Copper in PDB 9hs0: Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110

All present enzymatic activity of Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110:
1.7.2.1;

The structure of Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110, PDB code: 9hs0 was solved by C.Tolmie, F.M.Ferroni, D.J.Opperman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.27 / 1.30
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	105.808, 105.808, 105.808, 90, 90, 90
R / Rfree (%)	9 / 10.9

The binding sites of Copper atom in the Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 (pdb code 9hs0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110, PDB code: 9hs0:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:9.4 occ:1.00 ND1 A:HIS89 2.0 9.3 1.0 ND1 A:HIS140 2.1 8.6 1.0 SG A:CYS130 2.2 8.9 1.0 SD A:MET145 2.5 10.6 1.0 CE1 A:HIS140 3.0 9.2 1.0 CE1 A:HIS89 3.0 8.7 1.0 CG A:HIS140 3.1 8.6 1.0 CG A:HIS89 3.1 8.1 1.0 CB A:CYS130 3.3 8.2 1.0 CE A:MET145 3.3 11.1 1.0 CB A:HIS89 3.5 8.6 1.0 CB A:HIS140 3.5 7.5 1.0 CA A:HIS89 3.9 8.5 1.0 CG A:MET145 4.0 10.6 1.0 NE2 A:HIS140 4.1 10.0 1.0 NE2 A:HIS89 4.2 8.7 1.0 CD2 A:HIS140 4.2 9.9 1.0 CD2 A:HIS89 4.2 8.2 1.0 CG A:PRO132 4.2 9.3 0.7 O A:PRO88 4.3 10.8 1.0 CG A:PRO132 4.4 9.4 0.3 CB A:MET145 4.5 8.6 1.0 SD A:MET56 4.6 13.3 0.4 CD A:PRO132 4.7 8.7 0.7 CA A:CYS130 4.7 7.5 1.0 N A:ASN90 4.7 8.1 1.0 CD A:PRO132 4.7 9.1 0.3 CA A:HIS140 4.8 7.2 1.0 C A:HIS89 4.9 8.3 1.0 N A:HIS89 4.9 9.1 1.0 CE A:MET56 4.9 7.7 0.6 C A:PRO88 5.0 9.9 1.0

Copper binding site 2 out of 2 in the Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper-Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:8.3 occ:1.00 O A:HOH510 2.0 12.7 1.0 NE2 A:HIS94 2.0 7.1 1.0 NE2 A:HIS129 2.0 8.0 1.0 CE1 A:HIS94 3.0 7.0 1.0 CD2 A:HIS129 3.0 8.1 1.0 CE1 A:HIS129 3.1 7.4 1.0 CD2 A:HIS94 3.1 6.9 1.0 OD2 A:ASP92 3.7 12.1 1.0 O A:HOH763 4.1 38.4 0.5 ND1 A:HIS94 4.2 6.8 1.0 CG A:HIS129 4.2 6.9 1.0 ND1 A:HIS129 4.2 7.4 1.0 CG A:HIS94 4.2 6.6 1.0 CG A:ASP92 4.4 10.3 1.0 OD1 A:ASP92 4.6 10.4 1.0

C.S.Ramirez, C.Tolmie, M.G.Rivas, P.J.Gonzalez, D.H.Murgida, D.J.Opperman, C.D.Brondino, F.M.Ferroni. Structural Insights Into the Copper-Containing Nitrite Reductase From Bradyrhizobium Japonicum USDA110 and Its Role in the Low Nitrite Reductase Activity of Rhizobia. Arch.Biochem.Biophys. V. 770 10467 2025.
ISSN: ESSN 1096-0384
PubMed: 40381977
DOI: 10.1016/J.ABB.2025.110467