Copper in PDB 8rfv: High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy]

The structure of High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy], PDB code: 8rfv 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)	35.00 / 1.31
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	107.07, 107.07, 107.07, 90, 90, 90
R / Rfree (%)	13.9 / 17.3

The binding sites of Copper atom in the High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy] (pdb code 8rfv). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy], PDB code: 8rfv:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy]


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:15.6 occ:1.00 ND1 A:HIS140 2.0 14.1 1.0 ND1 A:HIS89 2.0 14.0 1.0 SG A:CYS130 2.2 15.1 1.0 SD A:MET145 2.5 16.0 1.0 CE1 A:HIS140 2.9 15.4 1.0 CE1 A:HIS89 3.0 14.8 1.0 CG A:HIS140 3.1 14.3 1.0 CG A:HIS89 3.1 14.2 1.0 CB A:CYS130 3.2 14.9 1.0 CE A:MET145 3.3 16.4 1.0 CB A:HIS89 3.5 15.1 1.0 CB A:HIS140 3.5 14.0 1.0 CA A:HIS89 3.8 13.7 1.0 CG A:MET145 4.0 15.7 1.0 NE2 A:HIS140 4.1 16.4 1.0 O A:PRO88 4.1 16.7 1.0 NE2 A:HIS89 4.1 15.3 1.0 CG A:PRO132 4.1 16.8 1.0 CD2 A:HIS140 4.2 17.4 1.0 CD2 A:HIS89 4.2 14.4 1.0 CB A:MET145 4.5 14.9 1.0 CD A:PRO132 4.5 15.8 1.0 CA A:CYS130 4.6 13.7 1.0 SD A:MET56 4.6 18.7 0.5 N A:ASN90 4.6 14.2 1.0 CA A:HIS140 4.7 13.2 1.0 C A:HIS89 4.8 14.6 1.0 N A:HIS89 4.8 15.8 1.0 C A:PRO88 4.9 16.0 1.0 CE A:MET56 4.9 15.9 0.5

Copper binding site 2 out of 2 in the High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy]


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High pH (8.0) As-Isolated Msox Movie Series Dataset 1 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[0.68 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:15.1 occ:0.95 O A:HOH503 1.9 28.9 1.0 NE2 A:HIS94 2.0 13.3 1.0 NE2 A:HIS129 2.0 13.0 1.0 O A:HOH799 2.3 24.0 0.5 CE1 A:HIS94 3.0 13.1 1.0 CD2 A:HIS129 3.0 13.5 1.0 CD2 A:HIS94 3.1 13.2 1.0 CE1 A:HIS129 3.1 14.3 1.0 OD2 A:ASP92 3.5 32.9 1.0 O A:HOH506 4.0 29.7 0.5 ND1 A:HIS94 4.1 11.8 1.0 CG A:HIS129 4.2 13.1 1.0 CG A:HIS94 4.2 11.7 1.0 ND1 A:HIS129 4.2 13.7 1.0 CG A:ASP92 4.2 23.8 1.0 OD1 A:ASP92 4.5 25.4 1.0

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