Copper in PDB 8rfu: Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final)

The structure of Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final), PDB code: 8rfu 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 / 2.18
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	104.52, 104.52, 64.69, 90, 90, 120
R / Rfree (%)	18.6 / 22.2

The binding sites of Copper atom in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final) (pdb code 8rfu). 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 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final), PDB code: 8rfu:
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 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final)


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 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:42.9 occ:0.95 ND1 A:HIS140 2.0 47.2 1.0 ND1 A:HIS89 2.1 38.2 1.0 SG A:CYS130 2.3 39.4 1.0 SD A:MET145 2.5 48.5 1.0 CE1 A:HIS140 3.0 46.5 1.0 CE1 A:HIS89 3.0 35.8 1.0 CG A:HIS140 3.1 47.5 1.0 CG A:HIS89 3.2 32.4 1.0 CB A:CYS130 3.4 35.8 1.0 CB A:HIS140 3.5 37.3 1.0 CB A:HIS89 3.5 34.6 1.0 CE A:MET145 3.6 54.5 1.0 CA A:HIS89 3.9 33.7 1.0 CG A:MET145 4.1 45.8 1.0 CG A:PRO132 4.1 54.1 1.0 NE2 A:HIS140 4.1 44.6 1.0 NE2 A:HIS89 4.1 34.9 1.0 CD2 A:HIS140 4.2 46.1 1.0 CD2 A:HIS89 4.2 33.3 1.0 O A:PRO88 4.4 40.2 1.0 CB A:MET145 4.5 40.3 1.0 SD A:MET56 4.5 56.6 0.5 CD A:PRO132 4.7 48.7 1.0 N A:ASN90 4.7 38.0 1.0 CA A:HIS140 4.7 37.9 1.0 CA A:CYS130 4.8 33.0 1.0 C A:HIS89 4.9 36.5 1.0 CE A:MET56 4.9 45.0 0.5 N A:HIS89 4.9 34.9 1.0

Copper binding site 2 out of 2 in the Low pH (5.5) Nitrite-Bound Msox Movie Series Dataset 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final)


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 40 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [40.80 Mgy] - Water Ligand + Decarboxylated Aspcat (Final) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:39.4 occ:0.95 O A:HOH556 1.9 42.9 1.0 NE2 A:HIS129 2.0 39.8 1.0 NE2 A:HIS94 2.0 36.9 1.0 CE1 A:HIS94 2.8 38.2 1.0 CD2 A:HIS129 3.0 39.2 1.0 CE1 A:HIS129 3.0 40.7 1.0 CD2 A:HIS94 3.2 36.2 1.0 ND1 A:HIS94 4.0 36.0 1.0 CG A:HIS129 4.1 37.0 1.0 ND1 A:HIS129 4.1 36.6 1.0 CG A:HIS94 4.2 35.4 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