Copper in PDB 8rfl: Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start)

The structure of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start), PDB code: 8rfl 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 / 1.16
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	104.06, 104.06, 64.25, 90, 90, 120
R / Rfree (%)	11.4 / 13.5

The binding sites of Copper atom in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start) (pdb code 8rfl). 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 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start), PDB code: 8rfl:
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 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start)


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 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:14.5 occ:0.95 ND1 A:HIS89 2.0 14.1 1.0 ND1 A:HIS140 2.0 13.6 1.0 SG A:CYS130 2.2 14.5 1.0 SD A:MET145 2.5 14.0 0.7 SD A:MET145 2.6 10.6 0.3 CE1 A:HIS89 2.9 14.0 1.0 CE1 A:HIS140 2.9 14.8 1.0 CG A:HIS140 3.1 13.5 1.0 CG A:HIS89 3.1 13.0 1.0 CB A:CYS130 3.2 13.2 1.0 CE A:MET145 3.3 14.9 0.7 CE A:MET145 3.4 11.6 0.3 CB A:HIS89 3.5 13.5 1.0 CB A:HIS140 3.5 12.8 1.0 CA A:HIS89 3.8 13.7 1.0 CG A:MET145 4.0 14.8 0.7 CG A:MET145 4.0 10.8 0.3 CG A:PRO132 4.1 15.4 0.6 O A:PRO88 4.1 16.5 1.0 NE2 A:HIS140 4.1 15.7 1.0 NE2 A:HIS89 4.1 14.8 1.0 CD2 A:HIS89 4.2 13.9 1.0 CD2 A:HIS140 4.2 15.7 1.0 CG A:PRO132 4.4 15.4 0.4 CB A:MET145 4.4 13.7 0.7 CB A:MET145 4.5 11.2 0.3 SD A:MET56 4.5 16.7 0.5 CD A:PRO132 4.6 14.1 0.6 CA A:CYS130 4.6 11.8 1.0 N A:ASN90 4.7 13.9 1.0 CA A:HIS140 4.7 12.6 1.0 CD A:PRO132 4.7 14.6 0.4 N A:HIS89 4.8 14.3 1.0 C A:HIS89 4.8 14.2 1.0 C A:PRO88 4.9 15.9 1.0 CE A:MET56 4.9 13.4 0.5

Copper binding site 2 out of 2 in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start)


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 1 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.02 Mgy] - Nitrite (Start) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:12.2 occ:0.95 O1 A:NO2403 2.0 20.1 0.7 NE2 A:HIS129 2.0 12.6 1.0 NE2 A:HIS94 2.0 11.0 1.0 N A:NO2403 2.0 23.7 0.7 O2 A:NO2403 2.4 24.4 0.7 CD2 A:HIS129 3.0 12.2 1.0 CE1 A:HIS94 3.0 11.9 1.0 CE1 A:HIS129 3.1 12.7 1.0 CD2 A:HIS94 3.1 11.8 1.0 OD2 A:ASP92 3.7 22.7 0.8 O A:HOH502 4.1 29.1 0.3 ND1 A:HIS94 4.1 11.5 1.0 CG A:HIS129 4.2 11.9 1.0 O A:HOH501 4.2 27.6 0.3 ND1 A:HIS129 4.2 12.0 1.0 CG A:HIS94 4.2 11.2 1.0 CG A:ASP92 4.3 17.3 0.8 OD1 A:ASP92 4.6 18.0 0.8 O A:HOH757 5.0 18.6 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