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Copper in PDB 2yqb: Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution

Enzymatic activity of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution

All present enzymatic activity of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution:
1.7.2.1;

Protein crystallography data

The structure of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution, PDB code: 2yqb was solved by S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.07 / 1.41
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 127.849, 127.849, 86.628, 90.00, 90.00, 120.00
R / Rfree (%) 11.2 / 14.7

Other elements in 2yqb:

The structure of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution also contains other interesting chemical elements:

Iron (Fe) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution (pdb code 2yqb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution, PDB code: 2yqb:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2yqb

Go back to Copper Binding Sites List in 2yqb
Copper binding site 1 out of 2 in the Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:6.6
occ:1.00
 ND1 A:HIS94 2.0 5.3 1.0
ND1 A:HIS143 2.1 5.4 1.0
SG A:CYS135 2.2 6.8 1.0
SD A:MET148 2.5 6.6 1.0
CE1 A:HIS143 3.0 6.7 1.0
CE1 A:HIS94 3.0 6.6 1.0
CG A:HIS94 3.1 5.5 1.0
CG A:HIS143 3.1 5.5 1.0
CB A:CYS135 3.2 5.8 1.0
CE A:MET148 3.4 6.9 1.0
CB A:HIS94 3.4 6.5 1.0
CB A:HIS143 3.5 6.5 1.0
CA A:HIS94 3.8 6.3 1.0
O A:ALA93 4.0 6.8 1.0
CG A:MET148 4.1 5.4 1.0
NE2 A:HIS143 4.1 5.2 1.0
NE2 A:HIS94 4.1 6.1 1.0
CD2 A:HIS143 4.2 7.0 1.0
CD2 A:HIS94 4.2 7.7 1.0
OG1 A:THR137 4.3 7.7 1.0
CB A:THR137 4.4 6.5 1.0
CE3 A:TRP61 4.5 5.8 1.0
CB A:MET148 4.6 5.2 1.0
CA A:HIS143 4.6 5.4 1.0
N A:ASN95 4.6 6.7 1.0
CA A:CYS135 4.6 4.9 1.0
N A:HIS94 4.8 7.1 1.0
C A:HIS94 4.8 7.0 1.0
C A:ALA93 4.8 7.6 1.0

Copper binding site 2 out of 2 in 2yqb

Go back to Copper Binding Sites List in 2yqb
Copper binding site 2 out of 2 in the Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of P93A Variant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:7.5
occ:1.00
 NE2 A:HIS134 2.0 5.5 1.0
NE2 A:HIS99 2.0 5.9 1.0
O A:HOH2277 2.0 9.2 1.0
CD2 A:HIS134 2.9 5.3 1.0
CE1 A:HIS99 3.0 7.9 1.0
CD2 A:HIS99 3.0 4.5 1.0
CE1 A:HIS134 3.1 6.3 1.0
OD2 A:ASP97 3.9 7.3 1.0
CG A:HIS134 4.1 5.2 1.0
ND1 A:HIS99 4.1 7.0 1.0
ND1 A:HIS134 4.1 5.4 1.0
CG A:HIS99 4.2 5.2 1.0
CG A:ASP97 4.4 7.9 1.0
OD1 A:ASP97 4.8 7.6 1.0

Reference:

S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain. Structures of Protein-Protein Complexes Involved in Electron Transfer. Nature V. 496 123 2013.
ISSN: ESSN 1476-4687
PubMed: 23535590
DOI: 10.1038/NATURE11996
Page generated: Wed Jul 31 00:25:53 2024

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