Atomistry » Copper » PDB 7xmb-8b9q » 7zcp
Atomistry »
  Copper »
    PDB 7xmb-8b9q »
      7zcp »

Copper in PDB 7zcp: Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate

Enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate

All present enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate:
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate, PDB code: 7zcp was solved by S.L.Rose, S.Baba, H.Okumura, S.V.Antonyuk, D.Sasaki, T.Tosha, T.Kumasaka, R.R.Eady, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.65 / 1.29
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.989, 106.989, 106.989, 90, 90, 90
R / Rfree (%) 13 / 16.1

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate (pdb code 7zcp). 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 Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate, PDB code: 7zcp:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 7zcp

Go back to Copper Binding Sites List in 7zcp
Copper binding site 1 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:15.0
occ:0.95
 ND1 A:HIS140 2.1 14.5 1.0
ND1 A:HIS89 2.1 13.8 1.0
SG A:CYS130 2.2 15.1 1.0
SD A:MET145 2.5 16.6 1.0
CE1 A:HIS140 3.0 16.6 1.0
CE1 A:HIS89 3.0 13.7 1.0
CG A:HIS140 3.1 13.5 1.0
CG A:HIS89 3.2 12.3 1.0
CB A:CYS130 3.2 14.8 1.0
CE A:MET145 3.3 14.1 1.0
CB A:HIS140 3.5 13.9 1.0
CB A:HIS89 3.5 12.7 1.0
CA A:HIS89 3.9 11.6 1.0
CG A:MET145 3.9 16.4 1.0
CG A:PRO132 4.1 16.9 0.5
NE2 A:HIS140 4.1 15.7 1.0
O A:PRO88 4.2 14.9 1.0
CD2 A:HIS140 4.2 15.8 1.0
NE2 A:HIS89 4.2 13.9 1.0
CD2 A:HIS89 4.3 14.1 1.0
CG A:PRO132 4.3 17.2 0.5
CB A:MET145 4.4 13.3 1.0
SD A:MET56 4.6 14.4 0.3
CA A:CYS130 4.6 12.7 1.0
CD A:PRO132 4.7 14.9 0.5
N A:ASN90 4.7 13.3 1.0
CD A:PRO132 4.7 15.3 0.5
CA A:HIS140 4.7 12.8 1.0
N A:HIS89 4.9 12.8 1.0
C A:HIS89 4.9 13.5 1.0
CE A:MET56 4.9 19.7 0.7
C A:PRO88 4.9 14.5 1.0

Copper binding site 2 out of 2 in 7zcp

Go back to Copper Binding Sites List in 7zcp
Copper binding site 2 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite-Bound Msox Movie Series Dataset 17 (13.6 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitric Oxide (No) Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:13.7
occ:0.90
 O A:NO410 2.0 29.7 0.7
NE2 A:HIS94 2.0 11.9 1.0
NE2 A:HIS129 2.1 11.8 1.0
N A:NO410 2.1 34.6 0.7
CE1 A:HIS94 3.0 13.4 1.0
CD2 A:HIS129 3.0 12.8 1.0
CD2 A:HIS94 3.1 13.8 1.0
CE1 A:HIS129 3.1 14.8 1.0
OD2 A:ASP92 3.7 32.2 0.9
O A:HOH862 4.0 34.9 0.7
ND1 A:HIS94 4.1 11.8 1.0
CG A:HIS129 4.2 11.8 1.0
CG A:HIS94 4.2 10.9 1.0
ND1 A:HIS129 4.2 12.9 1.0
CG A:ASP92 4.3 19.8 0.9
OD1 A:ASP92 4.6 23.0 0.9
O A:HOH760 5.0 23.1 1.0

Reference:

S.L.Rose, S.Baba, H.Okumura, S.V.Antonyuk, D.Sasaki, T.M.Hedison, M.Shanmugam, D.J.Heyes, N.S.Scrutton, T.Kumasaka, T.Tosha, R.R.Eady, M.Yamamoto, S.S.Hasnain. Single Crystal Spectroscopy and Multiple Structures From One Crystal (Msox) Define Catalysis in Copper Nitrite Reductases. Proc.Natl.Acad.Sci.Usa V. 119 64119 2022.
ISSN: ESSN 1091-6490
PubMed: 35862453
DOI: 10.1073/PNAS.2205664119
Page generated: Tue Apr 4 23:33:23 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy