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Copper in PDB 4yvu: Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6

Protein crystallography data

The structure of Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6, PDB code: 4yvu was solved by Z.C.Liu, T.Xie, G.G.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.38 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.730, 101.730, 135.572, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 18.7

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6 (pdb code 4yvu). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6, PDB code: 4yvu:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 4yvu

Go back to Copper Binding Sites List in 4yvu
Copper binding site 1 out of 3 in the Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6


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 Cota Native Enzyme in the Acid Condition, PH5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:15.7
occ:0.93
ND1 A:HIS419 2.0 21.6 1.0
ND1 A:HIS497 2.1 16.7 1.0
SG A:CYS492 2.2 16.0 1.0
CE1 A:HIS419 2.9 20.4 1.0
CE1 A:HIS497 3.0 16.3 1.0
CG A:HIS497 3.1 16.1 1.0
CG A:HIS419 3.1 20.1 1.0
SD A:MET502 3.2 16.3 1.0
CB A:CYS492 3.2 14.4 1.0
CB A:HIS497 3.5 16.6 1.0
CB A:HIS419 3.6 19.0 1.0
CD1 A:ILE494 3.8 13.9 1.0
CE A:MET502 3.9 17.0 1.0
NE2 A:HIS419 4.1 20.7 1.0
CB A:ILE494 4.1 13.4 1.0
NE2 A:HIS497 4.1 15.9 1.0
CD2 A:HIS419 4.2 20.8 1.0
CD2 A:HIS497 4.2 15.4 1.0
CA A:HIS419 4.2 17.9 1.0
CG1 A:ILE494 4.4 13.1 1.0
CA A:CYS492 4.6 14.4 1.0
CG A:MET502 4.6 15.3 1.0
O A:HOH751 4.6 25.9 1.0
CD A:PRO420 4.8 14.7 1.0
CD2 A:LEU386 4.8 30.9 1.0
N A:ILE494 4.9 13.5 1.0
O A:THR418 4.9 17.9 1.0
CG2 A:ILE494 4.9 13.5 1.0
CA A:HIS497 5.0 16.9 1.0

Copper binding site 2 out of 3 in 4yvu

Go back to Copper Binding Sites List in 4yvu
Copper binding site 2 out of 3 in the Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6


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 Cota Native Enzyme in the Acid Condition, PH5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:13.8
occ:0.20
NE2 A:HIS491 1.9 14.9 1.0
NE2 A:HIS424 1.9 12.4 1.0
NE2 A:HIS155 2.1 16.3 1.0
O A:HOH1009 2.2 18.0 1.0
CE1 A:HIS424 2.7 12.5 1.0
CD2 A:HIS491 2.8 15.7 1.0
CE1 A:HIS491 2.9 14.8 1.0
CD2 A:HIS155 3.0 16.8 1.0
CD2 A:HIS424 3.1 12.6 1.0
CE1 A:HIS155 3.2 16.1 1.0
CD2 A:HIS422 3.4 15.7 1.0
O A:HOH888 3.6 41.3 1.0
CG2 A:VAL489 3.9 12.2 0.5
ND1 A:HIS424 3.9 12.8 1.0
CG A:HIS491 3.9 15.4 1.0
ND1 A:HIS491 3.9 15.6 1.0
NE2 A:HIS422 4.0 15.9 1.0
CD2 A:HIS105 4.0 12.2 1.0
CG A:HIS424 4.1 13.2 1.0
NE2 A:HIS105 4.2 12.7 1.0
CG A:HIS155 4.2 15.3 1.0
ND1 A:HIS155 4.3 16.1 1.0
O A:HOH947 4.5 25.2 1.0
OE2 A:GLU498 4.6 17.9 1.0
CG A:HIS422 4.6 14.8 1.0
CU A:CU603 4.7 14.9 0.3
CG A:HIS105 4.7 11.6 1.0
CD2 A:HIS493 4.9 13.8 1.0
CE1 A:HIS105 4.9 12.7 1.0
CG1 A:VAL489 5.0 14.3 0.5

Copper binding site 3 out of 3 in 4yvu

Go back to Copper Binding Sites List in 4yvu
Copper binding site 3 out of 3 in the Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Cota Native Enzyme in the Acid Condition, PH5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:14.9
occ:0.35
ND1 A:HIS107 1.7 13.6 1.0
NE2 A:HIS153 2.2 11.0 1.0
NE2 A:HIS493 2.3 13.8 1.0
CE1 A:HIS107 2.4 12.9 1.0
O A:HOH1009 2.5 18.0 1.0
CG A:HIS107 2.9 12.9 1.0
CE1 A:HIS153 3.0 11.2 1.0
CD2 A:HIS493 3.1 13.8 1.0
CD2 A:HIS153 3.2 10.9 1.0
CE1 A:HIS493 3.3 13.2 1.0
CB A:HIS107 3.6 12.3 1.0
NE2 A:HIS107 3.6 12.9 1.0
CD2 A:HIS105 3.9 12.2 1.0
CD2 A:HIS107 3.9 13.2 1.0
O A:HOH888 3.9 41.3 1.0
CZ2 A:TRP151 4.0 10.4 1.0
ND1 A:HIS153 4.2 10.9 1.0
CD2 A:HIS422 4.2 15.7 1.0
CG A:HIS493 4.2 13.7 1.0
NE2 A:HIS422 4.3 15.9 1.0
CE2 A:TRP151 4.3 10.1 1.0
CG A:HIS153 4.3 10.8 1.0
ND1 A:HIS493 4.3 13.4 1.0
CB A:ALA297 4.3 11.7 1.0
NE1 A:TRP151 4.4 9.9 1.0
NE2 A:HIS105 4.5 12.7 1.0
CU A:CU602 4.7 13.8 0.2
CH2 A:TRP151 4.7 10.9 1.0
CA A:HIS107 4.7 12.3 1.0

Reference:

Z.Liu, T.Xie, Q.Zhong, G.Wang. Crystal Structure of Cota Laccase Complexed with 2,2-Azinobis-(3-Ethylbenzothiazoline-6-Sulfonate) at A Novel Binding Site Acta Crystallogr.,Sect.F V. 72 328 2016.
ISSN: ESSN 2053-230X
PubMed: 27050268
DOI: 10.1107/S2053230X1600426X
Page generated: Sun Dec 13 11:16:30 2020

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