Copper in PDB 6iqz: High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type

All present enzymatic activity of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type:
1.3.3.5;

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type, PDB code: 6iqz 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)	35.71 / 1.46
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.342, 83.553, 52.690, 90.00, 95.73, 90.00
R / Rfree (%)	13.1 / 17

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

Copper binding site 1 out of 4 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type


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 - Wild Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:19.1 occ:0.93 ND1 A:HIS462 2.1 19.8 1.0 ND1 A:HIS398 2.1 16.7 1.0 SG A:CYS457 2.2 19.0 1.0 CE1 A:HIS398 3.0 18.3 1.0 CG A:HIS462 3.0 19.5 1.0 CE1 A:HIS462 3.1 20.0 1.0 CG A:HIS398 3.1 16.7 1.0 CB A:CYS457 3.2 18.3 1.0 CB A:HIS462 3.3 17.9 1.0 SD A:MET467 3.4 22.1 1.0 CB A:HIS398 3.4 16.4 1.0 O A:THR397 3.6 17.7 1.0 CA A:HIS398 3.6 17.0 1.0 CB A:ASN459 3.9 18.2 1.0 NE2 A:HIS398 4.1 19.2 1.0 NE2 A:HIS462 4.2 20.9 1.0 CD2 A:HIS462 4.2 20.2 1.0 CD2 A:HIS398 4.2 17.8 1.0 CE A:MET467 4.4 20.7 1.0 C A:THR397 4.4 16.8 1.0 N A:HIS398 4.5 17.2 1.0 CA A:CYS457 4.6 17.1 1.0 CD A:PRO399 4.7 16.1 1.0 C A:HIS398 4.7 16.1 1.0 CG A:ASN459 4.7 17.8 1.0 CA A:HIS462 4.8 17.1 1.0 N A:ASN459 4.8 16.2 1.0 CG A:MET467 4.9 20.0 1.0 ND2 A:ASN459 5.0 18.0 1.0 CA A:ASN459 5.0 16.1 1.0 N A:PRO399 5.0 16.1 1.0

Copper binding site 2 out of 4 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type


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 - Wild Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:19.0 occ:0.76 NE2 A:HIS134 2.0 20.3 1.0 ND1 A:HIS96 2.0 17.1 1.0 NE2 A:HIS458 2.2 19.8 1.0 O A:HOH1096 2.7 29.8 1.0 CE1 A:HIS134 2.9 21.9 1.0 CE1 A:HIS96 2.9 17.6 1.0 CD2 A:HIS134 3.0 18.0 1.0 CG A:HIS96 3.1 17.4 1.0 CE1 A:HIS458 3.1 19.3 1.0 CD2 A:HIS458 3.3 18.1 1.0 CB A:HIS96 3.5 18.7 1.0 CZ2 A:TRP132 3.6 18.1 1.0 CD2 A:HIS94 3.7 25.6 1.0 CE2 A:TRP132 3.9 16.8 1.0 NE1 A:TRP132 3.9 17.4 1.0 ND1 A:HIS134 4.0 20.0 1.0 NE2 A:HIS96 4.1 18.6 1.0 CG A:HIS134 4.1 17.3 1.0 CD2 A:HIS96 4.2 17.8 1.0 CU A:CU604 4.2 18.2 0.1 ND1 A:HIS458 4.2 18.3 1.0 O A:HOH968 4.3 43.4 1.0 CB A:ALA274 4.3 15.7 1.0 CD2 A:HIS401 4.3 18.5 1.0 CG A:HIS458 4.3 17.6 1.0 NE2 A:HIS94 4.3 25.9 1.0 CH2 A:TRP132 4.5 17.0 1.0 NE2 A:HIS401 4.5 20.9 1.0 CA A:HIS96 4.7 16.8 1.0 CG A:HIS94 4.9 22.3 1.0 CD2 A:TRP132 4.9 18.2 1.0 CD1 A:TRP132 4.9 18.1 1.0 CU A:CU603 5.0 22.9 0.4

Copper binding site 3 out of 4 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type


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 - Wild Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:22.9 occ:0.43 NE2 A:HIS456 1.9 22.3 1.0 NE2 A:HIS403 2.0 23.1 1.0 NE2 A:HIS136 2.0 24.4 1.0 O A:HOH1096 2.3 29.8 1.0 CE1 A:HIS403 2.8 23.2 1.0 CD2 A:HIS456 2.8 22.2 1.0 CE1 A:HIS456 2.9 20.5 1.0 CD2 A:HIS136 3.0 26.0 1.0 CE1 A:HIS136 3.1 25.9 1.0 CD2 A:HIS403 3.2 21.5 1.0 CD2 A:HIS401 3.6 18.5 1.0 CE A:MET454 3.9 29.7 1.0 ND1 A:HIS403 4.0 21.7 1.0 CG A:HIS456 4.0 19.1 1.0 ND1 A:HIS456 4.0 20.7 1.0 CU A:CU604 4.0 18.2 0.1 CD2 A:HIS94 4.0 25.6 1.0 O A:HOH968 4.1 43.4 1.0 ND1 A:HIS136 4.1 29.4 1.0 CG A:HIS136 4.2 26.2 1.0 CG A:HIS403 4.2 21.5 1.0 NE2 A:HIS94 4.2 25.9 1.0 NE2 A:HIS401 4.2 20.9 1.0 CG A:HIS94 4.6 22.3 1.0 CG A:HIS401 4.7 19.0 1.0 CB A:MET454 4.7 21.4 1.0 OE2 A:GLU463 4.9 32.5 1.0 SD A:MET454 4.9 27.4 1.0 CE1 A:HIS94 4.9 26.3 1.0 CU A:CU602 5.0 19.0 0.8

Copper binding site 4 out of 4 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - Wild Type


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 - Wild Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:18.2 occ:0.15 NE2 A:HIS401 1.6 20.9 1.0 NE2 A:HIS94 1.7 25.9 1.0 CD2 A:HIS401 2.5 18.5 1.0 CD2 A:HIS94 2.7 25.6 1.0 CE1 A:HIS94 2.7 26.3 1.0 CE1 A:HIS401 2.7 19.7 1.0 O A:HOH995 3.1 27.6 1.0 NE2 A:HIS403 3.3 23.1 1.0 O A:HOH1096 3.3 29.8 1.0 CE1 A:HIS403 3.4 23.2 1.0 ND1 A:HIS96 3.5 17.1 1.0 CD2 A:HIS403 3.5 21.5 1.0 CG A:HIS96 3.5 17.4 1.0 CG A:HIS401 3.7 19.0 1.0 ND1 A:HIS401 3.7 21.1 1.0 ND1 A:HIS94 3.7 24.4 1.0 ND1 A:HIS403 3.7 21.7 1.0 CG A:HIS94 3.7 22.3 1.0 CG A:HIS403 3.8 21.5 1.0 CE1 A:HIS96 3.8 17.6 1.0 CA A:HIS96 3.9 16.8 1.0 CD2 A:HIS96 3.9 17.8 1.0 CB A:HIS96 4.0 18.7 1.0 CU A:CU603 4.0 22.9 0.4 NE2 A:HIS96 4.1 18.6 1.0 CU A:CU602 4.2 19.0 0.8 N A:GLY97 4.6 16.9 1.0 CB A:HIS403 4.7 19.2 1.0 O A:HOH887 4.7 25.3 1.0 CA A:HIS403 4.7 19.1 1.0 N A:HIS96 4.8 17.1 1.0 C A:HIS96 4.8 16.7 1.0 O A:HOH856 4.9 20.9 1.0

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