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Copper in PDB 7zcs: Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final)

Enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final)

All present enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final):
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final), PDB code: 7zcs 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) 75.78 / 1.61
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.176, 107.176, 107.176, 90, 90, 90
R / Rfree (%) 16.5 / 19.8

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final) (pdb code 7zcs). 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 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final), PDB code: 7zcs:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 7zcs

Go back to Copper Binding Sites List in 7zcs
Copper binding site 1 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final)


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 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:21.4
occ:0.95
 ND1 A:HIS140 2.0 20.7 1.0
ND1 A:HIS89 2.1 19.0 1.0
SG A:CYS130 2.2 23.0 1.0
SD A:MET145 2.4 23.8 1.0
CE1 A:HIS140 2.9 22.1 1.0
CE1 A:HIS89 3.0 17.9 1.0
CG A:HIS140 3.1 20.4 1.0
CG A:HIS89 3.1 17.7 1.0
CB A:CYS130 3.2 22.4 1.0
CE A:MET145 3.2 23.1 1.0
CB A:HIS140 3.5 19.1 1.0
CB A:HIS89 3.5 18.4 1.0
CA A:HIS89 3.8 17.8 1.0
CG A:MET145 4.0 23.2 1.0
NE2 A:HIS140 4.1 19.5 1.0
NE2 A:HIS89 4.2 18.0 1.0
CD2 A:HIS140 4.2 22.8 1.0
O A:PRO88 4.2 23.3 1.0
CD2 A:HIS89 4.2 17.4 1.0
CG A:PRO132 4.2 22.5 0.5
CG A:PRO132 4.4 21.6 0.5
CB A:MET145 4.4 20.3 1.0
SD A:MET56 4.6 22.4 0.3
CA A:CYS130 4.6 20.3 1.0
N A:ASN90 4.7 17.2 1.0
CA A:HIS140 4.7 17.6 1.0
CD A:PRO132 4.8 22.4 0.5
CD A:PRO132 4.8 23.1 0.5
N A:HIS89 4.8 19.6 1.0
C A:HIS89 4.8 19.3 1.0
C A:PRO88 4.9 21.6 1.0

Copper binding site 2 out of 2 in 7zcs

Go back to Copper Binding Sites List in 7zcs
Copper binding site 2 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final)


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 65 (52 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Water Ligand (Final) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:20.1
occ:0.90
 O A:HOH533 1.9 37.7 1.0
NE2 A:HIS94 2.0 19.1 1.0
NE2 A:HIS129 2.1 19.3 1.0
CE1 A:HIS94 2.9 19.8 1.0
CD2 A:HIS129 3.0 18.7 1.0
CD2 A:HIS94 3.1 17.9 1.0
CE1 A:HIS129 3.1 22.1 1.0
OD2 A:ASP92 3.7 48.9 0.9
O A:HOH915 3.9 30.0 0.5
ND1 A:HIS94 4.1 17.0 1.0
CG A:HIS94 4.2 17.8 1.0
CG A:HIS129 4.2 16.9 1.0
O A:HOH502 4.2 35.0 0.2
ND1 A:HIS129 4.2 19.4 1.0
CG A:ASP92 4.4 40.5 0.9
OD1 A:ASP92 4.6 38.0 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: Tue Apr 4 23:33:23 2023

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