Atomistry » Copper » PDB 6y6y-6zut » 6zar
Atomistry »
  Copper »
    PDB 6y6y-6zut »
      6zar »

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: Wed Jul 31 07:58:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy