Sodium in PDB 6y6y: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A:
1.7.2.4;

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A, PDB code: 6y6y was solved by L.Zhang, 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)	76.45 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.463, 76.453, 108.449, 90, 93.22, 90
R / Rfree (%)	17.1 / 20.3

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Zinc	(Zn)	1 atom
Copper	(Cu)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A (pdb code 6y6y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A, PDB code: 6y6y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:19.2 occ:0.72 O A:HOH1098 2.3 26.2 1.0 O A:HOH1242 2.4 36.2 1.0 O A:MET168 2.4 19.6 1.0 O A:HOH1058 2.4 19.9 1.0 O A:HOH1172 2.4 28.5 1.0 O A:HOH992 2.5 30.0 1.0 C A:MET168 3.6 18.2 1.0 O A:HOH1171 4.0 34.6 1.0 N A:MET168 4.1 17.1 1.0 O A:HOH1251 4.1 42.3 1.0 O A:ILE116 4.1 17.4 1.0 O A:HOH1130 4.2 42.6 1.0 O A:HOH1225 4.4 36.6 1.0 CA A:MET168 4.4 17.4 1.0 N A:ILE169 4.5 16.1 1.0 CA A:ILE169 4.5 15.8 1.0 O A:HOH1105 4.6 18.0 1.0 O A:HOH1162 4.6 44.0 1.0 CB A:ILE169 4.9 15.9 1.0 O A:MET227 4.9 23.0 1.0

Sodium binding site 2 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H129A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:34.9 occ:0.75 O B:HOH1140 2.3 41.6 1.0 O B:HOH933 2.3 37.3 1.0 O B:HOH1032 2.3 31.8 1.0 O B:HOH1180 2.3 38.3 1.0 O B:HOH1022 2.4 24.2 1.0 O B:MET168 2.5 21.1 1.0 C B:MET168 3.7 20.8 1.0 O B:HOH1120 4.1 38.8 1.0 O B:ILE116 4.1 19.7 1.0 N B:MET168 4.2 20.2 1.0 O B:HOH1167 4.2 43.9 1.0 O B:HOH1112 4.4 46.3 1.0 O B:HOH1134 4.4 43.4 1.0 CA B:ILE169 4.6 19.3 1.0 CA B:MET168 4.6 21.0 1.0 N B:ILE169 4.6 18.9 1.0 O B:HOH1060 4.7 21.5 1.0 CB B:ILE169 4.8 20.2 1.0 O B:MET227 5.0 25.0 1.0

L.Zhang, E.Bill, P.M.H.Kroneck, O.Einsle. A [3CU:2S] Cluster Provides Insight Into the Assembly and Function of the Cuz Site of Nitrous Oxide Reductase Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC05204C