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Copper in PDB 7zcn: Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start)

Enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start)

All present enzymatic activity of Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start):
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start), PDB code: 7zcn 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) 75.47 / 1.19
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.725, 106.725, 106.725, 90, 90, 90
R / Rfree (%) 10.8 / 13.4

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start) (pdb code 7zcn). 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 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start), PDB code: 7zcn:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 7zcn

Go back to Copper Binding Sites List in 7zcn
Copper binding site 1 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start)


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 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:11.8
occ:0.95
 ND1 A:HIS140 2.0 12.0 1.0
ND1 A:HIS89 2.0 11.0 1.0
SG A:CYS130 2.2 11.9 1.0
SD A:MET145 2.5 13.2 1.0
CE1 A:HIS89 3.0 11.9 1.0
CE1 A:HIS140 3.0 11.4 1.0
CG A:HIS140 3.1 11.5 1.0
CG A:HIS89 3.1 10.6 1.0
CB A:CYS130 3.2 11.6 1.0
CE A:MET145 3.3 13.6 1.0
CB A:HIS140 3.4 10.9 1.0
CB A:HIS89 3.5 11.0 1.0
CA A:HIS89 3.8 10.8 1.0
CG A:MET145 4.0 13.5 1.0
O A:PRO88 4.1 12.6 1.0
NE2 A:HIS140 4.1 12.4 1.0
CG A:PRO132 4.1 13.2 0.5
NE2 A:HIS89 4.1 11.2 1.0
CD2 A:HIS140 4.2 13.1 1.0
CD2 A:HIS89 4.2 11.3 1.0
CG A:PRO132 4.3 13.2 0.5
CB A:MET145 4.4 11.5 1.0
CD A:PRO132 4.6 13.1 0.5
SD A:MET56 4.6 9.4 0.3
CA A:CYS130 4.6 10.3 1.0
N A:ASN90 4.6 10.9 1.0
CD A:PRO132 4.7 11.8 0.5
CA A:HIS140 4.7 10.4 1.0
C A:HIS89 4.8 10.6 1.0
N A:HIS89 4.8 11.5 1.0
C A:PRO88 4.9 12.3 1.0
CE A:MET56 4.9 17.1 0.7

Copper binding site 2 out of 2 in 7zcn

Go back to Copper Binding Sites List in 7zcn
Copper binding site 2 out of 2 in the Nitrite-Bound Msox Movie Series Dataset 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start)


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 1 (0.8 Mgy) of the Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) - Nitrite (Start) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:11.1
occ:0.90
 O1 A:NO2407 1.8 23.3 0.7
NE2 A:HIS94 2.0 9.8 1.0
N A:NO2407 2.0 32.7 0.7
NE2 A:HIS129 2.1 10.8 1.0
O2 A:NO2407 2.2 22.8 0.7
CE1 A:HIS94 2.9 9.5 1.0
CD2 A:HIS129 3.1 10.9 1.0
CD2 A:HIS94 3.1 9.9 1.0
CE1 A:HIS129 3.1 11.4 1.0
OD2 A:ASP92 3.6 21.8 0.9
O A:HOH898 3.8 30.6 0.5
O A:HOH503 4.1 31.2 0.5
ND1 A:HIS94 4.1 9.3 1.0
CG A:HIS94 4.2 9.8 1.0
CG A:HIS129 4.2 10.5 1.0
ND1 A:HIS129 4.2 10.6 1.0
CG A:ASP92 4.2 14.3 0.9
OD1 A:ASP92 4.6 14.6 0.9
O A:HOH750 4.8 16.4 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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