Sodium in PDB 7aq8: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A, PDB code: 7aq8 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) 69.43 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.545, 76.667, 109.062, 90, 93.27, 90
R / Rfree (%) 15.8 / 21.7

Other elements in 7aq8:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A also contains other interesting chemical elements:

Potassium (K) 2 atoms
Calcium (Ca) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms
Copper (Cu) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A (pdb code 7aq8). 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, H583Y/D576A, PDB code: 7aq8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7aq8

Go back to Sodium Binding Sites List in 7aq8
Sodium binding site 1 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:32.7
occ:0.92
O A:HOH1208 2.2 41.7 1.0
O A:MET168 2.3 29.0 1.0
O A:HOH1154 2.4 28.8 1.0
O A:HOH994 2.5 25.0 1.0
O A:HOH931 2.5 18.9 1.0
O A:HOH1056 2.6 26.2 1.0
C A:MET168 3.5 21.4 1.0
O A:HOH1130 3.8 36.6 1.0
O A:HOH1219 3.9 55.3 1.0
O A:HOH1083 4.0 42.8 1.0
N A:MET168 4.1 19.4 1.0
O A:ILE116 4.1 21.6 1.0
O A:HOH1198 4.2 38.4 1.0
CA A:MET168 4.4 19.5 1.0
N A:ILE169 4.4 20.6 1.0
CA A:ILE169 4.4 26.8 1.0
O A:HOH1067 4.4 26.2 1.0
O A:HOH1139 4.8 41.3 1.0
CB A:ILE169 4.8 20.2 1.0

Sodium binding site 2 out of 2 in 7aq8

Go back to Sodium Binding Sites List in 7aq8
Sodium binding site 2 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H583Y/D576A


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, H583Y/D576A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:38.0
occ:0.70
O B:HOH1120 2.2 41.0 1.0
O B:MET168 2.4 24.4 1.0
O B:HOH965 2.4 27.6 1.0
O B:HOH1037 2.4 41.3 1.0
O B:HOH1081 2.5 44.6 1.0
O B:HOH1046 2.6 43.5 1.0
C B:MET168 3.6 23.0 1.0
O B:ILE116 4.1 27.6 1.0
N B:MET168 4.1 22.8 1.0
O B:HOH1115 4.3 43.4 1.0
O B:HOH1071 4.3 50.0 1.0
CA B:MET168 4.5 26.1 1.0
N B:ILE169 4.5 21.9 1.0
CA B:ILE169 4.5 23.6 1.0
O B:HOH1016 4.6 29.4 1.0
O B:HOH1059 4.6 49.7 1.0
CB B:ILE169 4.9 27.6 1.0

Reference:

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
Page generated: Mon Jan 25 15:51:23 2021

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