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Copper in PDB 6the: Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

All present enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the was solved by D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.57 / 2.87
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 125.141, 125.141, 125.141, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 23.4

Other elements in 6the:

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms
Yttrium (Y) 2 atoms
Erbium (Er) 4 atoms
Terbium (Tb) 1 atom
Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (pdb code 6the). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6the

Go back to Copper Binding Sites List in 6the
Copper binding site 1 out of 2 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:17.3
occ:1.00
ND1 A:HIS133 2.2 18.8 1.0
SG A:CYS125 2.2 19.0 1.0
ND1 A:HIS84 2.3 26.1 1.0
SD A:MET138 2.5 19.3 1.0
CE1 A:HIS133 3.1 18.8 1.0
CG A:HIS133 3.1 18.8 1.0
CE1 A:HIS84 3.1 26.1 1.0
CB A:CYS125 3.2 19.2 1.0
CG A:HIS84 3.3 26.1 1.0
CE A:MET138 3.4 19.2 1.0
CB A:HIS133 3.4 18.8 1.0
CB A:HIS84 3.7 26.2 1.0
CA A:HIS84 3.8 26.3 1.0
O A:ILE83 3.8 26.6 1.0
CG A:MET138 4.1 19.1 1.0
NE2 A:HIS133 4.2 18.8 1.0
CD2 A:HIS133 4.2 18.8 1.0
NE2 A:HIS84 4.3 26.1 1.0
CD2 A:HIS84 4.4 26.1 1.0
N A:SER85 4.5 26.2 1.0
CA A:HIS133 4.5 18.8 1.0
CE3 A:TRP51 4.5 19.1 1.0
CB A:MET138 4.6 19.0 1.0
OG1 A:THR127 4.6 19.8 1.0
CA A:CYS125 4.6 19.3 1.0
C A:ILE83 4.6 26.7 1.0
CB A:THR127 4.7 19.9 1.0
N A:HIS84 4.7 26.5 1.0
C A:HIS84 4.7 26.2 1.0

Copper binding site 2 out of 2 in 6the

Go back to Copper Binding Sites List in 6the
Copper binding site 2 out of 2 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:21.1
occ:0.70
O A:HOH610 2.0 11.2 1.0
NE2 A:HIS124 2.0 19.1 1.0
NE2 A:HIS89 2.1 26.4 1.0
CE1 A:HIS89 3.0 26.4 1.0
CE1 A:HIS124 3.0 19.1 1.0
CD2 A:HIS124 3.0 19.1 1.0
CD2 A:HIS89 3.2 26.5 1.0
OD2 A:ASP87 3.4 26.7 1.0
ND1 A:HIS89 4.1 26.5 1.0
ND1 A:HIS124 4.1 19.1 1.0
CG A:HIS124 4.2 19.1 1.0
CG A:HIS89 4.2 26.5 1.0
CG A:ASP87 4.2 26.7 1.0
O A:HOH617 4.6 25.3 1.0
OD1 A:ASP87 4.8 26.8 1.0

Reference:

D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain. Reverse Protein Engineering of A Novel 4-Domain Copper Nitrite Reductase Reveals Functional Regulation By Protein-Protein Interaction. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32255260
DOI: 10.1111/FEBS.15324
Page generated: Sun Dec 13 11:26:12 2020

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