Copper in PDB 8rg9: High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy]

The structure of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy], PDB code: 8rg9 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 / 1.25
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	107.08, 107.08, 107.08, 90, 90, 90
R / Rfree (%)	11.3 / 13.6

The binding sites of Copper atom in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy] (pdb code 8rg9). 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) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy], PDB code: 8rg9:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 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) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:13.8 occ:1.00 ND1 A:HIS140 2.0 12.4 1.0 ND1 A:HIS89 2.0 12.5 1.0 SG A:CYS130 2.2 13.5 1.0 SD A:MET145 2.5 14.9 1.0 CE1 A:HIS89 3.0 13.3 1.0 CE1 A:HIS140 3.0 13.4 1.0 CG A:HIS140 3.1 12.5 1.0 CG A:HIS89 3.1 12.7 1.0 CB A:CYS130 3.2 13.0 1.0 CE A:MET145 3.3 14.7 1.0 CB A:HIS140 3.5 12.3 1.0 CB A:HIS89 3.5 13.0 1.0 CA A:HIS89 3.8 13.3 1.0 CG A:MET145 4.0 14.4 1.0 NE2 A:HIS140 4.1 14.4 1.0 O A:PRO88 4.1 14.9 1.0 NE2 A:HIS89 4.1 13.5 1.0 CD2 A:HIS140 4.1 13.6 1.0 CG A:PRO132 4.2 15.4 1.0 CD2 A:HIS89 4.2 13.1 1.0 CB A:MET145 4.4 12.7 1.0 SD A:MET56 4.6 16.0 0.4 CA A:CYS130 4.6 11.5 1.0 CD A:PRO132 4.7 13.5 1.0 N A:ASN90 4.7 13.2 1.0 CA A:HIS140 4.7 11.5 1.0 N A:HIS89 4.8 13.7 1.0 C A:HIS89 4.8 13.2 1.0 C A:PRO88 4.9 13.6 1.0 CE A:MET56 5.0 14.0 0.6

Copper binding site 2 out of 2 in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 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) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[2.24 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:13.1 occ:0.95 O1 A:NO2503 2.0 22.2 0.7 N A:NO2503 2.0 22.4 0.7 NE2 A:HIS94 2.0 10.8 1.0 NE2 A:HIS129 2.1 11.1 1.0 O2 A:NO2503 2.1 21.1 0.7 CE1 A:HIS94 3.0 10.7 1.0 CD2 A:HIS129 3.1 11.6 1.0 CD2 A:HIS94 3.1 11.0 1.0 CE1 A:HIS129 3.1 11.8 1.0 OD2 A:ASP92 3.6 25.2 0.8 O A:HOH930 4.1 33.6 0.5 ND1 A:HIS94 4.1 10.8 1.0 CG A:HIS129 4.2 11.3 1.0 CG A:HIS94 4.2 10.5 1.0 ND1 A:HIS129 4.2 11.8 1.0 O A:HOH916 4.2 16.6 0.2 O A:HOH958 4.2 28.2 0.5 CG A:ASP92 4.3 20.2 0.8 OD1 A:ASP92 4.6 19.3 0.8 OD2 A:ASP92 4.7 16.3 0.2 O A:HOH887 5.0 19.9 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