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Copper in PDB 6iqy: High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared

Enzymatic activity of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared

All present enzymatic activity of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared:
1.3.3.5;

Protein crystallography data

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared, PDB code: 6iqy was solved by N.Shibata, M.Akter, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.298, 152.253, 69.908, 90.00, 91.66, 90.00
R / Rfree (%) 19.1 / 22.5

Other elements in 6iqy:

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared (pdb code 6iqy). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared, PDB code: 6iqy:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6iqy

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Copper binding site 1 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:9.7
occ:0.97
ND1 A:HIS462 2.0 10.6 1.0
ND1 A:HIS398 2.0 6.9 1.0
SG A:CYS457 2.2 9.4 1.0
OE1 A:GLN467 2.7 9.2 1.0
CE1 A:HIS398 3.0 11.7 1.0
CG A:HIS462 3.0 8.0 1.0
CE1 A:HIS462 3.0 11.2 1.0
CG A:HIS398 3.0 10.4 1.0
CB A:CYS457 3.2 13.1 1.0
CB A:HIS462 3.3 9.3 1.0
CB A:HIS398 3.4 8.9 1.0
O A:THR397 3.6 11.0 1.0
CA A:HIS398 3.7 9.5 1.0
CD A:GLN467 3.8 14.5 1.0
CB A:ASN459 4.1 10.8 1.0
NE2 A:HIS398 4.1 19.6 1.0
NE2 A:HIS462 4.1 9.0 1.0
CD2 A:HIS462 4.1 9.8 1.0
O A:HOH716 4.1 10.7 1.0
CD2 A:HIS398 4.1 17.7 1.0
C A:THR397 4.4 11.1 1.0
NE2 A:GLN467 4.4 12.4 1.0
N A:HIS398 4.5 9.3 1.0
CA A:CYS457 4.6 9.9 1.0
CD A:PRO399 4.8 9.0 1.0
CA A:HIS462 4.8 7.9 1.0
C A:HIS398 4.8 8.1 1.0
CG A:ASN459 4.9 9.0 1.0
CG A:GLN467 5.0 10.2 1.0
N A:ASN459 5.0 10.8 1.0

Copper binding site 2 out of 8 in 6iqy

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Copper binding site 2 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:12.5
occ:0.98
ND1 A:HIS96 2.0 8.8 1.0
NE2 A:HIS134 2.0 10.5 1.0
NE2 A:HIS458 2.2 8.8 1.0
O A:HOH1215 2.6 23.6 1.0
CE1 A:HIS96 2.8 8.3 1.0
CE1 A:HIS134 2.9 15.3 1.0
CD2 A:HIS134 3.0 8.3 1.0
CG A:HIS96 3.1 9.3 1.0
CE1 A:HIS458 3.1 11.3 1.0
CD2 A:HIS458 3.2 11.8 1.0
CB A:HIS96 3.5 6.7 1.0
CZ2 A:TRP132 3.6 9.4 1.0
CE2 A:TRP132 3.9 9.7 1.0
CD2 A:HIS94 4.0 10.8 1.0
NE1 A:TRP132 4.0 10.4 1.0
NE2 A:HIS96 4.0 9.6 1.0
ND1 A:HIS134 4.0 11.4 1.0
CG A:HIS134 4.1 11.9 1.0
CD2 A:HIS96 4.1 8.0 1.0
CU A:CU604 4.2 15.7 0.7
ND1 A:HIS458 4.2 9.3 1.0
CB A:ALA274 4.2 9.9 1.0
CG A:HIS458 4.3 7.4 1.0
CH2 A:TRP132 4.4 10.4 1.0
CD2 A:HIS401 4.4 9.2 1.0
O A:HOH893 4.4 25.2 1.0
NE2 A:HIS94 4.6 9.4 1.0
NE2 A:HIS401 4.6 7.9 1.0
CA A:HIS96 4.8 4.7 1.0
CU A:CU603 4.8 11.2 0.8
CD2 A:TRP132 4.9 10.3 1.0

Copper binding site 3 out of 8 in 6iqy

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Copper binding site 3 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:11.2
occ:0.79
NE2 A:HIS403 1.9 9.9 1.0
NE2 A:HIS136 2.0 10.2 1.0
NE2 A:HIS456 2.0 9.8 1.0
O A:HOH1215 2.2 23.6 1.0
CE1 A:HIS403 2.8 11.0 1.0
CD2 A:HIS456 3.0 4.3 1.0
CD2 A:HIS136 3.0 10.7 1.0
CE1 A:HIS456 3.0 7.4 1.0
CE1 A:HIS136 3.0 14.4 1.0
CD2 A:HIS403 3.1 11.1 1.0
CD2 A:HIS401 3.7 9.2 1.0
ND1 A:HIS403 4.0 12.7 1.0
CU A:CU604 4.0 15.7 0.7
CD2 A:HIS94 4.0 10.8 1.0
ND1 A:HIS456 4.1 8.9 1.0
ND1 A:HIS136 4.1 12.9 1.0
CG A:HIS456 4.1 9.4 1.0
CG A:HIS403 4.1 10.6 1.0
CG A:HIS136 4.1 10.2 1.0
CE A:MET454 4.2 11.4 1.0
O A:HOH893 4.2 25.2 1.0
NE2 A:HIS94 4.3 9.4 1.0
O A:HOH755 4.3 28.9 1.0
NE2 A:HIS401 4.4 7.9 1.0
CE A:MET468 4.6 12.2 0.5
CG A:HIS94 4.8 5.3 1.0
CU A:CU602 4.8 12.5 1.0
CG A:HIS401 4.8 10.8 1.0
OE2 A:GLU463 4.8 12.9 1.0
CB A:MET454 4.9 11.8 1.0
NE2 A:HIS458 4.9 8.8 1.0
CD2 A:HIS458 4.9 11.8 1.0

Copper binding site 4 out of 8 in 6iqy

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Copper binding site 4 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:15.7
occ:0.70
NE2 A:HIS401 1.8 7.9 1.0
NE2 A:HIS94 1.9 9.4 1.0
CD2 A:HIS401 2.7 9.2 1.0
O A:HOH1156 2.8 14.1 1.0
CD2 A:HIS94 2.8 10.8 1.0
CE1 A:HIS401 2.9 14.2 1.0
CE1 A:HIS94 2.9 15.1 1.0
NE2 A:HIS403 3.3 9.9 1.0
O A:HOH1215 3.3 23.6 1.0
ND1 A:HIS96 3.4 8.8 1.0
CE1 A:HIS403 3.5 11.0 1.0
CG A:HIS96 3.5 9.3 1.0
CD2 A:HIS403 3.5 11.1 1.0
CE1 A:HIS96 3.7 8.3 1.0
ND1 A:HIS403 3.7 12.7 1.0
CG A:HIS403 3.7 10.6 1.0
CD2 A:HIS96 3.8 8.0 1.0
CG A:HIS401 3.9 10.8 1.0
CA A:HIS96 3.9 4.7 1.0
ND1 A:HIS401 3.9 8.0 1.0
NE2 A:HIS96 3.9 9.6 1.0
CG A:HIS94 4.0 5.3 1.0
CB A:HIS96 4.0 6.7 1.0
ND1 A:HIS94 4.0 8.0 1.0
CU A:CU603 4.0 11.2 0.8
CU A:CU602 4.2 12.5 1.0
N A:GLY97 4.6 10.2 1.0
O A:HOH809 4.6 13.9 1.0
CA A:HIS403 4.6 11.4 1.0
O A:HOH852 4.6 11.1 1.0
CB A:HIS403 4.7 8.8 1.0
C A:HIS96 4.8 11.6 1.0
N A:HIS96 4.8 6.6 1.0

Copper binding site 5 out of 8 in 6iqy

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Copper binding site 5 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:10.3
occ:0.97
ND1 B:HIS398 2.0 8.9 1.0
ND1 B:HIS462 2.1 9.9 1.0
SG B:CYS457 2.3 10.2 1.0
OE1 B:GLN467 2.7 9.9 1.0
CE1 B:HIS398 3.0 16.8 1.0
CG B:HIS462 3.0 9.8 1.0
CG B:HIS398 3.0 10.1 1.0
CE1 B:HIS462 3.1 13.1 1.0
CB B:CYS457 3.2 11.9 1.0
CB B:HIS462 3.3 11.9 1.0
CB B:HIS398 3.4 11.9 1.0
O B:THR397 3.6 9.7 1.0
CA B:HIS398 3.7 9.5 1.0
CD B:GLN467 3.8 12.9 1.0
O B:HOH723 4.0 9.5 1.0
CB B:ASN459 4.1 7.5 1.0
NE2 B:HIS398 4.1 25.4 1.0
CD2 B:HIS398 4.2 18.4 1.0
CD2 B:HIS462 4.2 11.3 1.0
NE2 B:HIS462 4.2 9.7 1.0
C B:THR397 4.4 10.3 1.0
NE2 B:GLN467 4.4 11.2 1.0
N B:HIS398 4.5 8.8 1.0
CA B:CYS457 4.6 10.9 1.0
CA B:HIS462 4.8 8.9 1.0
CD B:PRO399 4.8 10.3 1.0
C B:HIS398 4.8 7.5 1.0
CG B:ASN459 4.9 9.8 1.0
N B:ASN459 5.0 8.9 1.0

Copper binding site 6 out of 8 in 6iqy

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Copper binding site 6 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:11.9
occ:0.92
NE2 B:HIS134 2.0 10.5 1.0
ND1 B:HIS96 2.0 7.6 1.0
NE2 B:HIS458 2.2 7.5 1.0
O B:HOH1235 2.6 23.9 1.0
CE1 B:HIS96 2.9 8.2 1.0
CE1 B:HIS134 2.9 13.6 1.0
CD2 B:HIS134 3.0 8.2 1.0
CE1 B:HIS458 3.0 9.5 1.0
CG B:HIS96 3.1 9.0 1.0
CD2 B:HIS458 3.2 11.2 1.0
CB B:HIS96 3.5 7.9 1.0
CZ2 B:TRP132 3.6 9.0 1.0
CD2 B:HIS94 3.9 9.3 1.0
CE2 B:TRP132 3.9 8.4 1.0
NE1 B:TRP132 3.9 9.0 1.0
ND1 B:HIS134 4.0 12.6 1.0
NE2 B:HIS96 4.1 8.8 1.0
CG B:HIS134 4.1 10.5 1.0
CD2 B:HIS96 4.1 7.1 1.0
CU B:CU604 4.2 16.1 0.7
O B:HOH1069 4.2 25.0 1.0
ND1 B:HIS458 4.2 12.4 1.0
CB B:ALA274 4.3 9.2 1.0
CG B:HIS458 4.3 7.9 1.0
CD2 B:HIS401 4.4 10.9 1.0
CH2 B:TRP132 4.4 10.3 1.0
NE2 B:HIS94 4.4 9.2 1.0
NE2 B:HIS401 4.5 10.7 1.0
CA B:HIS96 4.8 4.4 1.0
CU B:CU603 4.8 11.5 0.8
CD2 B:TRP132 4.9 10.8 1.0
CD1 B:TRP132 5.0 7.0 1.0

Copper binding site 7 out of 8 in 6iqy

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Copper binding site 7 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:11.5
occ:0.79
NE2 B:HIS403 1.9 8.1 1.0
NE2 B:HIS136 2.0 13.1 1.0
NE2 B:HIS456 2.1 8.2 1.0
O B:HOH1235 2.2 23.9 1.0
CE1 B:HIS403 2.8 10.0 1.0
CD2 B:HIS136 3.0 14.3 1.0
CE1 B:HIS456 3.0 9.7 1.0
CD2 B:HIS456 3.0 6.2 1.0
CE1 B:HIS136 3.1 13.1 1.0
CD2 B:HIS403 3.1 9.4 1.0
CD2 B:HIS401 3.6 10.9 1.0
ND1 B:HIS403 4.0 13.6 1.0
CU B:CU604 4.0 16.1 0.7
ND1 B:HIS456 4.1 11.9 1.0
CG B:HIS403 4.1 10.4 1.0
CG B:HIS136 4.1 9.9 1.0
CD2 B:HIS94 4.1 9.3 1.0
CG B:HIS456 4.1 11.0 1.0
ND1 B:HIS136 4.1 11.6 1.0
O B:HOH1069 4.2 25.0 1.0
CE B:MET454 4.2 10.3 1.0
O B:HOH716 4.2 17.1 1.0
NE2 B:HIS401 4.3 10.7 1.0
NE2 B:HIS94 4.4 9.2 1.0
CE B:MET468 4.7 13.3 0.3
CG B:HIS94 4.8 5.9 1.0
CU B:CU602 4.8 11.9 0.9
CG B:HIS401 4.8 9.1 1.0
OE2 B:GLU463 4.8 15.2 1.0
NE2 B:HIS458 4.8 7.5 1.0
CB B:MET454 4.9 12.4 1.0
CD2 B:HIS458 4.9 11.2 1.0

Copper binding site 8 out of 8 in 6iqy

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Copper binding site 8 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:16.1
occ:0.73
NE2 B:HIS401 1.8 10.7 1.0
NE2 B:HIS94 1.9 9.2 1.0
CD2 B:HIS401 2.8 10.9 1.0
CE1 B:HIS401 2.8 17.3 1.0
CE1 B:HIS94 2.9 13.0 1.0
CD2 B:HIS94 2.9 9.3 1.0
O B:HOH1143 2.9 15.8 1.0
O B:HOH1235 3.1 23.9 1.0
NE2 B:HIS403 3.2 8.1 1.0
CE1 B:HIS403 3.4 10.0 1.0
ND1 B:HIS96 3.4 7.6 1.0
CG B:HIS96 3.5 9.0 1.0
CD2 B:HIS403 3.5 9.4 1.0
ND1 B:HIS403 3.7 13.6 1.0
CG B:HIS403 3.8 10.4 1.0
CE1 B:HIS96 3.8 8.2 1.0
CA B:HIS96 3.9 4.4 1.0
CD2 B:HIS96 3.9 7.1 1.0
ND1 B:HIS401 3.9 7.6 1.0
CG B:HIS401 3.9 9.1 1.0
CB B:HIS96 3.9 7.9 1.0
ND1 B:HIS94 3.9 5.4 1.0
CG B:HIS94 4.0 5.9 1.0
CU B:CU603 4.0 11.5 0.8
NE2 B:HIS96 4.0 8.8 1.0
CU B:CU602 4.2 11.9 0.9
N B:GLY97 4.6 8.8 1.0
CA B:HIS403 4.6 10.5 1.0
CB B:HIS403 4.7 9.6 1.0
O B:HOH761 4.7 12.0 1.0
O B:HOH776 4.7 10.9 1.0
C B:HIS96 4.8 8.8 1.0
N B:HIS96 4.8 6.2 1.0

Reference:

M.Akter, T.Tokiwa, M.Shoji, K.Nishikawa, Y.Shigeta, T.Sakurai, Y.Higuchi, K.Kataoka, N.Shibata. Redox Potential-Dependent Formation of An Unusual His-Trp Bond in Bilirubin Oxidase. Chemistry V. 24 18052 2018.
ISSN: ISSN 1521-3765
PubMed: 30156345
DOI: 10.1002/CHEM.201803798
Page generated: Sun Dec 13 11:23:09 2020

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