Copper in PDB 8rfp: Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate

The structure of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate, PDB code: 8rfp 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 / 1.23
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	104.21, 104.21, 64.37, 90, 90, 120
R / Rfree (%)	11.4 / 13.8

The binding sites of Copper atom in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate (pdb code 8rfp). 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 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate, PDB code: 8rfp:
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 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate


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 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:15.3 occ:0.95 ND1 A:HIS89 2.1 14.2 1.0 ND1 A:HIS140 2.1 14.8 1.0 SG A:CYS130 2.2 15.2 1.0 SD A:MET145 2.5 16.8 1.0 CE1 A:HIS89 2.9 14.2 1.0 CE1 A:HIS140 3.0 15.5 1.0 CG A:HIS140 3.1 14.8 1.0 CG A:HIS89 3.1 13.7 1.0 CB A:CYS130 3.2 14.3 1.0 CE A:MET145 3.3 17.1 1.0 CB A:HIS89 3.5 14.3 1.0 CB A:HIS140 3.5 13.3 1.0 CA A:HIS89 3.8 13.9 1.0 CG A:MET145 4.0 18.6 1.0 NE2 A:HIS140 4.1 15.8 1.0 CG A:PRO132 4.1 18.4 0.6 NE2 A:HIS89 4.1 14.8 1.0 O A:PRO88 4.2 17.0 1.0 CD2 A:HIS140 4.2 16.0 1.0 CD2 A:HIS89 4.2 14.4 1.0 CG A:PRO132 4.2 18.8 0.4 CB A:MET145 4.5 14.8 1.0 SD A:MET56 4.6 18.7 0.5 CD A:PRO132 4.6 15.7 0.6 N A:ASN90 4.7 14.8 1.0 CA A:CYS130 4.7 12.3 1.0 CD A:PRO132 4.7 16.9 0.4 CA A:HIS140 4.7 13.0 1.0 N A:HIS89 4.8 14.4 1.0 C A:HIS89 4.8 14.4 1.0 C A:PRO88 4.9 15.8 1.0 CE A:MET56 4.9 14.7 0.5

Copper binding site 2 out of 2 in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate


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 3 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [3.06 Mgy] - Nitrite/No Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:12.7 occ:0.95 O1 A:NO2403 2.0 13.3 0.3 NE2 A:HIS94 2.0 11.6 1.0 N A:NO2403 2.0 15.5 0.3 NE2 A:HIS129 2.0 12.8 1.0 O A:NO406 2.2 28.4 0.4 N A:NO406 2.2 25.5 0.4 O2 A:NO2403 2.5 18.9 0.3 CD2 A:HIS129 3.0 12.6 1.0 CE1 A:HIS94 3.0 12.7 1.0 CE1 A:HIS129 3.0 13.3 1.0 CD2 A:HIS94 3.1 11.9 1.0 OD2 A:ASP92 3.7 25.7 0.8 O A:HOH512 4.1 21.9 0.3 O A:HOH512 4.1 28.0 0.3 ND1 A:HIS94 4.1 11.8 1.0 CG A:HIS129 4.2 11.9 1.0 ND1 A:HIS129 4.2 12.7 1.0 CG A:HIS94 4.2 11.5 1.0 CG A:ASP92 4.3 20.0 0.8 OD1 A:ASP92 4.6 20.2 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