OE1 B:GLU259 2.7 29.9 1.0 OD1 B:ASP273 2.8 31.1 1.0 CD B:GLU259 2.9 30.9 1.0 CG B:ASP273 3.0 33.0 1.0 C B:TYR256 3.5 23.4 1.0 CG B:ASN324 3.5 29.2 1.0 C B:MET267 3.5 28.7 1.0 ND2 B:ASN324 4.0 26.9 1.0 OG B:SER258 4.1 33.4 1.0 CA B:TYR256 4.3 24.3 1.0 N B:ASN257 4.3 26.4 1.0 CA B:ASN257 4.3 30.6 1.0 N B:SER258 4.3 31.8 1.0 N B:MET268 4.3 27.3 1.0 CA B:MET268 4.4 32.3 1.0 CA B:MET267 4.4 34.6 1.0 CG B:GLU259 4.4 26.7 1.0 CB B:ASP273 4.5 31.9 1.0 O B:ASN270 4.6 35.7 1.0 N B:ASN324 4.7 32.3 1.0 C B:MET268 4.7 32.5 1.0 CB B:ASN324 4.7 25.9 1.0 CA B:ASN324 4.7 24.5 1.0 N B:ASN270 4.8 32.2 1.0 N B:ARG269 4.8 39.4 1.0 C B:ASN257 4.8 35.0 1.0 CB B:TYR256 4.9 26.9 1.0 CB B:ASN270 4.9 29.2 1.0

L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle. Histidine-Gated Proton-Coupled Electron Transfer to the Cu A Site of Nitrous Oxide Reductase. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 33377777
DOI: 10.1021/JACS.0C10057