Sodium in PDB 6y7e: Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A:
1.7.2.4;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A, PDB code: 6y7e 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) 108.30 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.281, 76.61, 108.464, 90, 93.23, 90
R / Rfree (%) 15.3 / 18.9

Other elements in 6y7e:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 3 atoms
Chlorine (Cl) 2 atoms
Copper (Cu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A (pdb code 6y7e). 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, H494A, PDB code: 6y7e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6y7e

Go back to Sodium Binding Sites List in 6y7e
Sodium binding site 1 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A


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, H494A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na807

b:19.3
occ:0.70
O A:MET168 2.3 17.8 1.0
O A:HOH1201 2.4 23.0 1.0
O A:HOH1493 2.4 33.0 1.0
O A:HOH1383 2.4 29.0 1.0
O A:HOH1186 2.5 20.4 1.0
O A:HOH1250 2.5 25.0 1.0
C A:MET168 3.5 17.9 1.0
O A:HOH1357 3.9 34.0 1.0
O A:ILE116 4.1 15.4 1.0
N A:MET168 4.1 15.3 1.0
O A:HOH1273 4.1 40.2 1.0
O A:HOH1502 4.1 40.3 1.0
O A:HOH1360 4.1 51.2 1.0
O A:HOH1475 4.3 34.1 1.0
CA A:MET168 4.4 12.3 1.0
N A:ILE169 4.4 15.0 1.0
CA A:ILE169 4.5 15.4 1.0
O A:HOH1275 4.5 20.3 1.0
O A:HOH1362 4.7 35.9 1.0
CB A:ILE169 4.9 18.1 1.0

Sodium binding site 2 out of 2 in 6y7e

Go back to Sodium Binding Sites List in 6y7e
Sodium binding site 2 out of 2 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A


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, H494A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1305

b:22.8
occ:0.59
O B:HOH1796 2.3 38.9 1.0
O B:HOH1700 2.3 29.8 1.0
O B:HOH1883 2.4 44.4 1.0
O B:MET168 2.4 23.4 1.0
O B:HOH1628 2.4 34.4 1.0
O B:HOH1637 2.5 21.8 1.0
C B:MET168 3.6 17.6 1.0
O B:HOH1711 3.8 51.8 1.0
O B:HOH1780 4.1 52.8 1.0
N B:MET168 4.1 17.9 1.0
O B:ILE116 4.1 19.4 1.0
O B:HOH1861 4.1 40.9 1.0
O B:HOH1777 4.2 45.4 1.0
N B:ILE169 4.5 20.1 1.0
CA B:ILE169 4.5 20.1 1.0
CA B:MET168 4.5 17.7 1.0
O B:HOH1806 4.6 39.1 1.0
O B:HOH1689 4.6 23.3 1.0
CB B:ILE169 4.8 24.8 1.0
O B:MET227 4.9 28.3 1.0

Reference:

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
Page generated: Wed Mar 3 15:29:23 2021

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