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

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

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

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

Calcium	(Ca)	1 atom
Sodium	(Na)	2 atoms
Chlorine	(Cl)	2 atoms
Copper	(Cu)	4 atoms

The binding sites of Zinc atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A (pdb code 6y7e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A, PDB code: 6y7e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:33.6 occ:0.31 NE2 A:HIS326 2.0 35.3 1.0 O A:HOH1368 2.0 33.3 1.0 NE2 A:HIS382 2.1 28.8 1.0 O A:HOH1334 2.6 37.8 1.0 CD2 A:HIS326 2.9 34.9 1.0 CE1 A:HIS326 3.0 41.1 1.0 CE1 A:HIS382 3.0 29.4 1.0 CD2 A:HIS382 3.2 28.1 1.0 NE2 A:HIS433 3.3 31.9 1.0 ZN A:ZN803 3.4 29.3 0.2 O A:HOH1345 3.6 50.5 1.0 CD2 A:HIS433 3.7 34.4 1.0 CE1 A:HIS433 4.0 32.7 1.0 CG A:HIS326 4.1 33.4 1.0 ND1 A:HIS326 4.1 37.8 1.0 O A:HOH1379 4.1 39.4 1.0 ND1 A:HIS382 4.2 27.3 1.0 CG A:HIS382 4.3 23.4 1.0 ND2 A:ASN241 4.4 31.1 1.0 CG A:HIS433 4.5 27.3 1.0 ND1 A:HIS433 4.6 31.4 1.0

Zinc binding site 2 out of 3 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:29.3 occ:0.25 O A:HOH1334 2.0 37.8 1.0 NE2 A:HIS433 2.1 31.9 1.0 O A:HOH1379 2.2 39.4 1.0 NE2 A:HIS130 2.5 27.0 1.0 CE1 A:HIS433 2.9 32.7 1.0 CD2 A:HIS433 3.2 34.4 1.0 ZN A:ZN802 3.4 33.6 0.3 CD2 A:HIS130 3.4 17.7 1.0 CE1 A:HIS130 3.5 24.3 1.0 O A:HOH1345 3.9 50.5 1.0 ND1 A:HIS433 4.1 31.4 1.0 NE2 A:HIS178 4.1 46.9 1.0 OD1 A:ASN241 4.2 30.8 1.0 CG A:HIS433 4.2 27.3 1.0 NE2 A:HIS382 4.3 28.8 1.0 CB A:HIS129 4.4 22.0 1.0 O A:HOH1368 4.4 33.3 1.0 CE1 A:HIS382 4.4 29.4 1.0 O A:HOH1303 4.5 40.7 1.0 ND1 A:HIS130 4.6 21.8 1.0 CG A:HIS130 4.6 22.5 1.0 CB A:ALA494 4.7 33.3 1.0 CE1 A:HIS178 4.7 49.9 1.0 NE2 A:HIS326 4.8 35.3 1.0 CD2 A:HIS178 4.9 45.0 1.0 CG A:HIS129 4.9 27.6 1.0 CD2 A:HIS129 4.9 30.5 1.0 ND2 A:ASN241 5.0 31.1 1.0

Zinc binding site 3 out of 3 in the Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pseudomonas Stutzeri Nitrous Oxide Reductase Mutant, H494A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:83.3 occ:1.00 NE2 B:HIS326 2.0 47.2 1.0 CE1 B:HIS382 2.2 46.5 0.6 O B:HOH1812 2.5 50.6 1.0 CD2 B:HIS326 2.8 44.8 1.0 O B:HOH1447 2.9 39.7 1.0 NE2 B:HIS382 2.9 39.9 0.6 NE2 B:HIS433 3.0 44.1 1.0 CE1 B:HIS326 3.1 40.6 1.0 CD2 B:HIS433 3.3 45.9 1.0 ND1 B:HIS382 3.3 37.0 0.6 O B:HOH1770 3.8 45.0 1.0 CE1 B:HIS433 3.9 48.4 1.0 CG B:HIS326 4.0 39.3 1.0 ND1 B:HIS326 4.1 43.6 1.0 CD2 B:HIS382 4.2 33.9 0.6 OD1 B:ASN241 4.2 40.5 1.0 CG B:HIS433 4.3 35.8 1.0 CG B:HIS382 4.4 33.4 0.6 ND1 B:HIS433 4.6 42.0 1.0 CE2 A:PHE621 5.0 41.4 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