Copper in PDB 2xll: The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria

All present enzymatic activity of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria:
1.3.3.5;

The structure of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria, PDB code: 2xll was solved by T.P.Mcnamara, E.D.Lowe, J.A.Cracknell, C.F.Blanford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.801 / 2.305
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.793, 83.602, 143.148, 89.98, 89.89, 89.90
R / Rfree (%)	16.97 / 21.63

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria (pdb code 2xll). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria, PDB code: 2xll:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu535 b:16.0 occ:1.00 ND1 A:HIS398 2.0 10.2 1.0 ND1 A:HIS462 2.2 5.3 1.0 SG A:CYS457 2.3 14.3 1.0 CE1 A:HIS398 2.9 14.1 1.0 CG A:HIS462 3.0 8.4 1.0 CG A:HIS398 3.0 10.7 1.0 CE1 A:HIS462 3.2 6.5 1.0 CB A:CYS457 3.2 1.2 1.0 CB A:HIS462 3.2 8.2 1.0 SD A:MET467 3.4 16.8 1.0 CB A:HIS398 3.4 3.1 1.0 O A:THR397 3.6 23.7 1.0 CB A:ASN459 3.8 15.0 1.0 CA A:HIS398 3.8 4.4 1.0 NE2 A:HIS398 4.0 7.5 1.0 CD2 A:HIS398 4.1 13.0 1.0 CD2 A:HIS462 4.2 18.2 1.0 NE2 A:HIS462 4.3 21.3 1.0 C A:THR397 4.4 26.4 1.0 CE A:MET467 4.4 27.0 1.0 CG A:ASN459 4.6 18.6 1.0 N A:HIS398 4.6 8.5 1.0 CA A:CYS457 4.7 5.6 1.0 CD A:PRO399 4.7 6.9 1.0 CA A:HIS462 4.8 14.5 1.0 ND2 A:ASN459 4.8 14.1 1.0 N A:ASN459 4.9 19.6 1.0 CA A:ASN459 4.9 4.3 1.0 C A:HIS398 4.9 19.8 1.0 CG A:MET467 4.9 10.4 1.0 O A:HOH2224 5.0 15.2 1.0 O A:ASN459 5.0 8.6 1.0

Copper binding site 2 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu536 b:17.4 occ:1.00 NE2 A:HIS403 2.0 12.4 1.0 NE2 A:HIS456 2.1 16.8 1.0 NE2 A:HIS136 2.2 15.1 1.0 CE1 A:HIS403 3.0 19.1 1.0 CD2 A:HIS456 3.0 6.1 1.0 CD2 A:HIS403 3.0 10.7 1.0 CE1 A:HIS136 3.1 16.0 1.0 CE1 A:HIS456 3.1 2.7 1.0 CD2 A:HIS136 3.2 2.5 1.0 CD2 A:HIS401 3.6 36.5 1.0 CU A:CU538 4.1 25.4 1.0 ND1 A:HIS403 4.1 14.9 1.0 CE A:MET454 4.1 22.5 1.0 CG A:HIS403 4.1 12.4 1.0 CD2 A:HIS94 4.1 18.6 1.0 CG A:HIS456 4.2 17.5 1.0 ND1 A:HIS456 4.2 26.9 1.0 NE2 A:HIS401 4.2 33.9 1.0 ND1 A:HIS136 4.3 15.7 1.0 CG A:HIS136 4.3 15.5 1.0 NE2 A:HIS94 4.3 14.9 1.0 O A:HOH2258 4.5 38.7 1.0 CB A:MET454 4.7 8.8 1.0 CG A:HIS401 4.7 17.6 1.0 CU A:CU537 4.9 18.1 1.0 CG A:HIS94 4.9 15.1 1.0 CD2 A:HIS458 5.0 7.2 1.0 NE2 A:HIS458 5.0 20.4 1.0 SD A:MET454 5.0 17.7 1.0

Copper binding site 3 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu537 b:18.1 occ:1.00 ND1 A:HIS96 2.2 6.1 1.0 NE2 A:HIS134 2.2 12.1 1.0 NE2 A:HIS458 2.3 20.4 1.0 CE1 A:HIS96 3.1 9.3 1.0 CD2 A:HIS134 3.2 23.9 1.0 CE1 A:HIS458 3.2 2.7 1.0 CG A:HIS96 3.2 7.1 1.0 CE1 A:HIS134 3.2 12.4 1.0 CD2 A:HIS458 3.2 7.2 1.0 CB A:HIS96 3.5 10.4 1.0 CZ2 A:TRP132 3.6 12.8 1.0 CD2 A:HIS94 3.9 18.6 1.0 O A:HOH2258 3.9 38.7 1.0 CE2 A:TRP132 4.0 10.4 1.0 CU A:CU538 4.1 25.4 1.0 NE1 A:TRP132 4.1 8.7 1.0 NE2 A:HIS96 4.3 11.3 1.0 ND1 A:HIS458 4.3 11.4 1.0 ND1 A:HIS134 4.3 19.2 1.0 CD2 A:HIS96 4.3 15.7 1.0 CG A:HIS134 4.3 18.6 1.0 CG A:HIS458 4.3 11.3 1.0 CB A:ALA274 4.4 6.9 1.0 CH2 A:TRP132 4.4 25.0 1.0 NE2 A:HIS94 4.5 14.9 1.0 CD2 A:HIS401 4.5 36.5 1.0 NE2 A:HIS401 4.6 33.9 1.0 CA A:HIS96 4.8 9.9 1.0 CU A:CU536 4.9 17.4 1.0 CD2 A:TRP132 5.0 5.0 1.0

Copper binding site 4 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu538 b:25.4 occ:1.00 NE2 A:HIS401 2.0 33.9 1.0 NE2 A:HIS94 2.0 14.9 1.0 CE1 A:HIS401 2.9 11.8 1.0 CD2 A:HIS94 2.9 18.6 1.0 CD2 A:HIS401 2.9 36.5 1.0 CE1 A:HIS94 3.0 4.7 1.0 O A:HOH2059 3.1 11.3 1.0 ND1 A:HIS96 3.2 6.1 1.0 CG A:HIS96 3.2 7.1 1.0 NE2 A:HIS403 3.3 12.4 1.0 CD2 A:HIS403 3.5 10.7 1.0 CA A:HIS96 3.6 9.9 1.0 CE1 A:HIS403 3.6 19.1 1.0 CE1 A:HIS96 3.6 9.3 1.0 CB A:HIS96 3.6 10.4 1.0 CD2 A:HIS96 3.7 15.7 1.0 NE2 A:HIS96 3.9 11.3 1.0 CG A:HIS403 4.0 12.4 1.0 ND1 A:HIS401 4.0 20.4 1.0 ND1 A:HIS403 4.0 14.9 1.0 CG A:HIS401 4.0 17.6 1.0 CU A:CU537 4.1 18.1 1.0 ND1 A:HIS94 4.1 14.5 1.0 CU A:CU536 4.1 17.4 1.0 CG A:HIS94 4.1 15.1 1.0 N A:GLY97 4.4 13.7 1.0 C A:HIS96 4.5 12.9 1.0 N A:HIS96 4.6 7.2 1.0 O A:HOH2065 4.6 15.2 1.0 O A:HOH2225 4.7 3.8 1.0 CA A:HIS403 4.8 10.6 1.0 CB A:HIS403 4.9 2.3 1.0 O A:LEU95 5.0 4.7 1.0

Copper binding site 5 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu535 b:14.2 occ:1.00 ND1 B:HIS398 2.0 9.8 1.0 ND1 B:HIS462 2.2 3.4 1.0 SG B:CYS457 2.3 10.0 1.0 CE1 B:HIS398 2.9 8.8 1.0 CG B:HIS398 3.0 9.5 1.0 CG B:HIS462 3.1 11.8 1.0 CB B:CYS457 3.2 3.8 1.0 CE1 B:HIS462 3.2 4.8 1.0 CB B:HIS462 3.3 12.9 1.0 CB B:HIS398 3.4 2.0 1.0 SD B:MET467 3.4 15.7 1.0 O B:THR397 3.6 21.2 1.0 CA B:HIS398 3.8 8.8 1.0 CB B:ASN459 3.8 12.5 1.0 NE2 B:HIS398 4.0 5.1 1.0 CD2 B:HIS398 4.1 12.3 1.0 CD2 B:HIS462 4.3 19.5 1.0 NE2 B:HIS462 4.3 21.6 1.0 C B:THR397 4.4 29.0 1.0 CE B:MET467 4.4 26.4 1.0 N B:HIS398 4.6 5.0 1.0 CG B:ASN459 4.6 14.3 1.0 CA B:CYS457 4.6 6.4 1.0 CD B:PRO399 4.7 5.7 1.0 CA B:HIS462 4.8 13.9 1.0 N B:ASN459 4.9 15.0 1.0 ND2 B:ASN459 4.9 9.5 1.0 C B:HIS398 4.9 20.2 1.0 CA B:ASN459 4.9 1.8 1.0 CG B:MET467 4.9 13.6 1.0 O B:ASN459 5.0 7.0 1.0

Copper binding site 6 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu536 b:16.2 occ:1.00 NE2 B:HIS456 2.1 13.6 1.0 NE2 B:HIS403 2.1 12.2 1.0 NE2 B:HIS136 2.1 11.8 1.0 CD2 B:HIS456 3.0 1.6 1.0 CE1 B:HIS403 3.0 16.4 1.0 CE1 B:HIS136 3.0 17.9 1.0 CE1 B:HIS456 3.1 4.3 1.0 CD2 B:HIS403 3.1 9.2 1.0 CD2 B:HIS136 3.1 1.4 1.0 CD2 B:HIS401 3.6 35.1 1.0 CE B:MET454 4.1 20.8 1.0 CG B:HIS456 4.1 16.6 1.0 ND1 B:HIS456 4.1 25.1 1.0 ND1 B:HIS403 4.2 12.4 1.0 CU B:CU538 4.2 26.2 1.0 ND1 B:HIS136 4.2 15.8 1.0 CD2 B:HIS94 4.2 17.8 1.0 CG B:HIS403 4.2 8.0 1.0 CG B:HIS136 4.3 16.1 1.0 NE2 B:HIS401 4.3 33.9 1.0 NE2 B:HIS94 4.4 16.6 1.0 O B:HOH2265 4.6 25.6 1.0 CB B:MET454 4.7 9.2 1.0 CG B:HIS401 4.8 16.6 1.0 CU B:CU537 4.9 17.0 1.0 CG B:HIS94 4.9 12.8 1.0 SD B:MET454 4.9 17.4 1.0 CD2 B:HIS458 5.0 2.4 1.0 OE2 B:GLU463 5.0 29.3 1.0 NE2 B:HIS458 5.0 11.5 1.0

Copper binding site 7 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu537 b:17.0 occ:1.00 ND1 B:HIS96 2.2 3.7 1.0 NE2 B:HIS134 2.2 16.1 1.0 NE2 B:HIS458 2.3 11.5 1.0 CE1 B:HIS96 3.1 7.8 1.0 CD2 B:HIS134 3.2 23.7 1.0 CG B:HIS96 3.2 4.7 1.0 CE1 B:HIS458 3.2 5.7 1.0 CE1 B:HIS134 3.2 13.2 1.0 CD2 B:HIS458 3.2 2.4 1.0 CB B:HIS96 3.5 10.9 1.0 CZ2 B:TRP132 3.6 12.5 1.0 O B:HOH2265 3.9 25.6 1.0 CE2 B:TRP132 4.0 8.3 1.0 CD2 B:HIS94 4.0 17.8 1.0 CU B:CU538 4.0 26.2 1.0 NE1 B:TRP132 4.1 8.9 1.0 NE2 B:HIS96 4.2 9.8 1.0 ND1 B:HIS458 4.3 8.3 1.0 CD2 B:HIS96 4.3 10.5 1.0 ND1 B:HIS134 4.3 22.7 1.0 CG B:HIS134 4.3 15.3 1.0 CG B:HIS458 4.3 12.2 1.0 CB B:ALA274 4.4 6.9 1.0 CH2 B:TRP132 4.4 24.0 1.0 CD2 B:HIS401 4.5 35.1 1.0 NE2 B:HIS94 4.5 16.6 1.0 NE2 B:HIS401 4.6 33.9 1.0 CA B:HIS96 4.8 12.1 1.0 CU B:CU536 4.9 16.2 1.0 CD2 B:TRP132 5.0 2.4 1.0

Copper binding site 8 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu538 b:26.2 occ:1.00 NE2 B:HIS401 1.9 33.9 1.0 NE2 B:HIS94 2.1 16.6 1.0 CE1 B:HIS401 2.8 9.1 1.0 CD2 B:HIS401 2.9 35.1 1.0 CD2 B:HIS94 3.0 17.8 1.0 O B:HOH2066 3.1 9.6 1.0 CE1 B:HIS94 3.1 8.1 1.0 ND1 B:HIS96 3.1 3.7 1.0 CG B:HIS96 3.2 4.7 1.0 NE2 B:HIS403 3.3 12.2 1.0 CD2 B:HIS403 3.5 9.2 1.0 CE1 B:HIS96 3.6 7.8 1.0 CA B:HIS96 3.6 12.1 1.0 CB B:HIS96 3.6 10.9 1.0 CD2 B:HIS96 3.6 10.5 1.0 CE1 B:HIS403 3.7 16.4 1.0 NE2 B:HIS96 3.8 9.8 1.0 ND1 B:HIS401 3.9 21.0 1.0 CG B:HIS401 4.0 16.6 1.0 CG B:HIS403 4.0 8.0 1.0 ND1 B:HIS403 4.0 12.4 1.0 CU B:CU537 4.0 17.0 1.0 CG B:HIS94 4.1 12.8 1.0 ND1 B:HIS94 4.2 10.3 1.0 CU B:CU536 4.2 16.2 1.0 N B:GLY97 4.4 12.8 1.0 C B:HIS96 4.5 9.2 1.0 N B:HIS96 4.6 13.9 1.0 O B:HOH2242 4.7 3.9 1.0 O B:HOH2071 4.7 9.2 1.0 CA B:HIS403 4.8 11.4 1.0 CB B:HIS403 4.9 3.2 1.0

Copper binding site 9 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu535 b:15.3 occ:1.00 ND1 C:HIS398 1.9 9.7 1.0 ND1 C:HIS462 2.2 8.3 1.0 SG C:CYS457 2.3 15.2 1.0 CE1 C:HIS398 2.9 9.9 1.0 CG C:HIS398 3.0 12.8 1.0 CG C:HIS462 3.1 14.7 1.0 CB C:CYS457 3.2 1.8 1.0 CE1 C:HIS462 3.2 16.8 1.0 CB C:HIS462 3.3 10.7 1.0 CB C:HIS398 3.4 3.1 1.0 SD C:MET467 3.4 21.2 1.0 O C:THR397 3.6 20.3 1.0 CA C:HIS398 3.7 5.4 1.0 CB C:ASN459 3.9 18.8 1.0 NE2 C:HIS398 4.0 11.4 1.0 CD2 C:HIS398 4.1 14.5 1.0 CD2 C:HIS462 4.3 14.7 1.0 NE2 C:HIS462 4.3 21.8 1.0 C C:THR397 4.4 31.0 1.0 CE C:MET467 4.4 27.4 1.0 N C:HIS398 4.5 4.6 1.0 CA C:CYS457 4.6 10.4 1.0 CG C:ASN459 4.6 15.0 1.0 CD C:PRO399 4.7 8.4 1.0 CA C:HIS462 4.8 13.1 1.0 C C:HIS398 4.9 20.5 1.0 ND2 C:ASN459 4.9 10.2 1.0 N C:ASN459 4.9 11.6 1.0 CG C:MET467 4.9 13.1 1.0 O C:HOH2236 5.0 8.1 1.0 CA C:ASN459 5.0 8.4 1.0

Copper binding site 10 out of 16 in the The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of The Crystal Structure of Bilirubin Oxidase From Myrothecium Verrucaria within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu536 b:17.4 occ:1.00 NE2 C:HIS403 2.0 17.9 1.0 NE2 C:HIS136 2.1 15.1 1.0 NE2 C:HIS456 2.2 17.8 1.0 CE1 C:HIS403 2.9 16.2 1.0 CD2 C:HIS403 3.0 6.1 1.0 CD2 C:HIS456 3.0 2.5 1.0 CD2 C:HIS136 3.1 1.3 1.0 CE1 C:HIS136 3.1 15.8 1.0 CE1 C:HIS456 3.2 3.2 1.0 CD2 C:HIS401 3.6 34.6 1.0 CU C:CU538 4.0 27.3 1.0 ND1 C:HIS403 4.1 14.1 1.0 CE C:MET454 4.1 24.0 1.0 CD2 C:HIS94 4.1 13.8 1.0 CG C:HIS403 4.1 12.9 1.0 NE2 C:HIS401 4.2 33.8 1.0 CG C:HIS456 4.2 21.4 1.0 ND1 C:HIS136 4.2 15.4 1.0 ND1 C:HIS456 4.2 26.3 1.0 CG C:HIS136 4.3 16.3 1.0 NE2 C:HIS94 4.3 19.4 1.0 O C:HOH2265 4.5 30.9 1.0 CB C:MET454 4.7 8.1 1.0 CG C:HIS401 4.8 21.1 1.0 CG C:HIS94 4.8 14.6 1.0 CU C:CU537 4.9 18.3 1.0 SD C:MET454 5.0 16.6 1.0 CD2 C:HIS458 5.0 9.3 1.0

J.A.Cracknell, T.P.Mcnamara, E.D.Lowe, C.F.Blanford. Bilirubin Oxidase From Myrothecium Verrucaria: X- Ray Determination of the Complete Crystal Structure and A Rational Surface Modification For Enhanced Electrocatalytic O(2) Reduction. Dalton Trans V. 40 6668 2011.
ISSN: ISSN 1477-9226
PubMed: 21544308
DOI: 10.1039/C0DT01403F