Copper in PDB 8rfs: Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand

The structure of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand, PDB code: 8rfs was solved by S.L.Rose, F.M.Ferroni, S.V.Antonyuk, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.54
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	104.45, 104.45, 64.6, 90, 90, 120
R / Rfree (%)	14.5 / 17.2

The binding sites of Copper atom in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand (pdb code 8rfs). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand, PDB code: 8rfs:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:21.9 occ:0.95 ND1 A:HIS140 2.0 22.1 1.0 ND1 A:HIS89 2.1 18.0 1.0 SG A:CYS130 2.2 21.8 1.0 SD A:MET145 2.5 25.0 1.0 CE1 A:HIS89 3.0 20.1 1.0 CE1 A:HIS140 3.0 22.2 1.0 CG A:HIS140 3.1 22.1 1.0 CG A:HIS89 3.1 20.8 1.0 CB A:CYS130 3.3 19.4 1.0 CE A:MET145 3.3 23.5 1.0 CB A:HIS89 3.5 19.6 1.0 CB A:HIS140 3.5 19.6 1.0 CA A:HIS89 3.9 19.2 1.0 CG A:MET145 4.0 26.2 1.0 CG A:PRO132 4.1 25.7 0.6 NE2 A:HIS140 4.2 22.4 1.0 NE2 A:HIS89 4.2 18.5 1.0 CG A:PRO132 4.2 26.2 0.4 CD2 A:HIS140 4.2 26.0 1.0 CD2 A:HIS89 4.2 19.5 1.0 O A:PRO88 4.3 23.0 1.0 CB A:MET145 4.4 21.1 1.0 SD A:MET56 4.5 29.4 0.5 CA A:CYS130 4.7 16.2 1.0 CD A:PRO132 4.7 22.6 0.6 N A:ASN90 4.7 18.2 1.0 CD A:PRO132 4.7 24.2 0.4 CA A:HIS140 4.7 18.3 1.0 C A:HIS89 4.9 20.4 1.0 N A:HIS89 4.9 19.9 1.0 C A:PRO88 5.0 22.1 1.0 CE A:MET56 5.0 22.0 0.5

Copper binding site 2 out of 2 in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 11 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [11.22 Mgy] - Water Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:19.2 occ:0.95 O A:HOH523 1.9 31.6 1.0 NE2 A:HIS129 2.0 18.4 1.0 NE2 A:HIS94 2.0 18.6 1.0 CD2 A:HIS129 3.0 18.4 1.0 CE1 A:HIS94 3.0 20.3 1.0 CE1 A:HIS129 3.1 19.6 1.0 CD2 A:HIS94 3.1 17.6 1.0 OD2 A:ASP92 3.8 43.9 0.8 O A:HOH742 3.9 56.3 1.0 ND1 A:HIS94 4.1 18.3 1.0 CG A:HIS129 4.2 16.5 1.0 ND1 A:HIS129 4.2 16.9 1.0 CG A:HIS94 4.2 15.6 1.0 CG A:ASP92 4.4 38.2 0.8 OD1 A:ASP92 4.6 33.6 0.8

S.L.Rose, F.Martin Ferroni, S.Horrell, C.Dante Brondino, R.R.Eady, S.Jaho, M.A.Hough, R.L.Owen, S.V.Antonyuk, S.Samar Hasnain. Spectroscopically Validated pH-Dependent Msox Movies Provide Detailed Mechanism of Copper Nitrite Reductases. J.Mol.Biol. 68706 2024.
ISSN: ESSN 1089-8638
PubMed: 39002715
DOI: 10.1016/J.JMB.2024.168706