Atomistry » Copper » PDB 7xmc-8b9r » 7zcq
Atomistry »
  Copper »
    PDB 7xmc-8b9r »
      7zcq »

Copper in PDB 7zcq: Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate

Enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate

All present enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate:
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate, PDB code: 7zcq 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) 75.69 / 1.35
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.042, 107.042, 107.042, 90, 90, 90
R / Rfree (%) 13.1 / 15.7

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate (pdb code 7zcq). 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 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate, PDB code: 7zcq:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 7zcq

Go back to Copper Binding Sites List in 7zcq
Copper binding site 1 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water 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 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:16.3
occ:0.95
 ND1 A:HIS140 2.0 16.0 1.0
ND1 A:HIS89 2.1 15.3 1.0
SG A:CYS130 2.2 16.6 1.0
SD A:MET145 2.5 18.0 1.0
CE1 A:HIS140 3.0 17.5 1.0
CE1 A:HIS89 3.0 15.0 1.0
CG A:HIS140 3.1 14.7 1.0
CG A:HIS89 3.2 13.3 1.0
CB A:CYS130 3.2 16.0 1.0
CE A:MET145 3.3 15.7 1.0
CB A:HIS140 3.5 14.8 1.0
CB A:HIS89 3.5 14.9 1.0
CA A:HIS89 3.9 13.4 1.0
CG A:MET145 3.9 18.4 1.0
NE2 A:HIS140 4.1 16.9 1.0
NE2 A:HIS89 4.2 15.3 1.0
CD2 A:HIS140 4.2 17.6 1.0
CG A:PRO132 4.2 18.2 0.5
O A:PRO88 4.2 16.3 1.0
CD2 A:HIS89 4.2 15.5 1.0
CG A:PRO132 4.4 17.6 0.5
CB A:MET145 4.4 14.6 1.0
SD A:MET56 4.6 16.2 0.3
CA A:CYS130 4.6 14.0 1.0
N A:ASN90 4.7 14.3 1.0
CD A:PRO132 4.7 15.4 0.5
CD A:PRO132 4.7 16.2 0.5
CA A:HIS140 4.7 13.7 1.0
N A:HIS89 4.9 14.3 1.0
C A:HIS89 4.9 14.6 1.0
CE A:MET56 4.9 22.7 0.7
C A:PRO88 5.0 16.0 1.0

Copper binding site 2 out of 2 in 7zcq

Go back to Copper Binding Sites List in 7zcq
Copper binding site 2 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water 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 25 (20 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - No/Water Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:15.0
occ:0.90
 NE2 A:HIS94 2.0 13.1 1.0
O A:NO410 2.0 21.9 0.3
O A:HOH511 2.1 34.8 0.3
NE2 A:HIS129 2.1 13.0 1.0
N A:NO410 2.1 24.1 0.3
CE1 A:HIS94 3.0 14.8 1.0
CD2 A:HIS129 3.0 14.1 1.0
CD2 A:HIS94 3.0 15.2 1.0
CE1 A:HIS129 3.1 15.8 1.0
OD2 A:ASP92 3.7 36.3 0.9
O A:HOH891 3.9 34.5 0.5
O A:HOH509 4.0 35.1 0.5
ND1 A:HIS94 4.1 12.7 1.0
CG A:HIS94 4.2 11.8 1.0
CG A:HIS129 4.2 13.0 1.0
ND1 A:HIS129 4.2 14.2 1.0
CG A:ASP92 4.3 23.4 0.9
OD1 A:ASP92 4.6 26.4 0.9

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: Wed Jul 31 09:29:14 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