Copper in PDB 8rgd: High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy]

The structure of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy], PDB code: 8rgd 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 / 1.71
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	107.33, 107.33, 107.33, 90, 90, 90
R / Rfree (%)	15.6 / 18.9

The binding sites of Copper atom in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy] (pdb code 8rgd). 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 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy], PDB code: 8rgd:
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 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 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 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:25.1 occ:1.00 ND1 A:HIS140 2.0 23.6 1.0 ND1 A:HIS89 2.1 21.4 1.0 SG A:CYS130 2.2 24.0 1.0 SD A:MET145 2.5 26.9 1.0 CE1 A:HIS140 3.0 28.1 1.0 CE1 A:HIS89 3.0 22.8 1.0 CG A:HIS140 3.0 25.0 1.0 CG A:HIS89 3.1 22.1 1.0 CB A:CYS130 3.2 23.6 1.0 CE A:MET145 3.3 25.7 1.0 CB A:HIS89 3.5 22.4 1.0 CB A:HIS140 3.5 21.3 1.0 CA A:HIS89 3.9 20.3 1.0 CG A:MET145 3.9 26.1 1.0 NE2 A:HIS140 4.1 25.4 1.0 CD2 A:HIS140 4.1 27.1 1.0 NE2 A:HIS89 4.1 21.9 1.0 CD2 A:HIS89 4.2 21.5 1.0 CG A:PRO132 4.2 29.8 1.0 O A:PRO88 4.2 23.6 1.0 CB A:MET145 4.4 23.1 1.0 CE A:MET56 4.5 18.6 0.6 CA A:CYS130 4.6 21.3 1.0 N A:ASN90 4.7 20.5 1.0 CD A:PRO132 4.8 25.1 1.0 CA A:HIS140 4.8 22.4 1.0 C A:HIS89 4.9 23.0 1.0 N A:HIS89 4.9 24.2 1.0 C A:PRO88 5.0 23.4 1.0

Copper binding site 2 out of 2 in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 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 15 of the Copper Nitrite Reductase From Bradyrhizobium Sp. ORS375 (Two-Domain)[16.80 Mgy] within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:23.8 occ:0.95 N A:NO509 1.5 14.7 0.2 O A:NO509 1.9 16.3 0.2 O1 A:NO2503 2.0 25.0 0.2 NE2 A:HIS94 2.0 19.6 1.0 O2 A:NO2503 2.0 23.0 0.2 N A:NO2503 2.0 24.6 0.2 NE2 A:HIS129 2.1 21.4 1.0 CE1 A:HIS94 2.9 21.1 1.0 CD2 A:HIS129 3.1 21.0 1.0 CD2 A:HIS94 3.1 20.1 1.0 CE1 A:HIS129 3.1 21.7 1.0 O2 A:CO2508 3.5 28.0 0.3 C A:CO2508 3.9 26.6 0.3 ND1 A:HIS94 4.0 20.5 1.0 CG A:HIS94 4.2 19.0 1.0 CG A:HIS129 4.2 20.9 1.0 ND1 A:HIS129 4.3 21.9 1.0 O1 A:CO2508 4.6 22.6 0.3

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