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Copper in PDB 6zar: As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)

Enzymatic activity of As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)

All present enzymatic activity of As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx):
1.7.2.1;

Protein crystallography data

The structure of As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx), PDB code: 6zar 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) 30.00 / 1.10
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.716, 106.716, 106.716, 90, 90, 90
R / Rfree (%) 12.5 / 14.9

Copper Binding Sites:

The binding sites of Copper atom in the As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) (pdb code 6zar). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx), PDB code: 6zar:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6zar

Go back to Copper Binding Sites List in 6zar
Copper binding site 1 out of 2 in the As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:9.8
occ:1.00
 ND1 A:HIS140 2.0 9.1 1.0
ND1 A:HIS89 2.1 8.4 1.0
SG A:CYS130 2.2 9.1 1.0
SD A:MET145 2.6 9.2 1.0
CE1 A:HIS140 2.9 9.4 1.0
CE1 A:HIS89 3.0 9.5 1.0
CG A:HIS140 3.1 9.2 1.0
CG A:HIS89 3.1 8.7 1.0
CB A:CYS130 3.2 8.7 1.0
CE A:MET145 3.3 10.0 1.0
CB A:HIS140 3.5 9.5 1.0
CB A:HIS89 3.5 8.5 1.0
CA A:HIS89 3.8 8.4 1.0
O A:PRO88 4.1 10.4 1.0
CG A:MET145 4.1 9.2 1.0
NE2 A:HIS140 4.1 11.2 1.0
CG A:PRO132 4.1 10.1 0.6
NE2 A:HIS89 4.2 9.3 1.0
CD2 A:HIS140 4.2 12.7 1.0
CD2 A:HIS89 4.2 9.3 1.0
CG A:PRO132 4.2 10.0 0.3
CB A:MET145 4.5 8.2 1.0
CD A:PRO132 4.6 9.0 0.3
CD A:PRO132 4.6 10.1 0.6
CA A:CYS130 4.6 8.1 1.0
N A:ASN90 4.6 8.8 1.0
SD A:MET56 4.7 11.5 0.7
CA A:HIS140 4.7 8.4 1.0
N A:HIS89 4.8 9.0 1.0
C A:HIS89 4.8 8.2 1.0
C A:PRO88 4.8 9.1 1.0

Copper binding site 2 out of 2 in 6zar

Go back to Copper Binding Sites List in 6zar
Copper binding site 2 out of 2 in the As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.1 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:10.1
occ:1.00
 O A:HOH519 1.9 13.9 0.7
NE2 A:HIS94 2.0 7.6 1.0
O A:HOH882 2.0 20.5 0.3
NE2 A:HIS129 2.1 7.8 1.0
O A:HOH877 2.2 11.7 0.7
OD2 A:ASP92 2.8 15.2 0.3
CE1 A:HIS94 2.9 7.6 1.0
CD2 A:HIS94 3.1 7.7 1.0
CD2 A:HIS129 3.1 8.0 1.0
CE1 A:HIS129 3.1 7.8 1.0
O A:HOH954 3.6 26.5 0.5
OD2 A:ASP92 3.8 11.7 0.7
CG A:ASP92 3.9 12.3 0.3
ND1 A:HIS94 4.1 7.6 1.0
O A:HOH516 4.2 17.3 0.5
CG A:HIS94 4.2 7.4 1.0
ND1 A:HIS129 4.2 8.4 1.0
CG A:HIS129 4.2 8.2 1.0
CG A:ASP92 4.3 10.2 0.7
OD1 A:ASP92 4.4 8.4 0.3
OD1 A:ASP92 4.6 10.2 0.7
O A:HOH678 4.8 11.8 1.0

Reference:

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
Page generated: Mon Jul 14 07:35:11 2025

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