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

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

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

Protein crystallography data

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically Prepared, PDB code: 6iqx 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) 34.06 / 1.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.242, 152.579, 69.995, 90.00, 91.69, 90.00
R / Rfree (%) 16.1 / 19.9

Copper Binding Sites:

The binding sites of Copper atom in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically Prepared (pdb code 6iqx). 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, Aerobically Prepared, PDB code: 6iqx:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6iqx

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Copper binding site 1 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:7.5
occ:1.00
 ND1 A:HIS462 2.0 6.2 1.0
ND1 A:HIS398 2.1 5.3 1.0
SG A:CYS457 2.2 6.2 1.0
OE1 A:GLN467 2.7 7.2 1.0
CG A:HIS462 3.0 7.8 1.0
CE1 A:HIS462 3.0 5.9 1.0
CE1 A:HIS398 3.1 9.1 1.0
CG A:HIS398 3.1 8.5 1.0
CB A:CYS457 3.2 6.6 1.0
CB A:HIS462 3.3 7.9 1.0
CB A:HIS398 3.4 6.9 1.0
O A:THR397 3.6 6.5 1.0
CA A:HIS398 3.7 7.1 1.0
CD A:GLN467 3.8 7.3 1.0
O A:HOH714 4.0 10.6 1.0
CB A:ASN459 4.1 5.8 1.0
NE2 A:HIS462 4.1 6.5 1.0
CD2 A:HIS462 4.1 8.1 1.0
NE2 A:HIS398 4.2 12.7 1.0
CD2 A:HIS398 4.2 11.9 1.0
NE2 A:GLN467 4.3 6.1 1.0
C A:THR397 4.4 5.5 1.0
N A:HIS398 4.5 5.6 1.0
CA A:CYS457 4.6 4.1 1.0
CA A:HIS462 4.8 6.1 1.0
CD A:PRO399 4.8 5.2 1.0
C A:HIS398 4.8 4.1 1.0
CG A:ASN459 4.9 4.7 1.0
CG A:GLN467 4.9 8.7 1.0
N A:ASN459 5.0 4.5 1.0

Copper binding site 2 out of 8 in 6iqx

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Copper binding site 2 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:8.5
occ:0.88
 ND1 A:HIS96 2.0 5.5 1.0
NE2 A:HIS134 2.0 5.7 1.0
NE2 A:HIS458 2.2 8.5 1.0
O A:HOH1163 2.6 27.8 1.0
CE1 A:HIS134 2.9 8.2 1.0
CE1 A:HIS96 2.9 5.7 1.0
CD2 A:HIS134 3.1 5.7 1.0
CG A:HIS96 3.1 4.3 1.0
CE1 A:HIS458 3.1 6.7 1.0
CD2 A:HIS458 3.2 7.7 1.0
CB A:HIS96 3.5 5.7 1.0
CZ2 A:TRP132 3.5 8.7 1.0
CD2 A:HIS94 3.8 11.1 1.0
CE2 A:TRP132 3.8 6.6 1.0
NE1 A:TRP132 3.9 7.0 1.0
ND1 A:HIS134 4.0 9.4 1.0
NE2 A:HIS96 4.0 6.7 1.0
CG A:HIS134 4.1 6.9 1.0
CD2 A:HIS96 4.1 5.4 1.0
CB A:ALA274 4.2 7.2 1.0
ND1 A:HIS458 4.2 7.3 1.0
CU A:CU604 4.2 12.2 0.3
CG A:HIS458 4.3 6.8 1.0
CD2 A:HIS401 4.3 7.4 1.0
O A:HOH1067 4.3 19.1 1.0
CH2 A:TRP132 4.4 6.7 1.0
NE2 A:HIS94 4.4 11.0 1.0
NE2 A:HIS401 4.6 8.7 1.0
CA A:HIS96 4.8 3.6 1.0
CD2 A:TRP132 4.9 7.8 1.0
CD1 A:TRP132 4.9 6.5 1.0
CU A:CU603 4.9 11.0 0.6
CG A:HIS94 5.0 7.6 1.0

Copper binding site 3 out of 8 in 6iqx

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Copper binding site 3 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:11.0
occ:0.60
 NE2 A:HIS403 1.9 6.7 1.0
NE2 A:HIS456 2.0 7.0 1.0
NE2 A:HIS136 2.0 9.8 1.0
O A:HOH1163 2.3 27.8 1.0
CE1 A:HIS403 2.8 7.3 1.0
CE1 A:HIS456 3.0 7.0 1.0
CD2 A:HIS456 3.0 5.6 1.0
CD2 A:HIS136 3.0 10.5 1.0
CE1 A:HIS136 3.0 12.3 1.0
CD2 A:HIS403 3.1 6.6 1.0
CD2 A:HIS401 3.5 7.4 1.0
ND1 A:HIS403 3.9 8.5 1.0
ND1 A:HIS456 4.0 6.5 1.0
CU A:CU604 4.1 12.2 0.3
CG A:HIS456 4.1 7.9 1.0
ND1 A:HIS136 4.1 12.7 1.0
CG A:HIS136 4.1 9.8 1.0
CE A:MET454 4.1 8.9 1.0
CG A:HIS403 4.1 6.9 1.0
CD2 A:HIS94 4.2 11.1 1.0
NE2 A:HIS401 4.3 8.7 1.0
O A:HOH1067 4.3 19.1 1.0
NE2 A:HIS94 4.4 11.0 1.0
CG A:HIS401 4.6 7.2 1.0
CE A:MET468 4.6 13.2 0.5
CG A:HIS94 4.7 7.6 1.0
CB A:MET454 4.8 8.0 1.0
OE2 A:GLU463 4.9 13.8 1.0
CD2 A:HIS458 4.9 7.7 1.0
NE2 A:HIS458 4.9 8.5 1.0
CU A:CU602 4.9 8.5 0.9
SD A:MET454 5.0 9.9 1.0

Copper binding site 4 out of 8 in 6iqx

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Copper binding site 4 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:12.2
occ:0.35
 NE2 A:HIS401 1.6 8.7 1.0
NE2 A:HIS94 1.7 11.0 1.0
CD2 A:HIS401 2.5 7.4 1.0
CE1 A:HIS94 2.7 9.8 1.0
CE1 A:HIS401 2.7 9.1 1.0
CD2 A:HIS94 2.7 11.1 1.0
O A:HOH1059 3.0 14.1 1.0
NE2 A:HIS403 3.3 6.7 1.0
CE1 A:HIS403 3.4 7.3 1.0
ND1 A:HIS96 3.5 5.5 1.0
CG A:HIS96 3.5 4.3 1.0
O A:HOH1163 3.5 27.8 1.0
CD2 A:HIS403 3.6 6.6 1.0
ND1 A:HIS403 3.7 8.5 1.0
CG A:HIS401 3.7 7.2 1.0
ND1 A:HIS401 3.7 8.8 1.0
CE1 A:HIS96 3.7 5.7 1.0
ND1 A:HIS94 3.8 8.8 1.0
CD2 A:HIS96 3.8 5.4 1.0
CG A:HIS403 3.8 6.9 1.0
CG A:HIS94 3.8 7.6 1.0
CA A:HIS96 3.9 3.6 1.0
NE2 A:HIS96 3.9 6.7 1.0
CB A:HIS96 4.0 5.7 1.0
CU A:CU603 4.1 11.0 0.6
CU A:CU602 4.2 8.5 0.9
N A:GLY97 4.6 4.7 1.0
O A:HOH766 4.7 10.2 1.0
CA A:HIS403 4.7 5.3 1.0
O A:HOH885 4.7 8.8 1.0
CB A:HIS403 4.8 6.3 1.0
C A:HIS96 4.8 4.3 1.0
N A:HIS96 4.8 4.9 1.0

Copper binding site 5 out of 8 in 6iqx

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Copper binding site 5 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:7.1
occ:1.00
 ND1 B:HIS462 2.0 6.2 1.0
ND1 B:HIS398 2.1 7.0 1.0
SG B:CYS457 2.2 6.8 1.0
OE1 B:GLN467 2.7 6.5 1.0
CG B:HIS462 3.0 6.2 1.0
CE1 B:HIS462 3.0 6.3 1.0
CE1 B:HIS398 3.0 7.1 1.0
CG B:HIS398 3.1 5.4 1.0
CB B:CYS457 3.2 7.3 1.0
CB B:HIS462 3.3 6.7 1.0
CB B:HIS398 3.4 4.8 1.0
O B:THR397 3.6 6.5 1.0
CA B:HIS398 3.7 5.4 1.0
CD B:GLN467 3.8 6.8 1.0
O B:HOH710 4.1 13.7 1.0
CB B:ASN459 4.1 5.3 1.0
NE2 B:HIS462 4.1 6.4 1.0
CD2 B:HIS462 4.1 6.1 1.0
NE2 B:HIS398 4.1 10.0 1.0
CD2 B:HIS398 4.2 10.2 1.0
C B:THR397 4.4 5.7 1.0
NE2 B:GLN467 4.4 7.5 1.0
N B:HIS398 4.5 6.0 1.0
CA B:CYS457 4.6 5.4 1.0
CA B:HIS462 4.8 5.3 1.0
CD B:PRO399 4.8 5.5 1.0
C B:HIS398 4.8 2.7 1.0
CG B:ASN459 4.9 4.6 1.0
N B:ASN459 5.0 5.8 1.0
CG B:GLN467 5.0 7.2 1.0

Copper binding site 6 out of 8 in 6iqx

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Copper binding site 6 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:7.5
occ:0.84
 ND1 B:HIS96 2.0 6.1 1.0
NE2 B:HIS134 2.0 7.1 1.0
NE2 B:HIS458 2.2 6.8 1.0
O B:HOH1109 2.4 30.0 1.0
CE1 B:HIS96 2.9 6.7 1.0
CE1 B:HIS134 2.9 9.3 1.0
CD2 B:HIS134 3.0 6.9 1.0
CG B:HIS96 3.0 4.3 1.0
CE1 B:HIS458 3.1 6.4 1.0
CD2 B:HIS458 3.2 7.7 1.0
CB B:HIS96 3.5 4.7 1.0
CZ2 B:TRP132 3.5 7.7 1.0
CD2 B:HIS94 3.8 9.6 1.0
CE2 B:TRP132 3.8 6.6 1.0
NE1 B:TRP132 3.9 9.6 1.0
NE2 B:HIS96 4.0 6.2 1.0
ND1 B:HIS134 4.0 9.8 1.0
CD2 B:HIS96 4.1 6.0 1.0
CG B:HIS134 4.1 7.7 1.0
CB B:ALA274 4.2 7.8 1.0
ND1 B:HIS458 4.2 5.9 1.0
CD2 B:HIS401 4.3 8.0 1.0
O B:HOH1093 4.3 21.8 1.0
CU B:CU604 4.3 10.9 0.3
CG B:HIS458 4.3 6.6 1.0
CH2 B:TRP132 4.4 7.7 1.0
NE2 B:HIS94 4.4 9.3 1.0
NE2 B:HIS401 4.5 8.1 1.0
CA B:HIS96 4.8 4.7 1.0
CD2 B:TRP132 4.9 6.0 1.0
CU B:CU603 4.9 11.9 0.6
CD1 B:TRP132 4.9 7.6 1.0
CG B:HIS94 5.0 6.4 1.0

Copper binding site 7 out of 8 in 6iqx

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Copper binding site 7 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:11.9
occ:0.64
 NE2 B:HIS456 2.0 7.7 1.0
NE2 B:HIS403 2.0 7.7 1.0
NE2 B:HIS136 2.1 11.0 1.0
O B:HOH1109 2.6 30.0 1.0
CE1 B:HIS403 2.8 8.0 1.0
CE1 B:HIS456 2.9 6.6 1.0
CD2 B:HIS456 2.9 6.4 1.0
CD2 B:HIS136 3.0 12.2 1.0
CE1 B:HIS136 3.1 12.5 1.0
CD2 B:HIS403 3.1 7.8 1.0
CD2 B:HIS401 3.5 8.0 1.0
ND1 B:HIS403 4.0 8.8 1.0
ND1 B:HIS456 4.0 7.1 1.0
CG B:HIS456 4.0 7.2 1.0
CU B:CU604 4.1 10.9 0.3
CD2 B:HIS94 4.1 9.6 1.0
CG B:HIS403 4.1 6.5 1.0
ND1 B:HIS136 4.2 13.4 1.0
CE B:MET454 4.2 12.9 1.0
CG B:HIS136 4.2 11.8 1.0
NE2 B:HIS401 4.3 8.1 1.0
NE2 B:HIS94 4.3 9.3 1.0
O B:HOH1093 4.4 21.8 1.0
CG B:HIS401 4.6 8.9 1.0
CG B:HIS94 4.7 6.4 1.0
CB B:MET454 4.8 5.7 1.0
OE2 B:GLU463 4.9 13.6 1.0
CU B:CU602 4.9 7.5 0.8
NE2 B:HIS458 4.9 6.8 1.0
CD2 B:HIS458 4.9 7.7 1.0

Copper binding site 8 out of 8 in 6iqx

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Copper binding site 8 out of 8 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Aerobically 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, Aerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:10.9
occ:0.32
 NE2 B:HIS401 1.6 8.1 1.0
NE2 B:HIS94 1.7 9.3 1.0
CD2 B:HIS401 2.6 8.0 1.0
CE1 B:HIS94 2.7 7.3 1.0
CE1 B:HIS401 2.7 9.3 1.0
CD2 B:HIS94 2.8 9.6 1.0
O B:HOH1011 2.8 13.8 1.0
NE2 B:HIS403 3.3 7.7 1.0
CE1 B:HIS403 3.4 8.0 1.0
CG B:HIS96 3.5 4.3 1.0
CD2 B:HIS403 3.5 7.8 1.0
ND1 B:HIS96 3.5 6.1 1.0
O B:HOH1109 3.6 30.0 1.0
ND1 B:HIS403 3.7 8.8 1.0
CG B:HIS401 3.7 8.9 1.0
ND1 B:HIS401 3.7 9.4 1.0
CG B:HIS403 3.8 6.5 1.0
ND1 B:HIS94 3.8 7.6 1.0
CD2 B:HIS96 3.8 6.0 1.0
CE1 B:HIS96 3.8 6.7 1.0
CG B:HIS94 3.8 6.4 1.0
CA B:HIS96 3.9 4.7 1.0
NE2 B:HIS96 4.0 6.2 1.0
CB B:HIS96 4.0 4.7 1.0
CU B:CU603 4.1 11.9 0.6
CU B:CU602 4.3 7.5 0.8
O B:HOH832 4.5 10.4 1.0
N B:GLY97 4.6 6.0 1.0
CA B:HIS403 4.6 6.5 1.0
O B:HOH927 4.6 7.2 1.0
CB B:HIS403 4.7 5.7 1.0
C B:HIS96 4.8 6.3 1.0
N B:HIS96 4.8 5.2 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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