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Copper in PDB 2bhf: 3D Structure of the Reduced Form of Cota

Protein crystallography data

The structure of 3D Structure of the Reduced Form of Cota, PDB code: 2bhf was solved by I.Bento, L.O.Martins, G.G.Lopes, M.A.Carrondo, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 2.5
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.101, 102.101, 136.257, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21.3

Copper Binding Sites:

The binding sites of Copper atom in the 3D Structure of the Reduced Form of Cota (pdb code 2bhf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the 3D Structure of the Reduced Form of Cota, PDB code: 2bhf:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2bhf

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Copper binding site 1 out of 4 in the 3D Structure of the Reduced Form of Cota


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 3D Structure of the Reduced Form of Cota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1512

b:42.8
occ:1.00
ND1 A:HIS419 2.0 42.7 1.0
ND1 A:HIS497 2.0 44.1 1.0
SG A:CYS492 2.3 42.4 1.0
CE1 A:HIS419 2.7 41.2 1.0
CE1 A:HIS497 3.0 43.3 1.0
CG A:HIS497 3.0 43.8 1.0
CG A:HIS419 3.2 44.1 1.0
CB A:CYS492 3.3 42.2 1.0
SD A:MET502 3.3 43.1 1.0
CB A:HIS497 3.3 43.1 1.0
CB A:HIS419 3.7 44.9 1.0
CD1 A:ILE494 3.9 37.4 1.0
NE2 A:HIS419 3.9 40.7 1.0
CE A:MET502 4.0 42.7 1.0
CB A:ILE494 4.0 39.1 1.0
NE2 A:HIS497 4.1 43.7 1.0
CD2 A:HIS497 4.1 41.9 1.0
CD2 A:HIS419 4.2 42.1 1.0
CA A:HIS419 4.2 45.0 1.0
CG1 A:ILE494 4.4 39.1 1.0
CA A:CYS492 4.6 41.7 1.0
CD A:PRO420 4.6 44.2 1.0
CG2 A:ILE494 4.7 39.6 1.0
CG A:MET502 4.8 44.2 1.0
CA A:HIS497 4.9 43.4 1.0
O A:THR418 4.9 46.8 1.0
N A:ILE494 4.9 39.6 1.0
O A:ILE494 5.0 39.7 1.0

Copper binding site 2 out of 4 in 2bhf

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Copper binding site 2 out of 4 in the 3D Structure of the Reduced Form of Cota


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 3D Structure of the Reduced Form of Cota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1513

b:46.7
occ:0.80
ND1 A:HIS107 2.0 42.5 1.0
NE2 A:HIS493 2.0 41.3 1.0
NE2 A:HIS153 2.0 39.9 1.0
CE1 A:HIS493 2.9 38.8 1.0
CE1 A:HIS107 2.9 44.5 1.0
CE1 A:HIS153 3.0 37.4 1.0
CG A:HIS107 3.0 41.3 1.0
CD2 A:HIS153 3.1 36.8 1.0
CD2 A:HIS493 3.1 39.7 1.0
CB A:HIS107 3.4 40.7 1.0
CD2 A:HIS105 3.8 39.6 1.0
CZ2 A:TRP151 3.8 32.0 1.0
ND1 A:HIS493 4.0 39.4 1.0
NE2 A:HIS107 4.1 44.2 1.0
ND1 A:HIS153 4.1 36.7 1.0
CD2 A:HIS107 4.1 42.3 1.0
CE2 A:TRP151 4.1 31.3 1.0
NE1 A:TRP151 4.2 31.1 1.0
CG A:HIS493 4.2 41.1 1.0
CU A:CU11515 4.2 43.5 0.5
CG A:HIS153 4.2 35.1 1.0
NE2 A:HIS105 4.3 40.8 1.0
CB A:ALA297 4.4 34.0 1.0
CA A:HIS107 4.5 40.4 1.0
CH2 A:TRP151 4.6 32.0 1.0
CD2 A:HIS422 4.7 43.0 1.0
NE2 A:HIS422 4.8 42.3 1.0

Copper binding site 3 out of 4 in 2bhf

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Copper binding site 3 out of 4 in the 3D Structure of the Reduced Form of Cota


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 3D Structure of the Reduced Form of Cota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1514

b:48.5
occ:0.30
NE2 A:HIS491 2.0 44.9 1.0
NE2 A:HIS155 2.0 45.7 1.0
NE2 A:HIS424 2.0 52.9 1.0
CE1 A:HIS424 2.7 54.6 1.0
CD2 A:HIS491 2.8 45.2 1.0
CD2 A:HIS155 2.9 44.8 1.0
CE1 A:HIS491 3.0 46.2 1.0
CE1 A:HIS155 3.0 45.3 1.0
CD2 A:HIS424 3.2 53.6 1.0
CG2 A:VAL489 3.6 41.4 1.0
CG A:HIS491 3.9 44.3 1.0
CD2 A:HIS105 3.9 39.6 1.0
ND1 A:HIS491 3.9 45.6 1.0
ND1 A:HIS424 3.9 53.7 1.0
NE2 A:HIS105 4.0 40.8 1.0
CD2 A:HIS422 4.0 43.0 1.0
ND1 A:HIS155 4.1 44.7 1.0
CG A:HIS155 4.1 40.9 1.0
CG A:HIS424 4.2 53.1 1.0
CU A:CU11515 4.2 43.5 0.5
O A:HOH2109 4.3 71.0 1.0
NE2 A:HIS422 4.6 42.3 1.0
CG A:HIS105 4.6 38.4 1.0
CE1 A:HIS105 4.7 40.6 1.0
OE2 A:GLU498 4.7 46.6 1.0

Copper binding site 4 out of 4 in 2bhf

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Copper binding site 4 out of 4 in the 3D Structure of the Reduced Form of Cota


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of 3D Structure of the Reduced Form of Cota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1515

b:43.5
occ:0.50
NE2 A:HIS105 2.0 40.8 1.0
NE2 A:HIS422 2.0 42.3 1.0
O A:HOH2099 2.8 60.2 1.0
CE1 A:HIS105 2.8 40.6 1.0
CE1 A:HIS422 2.9 42.1 1.0
CD2 A:HIS422 2.9 43.0 1.0
CD2 A:HIS105 3.1 39.6 1.0
NE2 A:HIS424 3.2 52.9 1.0
CD2 A:HIS424 3.2 53.6 1.0
ND1 A:HIS107 3.5 42.5 1.0
CG A:HIS107 3.5 41.3 1.0
CA A:HIS107 3.6 40.4 1.0
CE1 A:HIS424 3.7 54.6 1.0
CG A:HIS424 3.8 53.1 1.0
CE1 A:HIS107 3.9 44.5 1.0
CB A:HIS107 3.9 40.7 1.0
CD2 A:HIS107 4.0 42.3 1.0
N A:GLY108 4.0 41.7 1.0
ND1 A:HIS105 4.0 40.9 1.0
ND1 A:HIS422 4.0 42.8 1.0
CG A:HIS422 4.0 43.9 1.0
ND1 A:HIS424 4.0 53.7 1.0
CG A:HIS105 4.1 38.4 1.0
NE2 A:HIS107 4.1 44.2 1.0
CU A:CU11513 4.2 46.7 0.8
CU A:CU11514 4.2 48.5 0.3
C A:HIS107 4.3 41.1 1.0
CA A:HIS424 4.5 51.0 1.0
N A:HIS107 4.6 39.3 1.0
O A:HOH2269 4.6 50.2 1.0
CB A:HIS424 4.6 51.1 1.0
O A:LEU106 4.9 37.9 1.0
NE2 A:HIS491 4.9 44.9 1.0
N A:HIS424 5.0 50.3 1.0

Reference:

I.Bento, L.O.Martins, G.G.Lopes, M.A.Carrondo, P.F.Lindley. Dioxygen Reduction By Multi-Copper Oxidases; A Structural Perspective. Dalton Trans. V. 7 3507 2005.
ISSN: ISSN 1477-9226
PubMed: 16234932
DOI: 10.1039/B504806K
Page generated: Thu Sep 3 16:31:04 2020
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