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Copper in PDB 7zco: Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate

Enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate

All present enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate:
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate, PDB code: 7zco 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) 75.58 / 1.22
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.881, 106.881, 106.881, 90, 90, 90
R / Rfree (%) 12.9 / 15.8

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate (pdb code 7zco). 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 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate, PDB code: 7zco:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 7zco

Go back to Copper Binding Sites List in 7zco
Copper binding site 1 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/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 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:13.5
occ:0.95
 ND1 A:HIS140 2.0 13.7 1.0
ND1 A:HIS89 2.1 12.3 1.0
SG A:CYS130 2.2 13.5 1.0
SD A:MET145 2.5 14.8 1.0
CE1 A:HIS140 3.0 13.2 1.0
CE1 A:HIS89 3.0 12.2 1.0
CG A:HIS140 3.1 12.8 1.0
CG A:HIS89 3.1 11.8 1.0
CB A:CYS130 3.2 13.1 1.0
CE A:MET145 3.3 12.9 1.0
CB A:HIS140 3.5 12.2 1.0
CB A:HIS89 3.5 11.8 1.0
CA A:HIS89 3.8 11.4 1.0
CG A:MET145 3.9 14.7 1.0
CG A:PRO132 4.1 14.9 0.5
NE2 A:HIS140 4.1 14.4 1.0
O A:PRO88 4.2 13.9 1.0
CD2 A:HIS140 4.2 14.5 1.0
NE2 A:HIS89 4.2 12.7 1.0
CD2 A:HIS89 4.2 12.5 1.0
CG A:PRO132 4.3 15.0 0.5
CB A:MET145 4.4 12.1 1.0
CD A:PRO132 4.6 14.5 0.5
SD A:MET56 4.6 12.2 0.3
CA A:CYS130 4.6 11.0 1.0
N A:ASN90 4.7 11.6 1.0
CD A:PRO132 4.7 13.8 0.5
CA A:HIS140 4.7 11.8 1.0
N A:HIS89 4.9 12.3 1.0
C A:HIS89 4.9 12.1 1.0
C A:PRO88 4.9 12.3 1.0
CE A:MET56 5.0 17.7 0.7

Copper binding site 2 out of 2 in 7zco

Go back to Copper Binding Sites List in 7zco
Copper binding site 2 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/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 8 (6.4 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite/No Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:12.4
occ:0.90
 O1 A:NO2421 1.8 21.6 0.3
NE2 A:HIS94 2.0 10.5 1.0
N A:NO410 2.0 24.9 0.3
NE2 A:HIS129 2.1 11.3 1.0
N A:NO2421 2.1 25.8 0.3
O A:NO410 2.3 25.2 0.3
O2 A:NO2421 2.4 23.0 0.3
CE1 A:HIS94 2.9 11.0 1.0
CD2 A:HIS129 3.0 12.6 1.0
CD2 A:HIS94 3.1 11.5 1.0
CE1 A:HIS129 3.1 12.9 1.0
OD2 A:ASP92 3.6 27.9 0.9
O A:HOH530 3.9 32.6 0.5
O A:HOH505 4.1 23.2 0.5
ND1 A:HIS94 4.1 10.4 1.0
CG A:HIS129 4.2 10.9 1.0
CG A:HIS94 4.2 10.8 1.0
ND1 A:HIS129 4.2 11.7 1.0
CG A:ASP92 4.3 17.0 0.9
OD1 A:ASP92 4.6 18.4 0.9
O A:HOH749 5.0 19.4 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: Wed Jul 31 09:29:14 2024

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