Copper in PDB 6zax: Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy)

All present enzymatic activity of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy):
1.7.2.1;

The structure of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy), PDB code: 6zax was solved by S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.15 / 1.48
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	107.566, 107.566, 107.566, 90, 90, 90
R / Rfree (%)	14.7 / 17.6

The binding sites of Copper atom in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy) (pdb code 6zax). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy), PDB code: 6zax:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:17.1 occ:1.00 ND1 A:HIS140 2.0 17.1 1.0 ND1 A:HIS89 2.0 13.3 1.0 SG A:CYS130 2.2 16.1 1.0 SD A:MET145 2.5 17.3 1.0 CE1 A:HIS89 2.9 15.2 1.0 CE1 A:HIS140 2.9 16.9 1.0 CG A:HIS140 3.0 17.5 1.0 CG A:HIS89 3.1 15.7 1.0 CB A:CYS130 3.2 14.6 1.0 CE A:MET145 3.3 16.9 1.0 CB A:HIS140 3.4 15.5 1.0 CB A:HIS89 3.5 15.7 1.0 CA A:HIS89 3.8 16.0 1.0 CG A:MET145 4.0 16.9 1.0 O A:PRO88 4.1 18.3 1.0 NE2 A:HIS140 4.1 19.0 1.0 NE2 A:HIS89 4.1 15.1 1.0 CD2 A:HIS140 4.1 18.0 1.0 CG A:PRO132 4.1 16.7 1.0 CD2 A:HIS89 4.2 14.5 1.0 CB A:MET145 4.4 15.7 1.0 CA A:CYS130 4.6 15.8 1.0 SD A:MET56 4.6 17.9 0.6 CD A:PRO132 4.7 15.1 1.0 N A:ASN90 4.7 15.5 1.0 CA A:HIS140 4.7 15.4 1.0 CE A:MET56 4.8 23.4 0.6 N A:HIS89 4.8 17.5 1.0 C A:HIS89 4.8 16.9 1.0 C A:PRO88 4.8 16.9 1.0

Copper binding site 2 out of 2 in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at Low Dose (0.5 Mgy) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:15.5 occ:0.95 N A:NO2409 1.8 36.5 0.8 O2 A:NO2409 1.9 24.6 0.8 NE2 A:HIS94 2.0 12.9 1.0 NE2 A:HIS129 2.1 16.4 1.0 O1 A:NO2409 2.3 27.0 0.8 CE1 A:HIS94 3.0 13.5 1.0 CE1 A:HIS129 3.1 15.2 1.0 CD2 A:HIS129 3.1 15.8 1.0 CD2 A:HIS94 3.1 14.0 1.0 OD2 A:ASP92 3.3 15.2 0.2 OD2 A:ASP92 3.8 21.8 0.6 O A:HOH502 4.1 23.2 0.2 ND1 A:HIS94 4.1 14.1 1.0 O A:HOH502 4.2 23.5 0.2 CG A:HIS94 4.2 13.9 1.0 ND1 A:HIS129 4.2 15.4 1.0 CG A:HIS129 4.2 14.6 1.0 CG A:ASP92 4.3 15.7 0.2 CG A:ASP92 4.3 20.1 0.6 OD1 A:ASP92 4.5 16.4 0.6 OD1 A:ASP92 4.9 16.7 0.2

S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain. An Unprecedented Insight Into the Catalytic Mechanism of Copper Nitrite Reductase From Atomic-Resolution and Damage-Free Structures Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABD8523