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Copper in PDB 6i3l: Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F

Enzymatic activity of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F

All present enzymatic activity of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F:
1.3.3.5;

Protein crystallography data

The structure of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F, PDB code: 6i3l was solved by T.Koval, L.Svecova, T.Skalova, P.Kolenko, J.Duskova, L.H.Ostergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.54 / 2.10
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 136.250, 200.663, 217.121, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.6

Other elements in 6i3l:

The structure of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F also contains other interesting chemical elements:

Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F (pdb code 6i3l). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F, PDB code: 6i3l:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6i3l

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Copper binding site 1 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:16.5
occ:1.00
 ND1 A:HIS398 1.9 16.1 1.0
ND1 A:HIS462 2.0 15.1 1.0
SG A:CYS457 2.2 12.1 1.0
CE1 A:HIS398 2.8 17.8 1.0
CE1 A:HIS462 3.0 15.6 1.0
CG A:HIS462 3.0 15.0 1.0
CG A:HIS398 3.0 16.1 1.0
CB A:CYS457 3.2 12.8 1.0
CB A:HIS462 3.3 15.3 1.0
SD A:MET467 3.4 16.6 1.0
CB A:HIS398 3.4 14.4 1.0
O A:THR397 3.5 16.3 1.0
CA A:HIS398 3.6 15.0 1.0
NE2 A:HIS398 4.0 17.1 1.0
CB A:ASN459 4.0 13.6 1.0
CD2 A:HIS398 4.1 16.6 1.0
NE2 A:HIS462 4.1 15.0 1.0
CD2 A:HIS462 4.1 15.2 1.0
C A:THR397 4.2 15.2 1.0
N A:HIS398 4.4 14.9 1.0
CE A:MET467 4.4 16.2 1.0
CA A:CYS457 4.6 13.5 1.0
C A:HIS398 4.8 13.4 1.0
CA A:HIS462 4.8 14.8 1.0
CD A:PRO399 4.8 13.1 1.0
CG A:ASN459 4.9 13.8 1.0
CG A:MET467 4.9 16.2 1.0
N A:ASN459 5.0 13.4 1.0

Copper binding site 2 out of 8 in 6i3l

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Copper binding site 2 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:16.7
occ:1.00
 NE2 A:HIS136 2.0 18.2 1.0
NE2 A:HIS403 2.0 11.7 1.0
NE2 A:HIS456 2.1 13.9 1.0
O2 A:OXY617 2.3 15.3 1.0
O1 A:OXY617 2.6 9.4 1.0
CE1 A:HIS403 2.9 10.8 1.0
CD2 A:HIS136 2.9 17.1 1.0
CE1 A:HIS456 3.0 14.3 1.0
CD2 A:HIS456 3.1 13.9 1.0
CE1 A:HIS136 3.1 18.4 1.0
CD2 A:HIS403 3.2 12.0 1.0
CD2 A:HIS401 3.7 13.5 1.0
O A:HOH786 3.9 20.7 1.0
CU A:CU604 4.0 18.9 1.0
CE A:MET454 4.0 15.8 1.0
ND1 A:HIS403 4.1 10.5 1.0
ND1 A:HIS456 4.1 14.7 1.0
CG A:HIS136 4.1 16.5 1.0
CG A:HIS456 4.2 14.0 1.0
ND1 A:HIS136 4.2 16.9 1.0
CG A:HIS403 4.2 11.3 1.0
CD2 A:HIS94 4.3 15.5 1.0
NE2 A:HIS401 4.3 14.4 1.0
NE2 A:HIS94 4.5 16.7 1.0
OE2 A:GLU463 4.8 19.3 1.0
CB A:MET454 4.8 14.3 1.0
CG A:HIS94 4.9 15.6 1.0
CU A:CU603 4.9 15.8 1.0
CG A:HIS401 4.9 13.6 1.0

Copper binding site 3 out of 8 in 6i3l

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Copper binding site 3 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:15.8
occ:1.00
 ND1 A:HIS96 2.0 12.4 1.0
NE2 A:HIS134 2.1 12.8 1.0
NE2 A:HIS458 2.2 14.0 1.0
O1 A:OXY617 2.4 9.4 1.0
O2 A:OXY617 2.8 15.3 1.0
CE1 A:HIS96 2.9 12.4 1.0
CE1 A:HIS134 2.9 12.4 1.0
CG A:HIS96 3.1 12.8 1.0
CD2 A:HIS134 3.1 12.6 1.0
CD2 A:HIS458 3.2 14.0 1.0
CE1 A:HIS458 3.2 14.6 1.0
CB A:HIS96 3.5 12.9 1.0
CZ2 A:TRP132 3.6 16.5 1.0
CD2 A:HIS94 3.9 15.5 1.0
CE2 A:TRP132 3.9 15.3 1.0
NE1 A:TRP132 4.0 14.6 1.0
NE2 A:HIS96 4.0 12.7 1.0
CU A:CU604 4.1 18.9 1.0
ND1 A:HIS134 4.1 12.8 1.0
CD2 A:HIS96 4.1 12.7 1.0
O A:HOH786 4.2 20.7 1.0
CG A:HIS134 4.2 12.4 1.0
CB A:ALA274 4.3 14.1 1.0
ND1 A:HIS458 4.3 13.9 1.0
CG A:HIS458 4.3 14.0 1.0
CH2 A:TRP132 4.4 16.8 1.0
NE2 A:HIS94 4.4 16.7 1.0
CD2 A:HIS401 4.5 13.5 1.0
NE2 A:HIS401 4.6 14.4 1.0
CA A:HIS96 4.8 12.8 1.0
CU A:CU602 4.9 16.7 1.0
CD2 A:TRP132 4.9 14.6 1.0

Copper binding site 4 out of 8 in 6i3l

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Copper binding site 4 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:18.9
occ:1.00
 NE2 A:HIS94 1.9 16.7 1.0
NE2 A:HIS401 1.9 14.4 1.0
O2 A:OXY617 2.5 15.3 1.0
CD2 A:HIS401 2.8 13.5 1.0
CD2 A:HIS94 2.8 15.5 1.0
CE1 A:HIS94 2.9 16.6 1.0
CE1 A:HIS401 3.0 13.2 1.0
O A:HOH1112 3.1 14.2 1.0
ND1 A:HIS96 3.3 12.4 1.0
NE2 A:HIS403 3.3 11.7 1.0
CG A:HIS96 3.4 12.8 1.0
CE1 A:HIS403 3.4 10.8 1.0
CD2 A:HIS403 3.7 12.0 1.0
CE1 A:HIS96 3.7 12.4 1.0
CD2 A:HIS96 3.7 12.7 1.0
ND1 A:HIS403 3.8 10.5 1.0
O1 A:OXY617 3.8 9.4 1.0
CB A:HIS96 3.8 12.9 1.0
CA A:HIS96 3.8 12.8 1.0
CG A:HIS403 3.9 11.3 1.0
NE2 A:HIS96 3.9 12.7 1.0
CG A:HIS94 3.9 15.6 1.0
ND1 A:HIS94 3.9 15.9 1.0
CG A:HIS401 3.9 13.6 1.0
CU A:CU602 4.0 16.7 1.0
ND1 A:HIS401 4.0 12.8 1.0
CU A:CU603 4.1 15.8 1.0
N A:GLY97 4.7 13.0 1.0
O A:HOH816 4.8 10.6 1.0
CA A:HIS403 4.8 12.6 1.0
N A:HIS96 4.8 13.0 1.0
C A:HIS96 4.8 13.0 1.0
O A:HOH875 4.8 14.6 1.0
CB A:HIS403 4.9 11.9 1.0

Copper binding site 5 out of 8 in 6i3l

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Copper binding site 5 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:17.4
occ:1.00
 ND1 B:HIS398 2.0 16.4 1.0
ND1 B:HIS462 2.0 18.2 1.0
SG B:CYS457 2.2 15.7 1.0
CE1 B:HIS398 2.9 16.9 1.0
CG B:HIS462 2.9 18.1 1.0
CE1 B:HIS462 3.0 18.4 1.0
CG B:HIS398 3.0 17.1 1.0
CB B:CYS457 3.2 16.0 1.0
CB B:HIS462 3.2 17.5 1.0
CB B:HIS398 3.4 16.1 1.0
SD B:MET467 3.4 20.6 1.0
O B:THR397 3.5 14.6 1.0
CA B:HIS398 3.6 15.6 1.0
CB B:ASN459 4.0 15.3 1.0
NE2 B:HIS398 4.0 16.9 1.0
CD2 B:HIS462 4.1 18.5 1.0
CD2 B:HIS398 4.1 18.1 1.0
NE2 B:HIS462 4.1 18.3 1.0
C B:THR397 4.2 16.1 1.0
N B:HIS398 4.3 16.2 1.0
CE B:MET467 4.5 21.9 1.0
CA B:CYS457 4.6 15.5 1.0
CA B:HIS462 4.7 17.9 1.0
C B:HIS398 4.8 15.7 1.0
CG B:ASN459 4.8 15.3 1.0
CD B:PRO399 4.9 16.1 1.0
N B:ASN459 4.9 15.0 1.0
CG B:MET467 4.9 20.3 1.0
ND2 B:ASN459 5.0 15.6 1.0

Copper binding site 6 out of 8 in 6i3l

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Copper binding site 6 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:18.4
occ:1.00
 NE2 B:HIS403 2.0 14.5 1.0
NE2 B:HIS456 2.0 16.1 1.0
NE2 B:HIS136 2.0 18.1 1.0
O1 B:OXY617 2.4 15.1 1.0
O2 B:OXY617 2.5 10.9 1.0
CE1 B:HIS403 2.9 15.0 1.0
CE1 B:HIS456 2.9 16.7 1.0
CD2 B:HIS136 2.9 18.8 1.0
CD2 B:HIS456 3.0 16.7 1.0
CD2 B:HIS403 3.1 15.4 1.0
CE1 B:HIS136 3.1 18.2 1.0
CD2 B:HIS401 3.7 12.8 1.0
O B:HOH713 3.8 21.3 1.0
CU B:CU604 4.0 20.4 1.0
ND1 B:HIS456 4.0 15.5 1.0
ND1 B:HIS403 4.0 14.3 1.0
CE B:MET454 4.0 20.6 1.0
CG B:HIS456 4.1 15.9 1.0
CG B:HIS136 4.1 17.6 1.0
CG B:HIS403 4.1 15.1 1.0
CD2 B:HIS94 4.2 15.4 1.0
ND1 B:HIS136 4.2 17.8 1.0
NE2 B:HIS401 4.3 12.8 1.0
NE2 B:HIS94 4.4 16.5 1.0
OE2 B:GLU463 4.7 22.8 1.0
CB B:MET454 4.8 18.0 1.0
CG B:HIS94 4.8 14.9 1.0
CG B:HIS401 4.9 14.0 1.0
CU B:CU603 4.9 18.9 1.0
SD B:MET454 5.0 19.4 1.0

Copper binding site 7 out of 8 in 6i3l

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Copper binding site 7 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:18.9
occ:1.00
 NE2 B:HIS134 2.0 15.3 1.0
ND1 B:HIS96 2.0 15.7 1.0
NE2 B:HIS458 2.3 13.8 1.0
O2 B:OXY617 2.6 10.9 1.0
O1 B:OXY617 2.7 15.1 1.0
CE1 B:HIS134 2.9 16.1 1.0
CE1 B:HIS96 2.9 14.8 1.0
CD2 B:HIS134 3.0 16.1 1.0
CG B:HIS96 3.1 14.7 1.0
CE1 B:HIS458 3.2 13.9 1.0
CD2 B:HIS458 3.3 14.0 1.0
CB B:HIS96 3.4 14.3 1.0
CZ2 B:TRP132 3.7 15.3 1.0
NE1 B:TRP132 3.9 15.1 1.0
CE2 B:TRP132 3.9 15.1 1.0
CD2 B:HIS94 4.0 15.4 1.0
ND1 B:HIS134 4.1 15.7 1.0
CU B:CU604 4.1 20.4 1.0
NE2 B:HIS96 4.1 14.5 1.0
CG B:HIS134 4.1 16.6 1.0
O B:HOH713 4.2 21.3 1.0
CD2 B:HIS96 4.2 14.2 1.0
CB B:ALA274 4.2 14.6 1.0
ND1 B:HIS458 4.3 13.6 1.0
CG B:HIS458 4.4 14.3 1.0
CD2 B:HIS401 4.4 12.8 1.0
CH2 B:TRP132 4.5 14.8 1.0
NE2 B:HIS401 4.6 12.8 1.0
NE2 B:HIS94 4.6 16.5 1.0
CA B:HIS96 4.8 13.8 1.0
CU B:CU602 4.9 18.4 1.0
CD2 B:TRP132 4.9 15.6 1.0
CD1 B:TRP132 4.9 16.1 1.0

Copper binding site 8 out of 8 in 6i3l

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Copper binding site 8 out of 8 in the Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Bilirubin Oxidase From Myrothecium Verrucaria, Mutant W396F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:20.4
occ:1.00
 NE2 B:HIS401 1.9 12.8 1.0
NE2 B:HIS94 1.9 16.5 1.0
O1 B:OXY617 2.6 15.1 1.0
CD2 B:HIS94 2.7 15.4 1.0
CD2 B:HIS401 2.8 12.8 1.0
CE1 B:HIS401 2.9 12.5 1.0
CE1 B:HIS94 3.0 16.6 1.0
O B:HOH1018 3.1 21.3 1.0
ND1 B:HIS96 3.3 15.7 1.0
NE2 B:HIS403 3.4 14.5 1.0
CG B:HIS96 3.4 14.7 1.0
CE1 B:HIS403 3.5 15.0 1.0
CD2 B:HIS403 3.6 15.4 1.0
CD2 B:HIS96 3.7 14.2 1.0
CE1 B:HIS96 3.8 14.8 1.0
ND1 B:HIS403 3.8 14.3 1.0
CA B:HIS96 3.8 13.8 1.0
CB B:HIS96 3.8 14.3 1.0
CG B:HIS403 3.8 15.1 1.0
O2 B:OXY617 3.8 10.9 1.0
CG B:HIS94 3.9 14.9 1.0
CG B:HIS401 3.9 14.0 1.0
NE2 B:HIS96 3.9 14.5 1.0
ND1 B:HIS401 4.0 13.3 1.0
CU B:CU602 4.0 18.4 1.0
ND1 B:HIS94 4.0 15.4 1.0
CU B:CU603 4.1 18.9 1.0
N B:GLY97 4.7 13.4 1.0
CA B:HIS403 4.7 15.6 1.0
N B:HIS96 4.7 13.9 1.0
CB B:HIS403 4.7 16.4 1.0
C B:HIS96 4.8 14.1 1.0
O B:HOH854 4.8 11.3 1.0
O B:HOH920 4.8 10.5 1.0

Reference:

T.Koval, L.Svecova, L.H.Ostergaard, T.Skalova, J.Duskova, J.Hasek, P.Kolenko, K.Fejfarova, J.Stransky, M.Trundova, J.Dohnalek. Trp-His Covalent Adduct in Bilirubin Oxidase Is Crucial For Effective Bilirubin Binding But Has A Minor Role in Electron Transfer. Sci Rep V. 9 13700 2019.
ISSN: ESSN 2045-2322
PubMed: 31548583
DOI: 10.1038/S41598-019-50105-3
Page generated: Mon Jul 14 06:14:53 2025

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