Copper in PDB 7z5p: Bilirubin Oxidase From Bacillus Pumilus

The structure of Bilirubin Oxidase From Bacillus Pumilus, PDB code: 7z5p was solved by S.Gihaz, N.S.Herzallh, Y.Cohen, O.Bachar, A.Fishman, O.Yehezkeli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.22 / 2.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	198.96, 63.51, 115.96, 90, 124.57, 90
R / Rfree (%)	25.4 / 26.7

The binding sites of Copper atom in the Bilirubin Oxidase From Bacillus Pumilus (pdb code 7z5p). 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 Bacillus Pumilus, PDB code: 7z5p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:96.6 occ:1.00 NE2 A:HIS103 2.0 72.2 1.0 NE2 A:HIS422 2.1 81.3 1.0 CE1 A:HIS424 2.4 76.8 1.0 ND1 A:HIS424 2.5 77.8 1.0 CD2 A:HIS103 2.8 72.9 1.0 CE1 A:HIS103 3.0 71.4 1.0 ND1 A:HIS105 3.0 75.6 1.0 CE1 A:HIS422 3.0 79.3 1.0 CD2 A:HIS422 3.0 79.7 1.0 CA A:HIS105 3.5 72.3 1.0 NE2 A:HIS424 3.5 79.0 1.0 CG A:HIS105 3.6 74.2 1.0 CU A:CU603 3.7 96.6 1.0 CU A:CU602 3.7 96.6 1.0 CG A:HIS424 3.7 76.0 1.0 CE1 A:HIS105 3.8 75.5 1.0 CB A:HIS105 3.8 69.0 1.0 CG A:HIS103 3.9 73.7 1.0 ND1 A:HIS103 3.9 72.6 1.0 N A:GLY106 4.0 65.7 1.0 ND1 A:HIS422 4.1 79.8 1.0 CD2 A:HIS424 4.2 79.8 1.0 CG A:HIS422 4.2 81.1 1.0 C A:HIS105 4.3 71.2 1.0 N A:HIS105 4.3 72.7 1.0 CD2 A:HIS105 4.6 75.7 1.0 CA A:HIS424 4.6 73.3 1.0 NE2 A:HIS105 4.7 77.7 1.0 CB A:HIS424 4.7 74.6 1.0 O A:LEU104 4.8 69.1 1.0 NE2 A:HIS151 4.8 79.5 1.0 C A:LEU104 4.9 68.3 1.0

Copper binding site 2 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:96.6 occ:1.00 CE1 A:HIS424 2.1 76.8 1.0 NE2 A:HIS491 2.2 82.5 1.0 NE2 A:HIS424 2.3 79.0 1.0 NE2 A:HIS153 2.4 108.7 1.0 CD2 A:HIS153 2.7 93.5 1.0 CE1 A:HIS491 3.1 85.9 1.0 CD2 A:HIS491 3.2 77.9 1.0 ND1 A:HIS424 3.4 77.8 1.0 CE1 A:HIS153 3.6 109.0 1.0 CD2 A:HIS424 3.6 79.8 1.0 CU A:CU601 3.7 96.6 1.0 CD2 A:HIS422 3.7 79.7 1.0 CG A:HIS153 3.9 100.4 1.0 CU A:CU603 4.1 96.6 1.0 CG A:HIS424 4.1 76.0 1.0 NE2 A:HIS422 4.2 81.3 1.0 ND1 A:HIS491 4.3 83.1 1.0 ND1 A:HIS153 4.3 99.8 1.0 CG A:HIS491 4.3 75.6 1.0 CD2 A:HIS103 4.4 72.9 1.0 NE2 A:HIS103 4.4 72.2 1.0 OE2 A:GLU498 4.7 84.3 1.0 CE1 A:HIS151 4.7 84.7 1.0 CG A:HIS103 4.7 73.7 1.0 CE1 A:HIS103 4.8 71.4 1.0 OE1 A:GLU498 4.9 85.2 1.0 NE2 A:HIS151 5.0 79.5 1.0 ND1 A:HIS103 5.0 72.6 1.0 CG A:HIS422 5.0 81.1 1.0

Copper binding site 3 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:96.6 occ:1.00 NE2 A:HIS151 2.1 79.5 1.0 NE2 A:HIS493 2.3 83.3 1.0 ND1 A:HIS105 2.3 75.6 1.0 CE1 A:HIS151 2.8 84.7 1.0 CG A:HIS105 3.1 74.2 1.0 CD2 A:HIS493 3.1 88.5 1.0 CD2 A:HIS151 3.2 79.8 1.0 CE1 A:HIS493 3.2 84.7 1.0 CE1 A:HIS105 3.3 75.5 1.0 CB A:HIS105 3.4 69.0 1.0 CU A:CU601 3.7 96.6 1.0 ND1 A:HIS151 4.0 81.3 1.0 CU A:CU602 4.1 96.6 1.0 CD2 A:HIS103 4.1 72.9 1.0 CZ2 A:TRP149 4.1 77.1 1.0 CD2 A:HIS105 4.2 75.7 1.0 CG A:HIS151 4.2 78.1 1.0 NE2 A:HIS105 4.2 77.7 1.0 CG A:HIS493 4.3 84.2 1.0 CD2 A:HIS422 4.3 79.7 1.0 ND1 A:HIS493 4.3 89.5 1.0 NE2 A:HIS422 4.3 81.3 1.0 CA A:HIS105 4.4 72.3 1.0 CE2 A:TRP149 4.5 76.3 1.0 NE2 A:HIS103 4.6 72.2 1.0 NE1 A:TRP149 4.7 79.6 1.0 CB A:ALA297 4.7 71.0 1.0 CE1 A:HIS424 4.8 76.8 1.0 CH2 A:TRP149 4.8 76.2 1.0 CD2 A:HIS153 4.9 93.5 1.0

Copper binding site 4 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:104.7 occ:1.00 SG A:CYS492 1.7 78.5 1.0 ND1 A:HIS419 2.6 117.4 1.0 ND1 A:HIS497 2.6 78.2 1.0 CB A:CYS492 2.8 77.6 1.0 CB A:HIS497 3.2 77.9 1.0 CG A:HIS497 3.3 78.8 1.0 SD A:MET502 3.3 86.0 1.0 CE1 A:HIS419 3.4 113.1 1.0 CG A:HIS419 3.4 91.4 1.0 CB A:HIS419 3.7 86.3 1.0 CE1 A:HIS497 3.7 76.4 1.0 CB A:ILE494 3.9 73.4 1.0 CA A:HIS419 4.0 85.8 1.0 CA A:CYS492 4.1 81.2 1.0 CG1 A:ILE494 4.2 71.2 1.0 CD1 A:ILE494 4.4 70.5 1.0 CE A:MET502 4.4 80.2 1.0 C A:CYS492 4.4 77.3 1.0 NE2 A:HIS419 4.5 95.4 1.0 N A:ILE494 4.5 78.2 1.0 CD2 A:HIS419 4.5 93.5 1.0 CD2 A:HIS497 4.5 72.3 1.0 CG A:MET502 4.5 75.0 1.0 O A:ILE494 4.6 72.9 1.0 CD A:PRO420 4.6 79.9 1.0 C A:HIS419 4.7 82.2 1.0 CA A:HIS497 4.7 74.0 1.0 NE2 A:HIS497 4.7 73.5 1.0 CA A:ILE494 4.7 77.1 1.0 CB A:MET502 4.7 73.8 1.0 O A:PRO420 4.8 86.1 1.0 O A:CYS492 4.8 78.5 1.0 N A:PRO420 4.8 84.0 1.0 N A:HIS493 4.9 78.3 1.0 CG2 A:ILE494 4.9 70.5 1.0

Copper binding site 5 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu601 b:114.6 occ:1.00 NE2 B:HIS422 2.1 79.4 1.0 NE2 B:HIS103 2.1 69.0 1.0 CE1 B:HIS424 2.3 80.5 1.0 ND1 B:HIS105 2.5 95.4 1.0 ND1 B:HIS424 2.6 77.3 1.0 CD2 B:HIS103 2.9 67.4 1.0 CE1 B:HIS422 3.0 83.1 1.0 CD2 B:HIS422 3.0 79.0 1.0 CE1 B:HIS103 3.1 72.6 1.0 CA B:HIS105 3.4 68.8 1.0 CE1 B:HIS105 3.4 88.2 1.0 CG B:HIS105 3.5 71.4 1.0 NE2 B:HIS424 3.5 78.3 1.0 CU B:CU602 3.7 96.6 1.0 CU B:CU603 3.7 96.6 1.0 CB B:HIS105 3.7 69.0 1.0 CG B:HIS424 3.9 77.4 1.0 N B:GLY106 3.9 76.2 1.0 CG B:HIS103 4.0 68.9 1.0 ND1 B:HIS422 4.1 77.7 1.0 ND1 B:HIS103 4.1 73.3 1.0 CG B:HIS422 4.1 72.8 1.0 C B:HIS105 4.2 71.2 1.0 N B:HIS105 4.3 68.8 1.0 CD2 B:HIS424 4.3 75.7 1.0 NE2 B:HIS105 4.5 72.8 1.0 CD2 B:HIS105 4.6 72.9 1.0 NE2 B:HIS151 4.8 70.9 1.0 O B:LEU104 4.8 76.2 1.0 CA B:HIS424 4.8 70.8 1.0 C B:LEU104 4.9 74.5 1.0 CB B:HIS424 4.9 72.1 1.0

Copper binding site 6 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:96.6 occ:1.00 NE2 B:HIS493 2.1 71.5 1.0 NE2 B:HIS151 2.4 70.9 1.0 ND1 B:HIS105 2.4 95.4 1.0 CG B:HIS105 2.7 71.4 1.0 CE1 B:HIS105 3.0 88.2 1.0 CE1 B:HIS493 3.1 68.6 1.0 CD2 B:HIS493 3.1 71.5 1.0 CE1 B:HIS151 3.2 73.8 1.0 CB B:HIS105 3.2 69.0 1.0 CD2 B:HIS151 3.4 72.2 1.0 CD2 B:HIS105 3.5 72.9 1.0 NE2 B:HIS105 3.6 72.8 1.0 CU B:CU601 3.7 114.6 1.0 CZ2 B:TRP149 3.8 68.0 1.0 ND1 B:HIS493 4.2 68.6 1.0 CG B:HIS493 4.2 69.9 1.0 CE2 B:TRP149 4.2 68.9 1.0 NE1 B:TRP149 4.2 68.4 1.0 ND1 B:HIS151 4.3 74.6 1.0 CB B:ALA297 4.3 75.1 1.0 CA B:HIS105 4.3 68.8 1.0 CD2 B:HIS422 4.3 79.0 1.0 NE2 B:HIS422 4.3 79.4 1.0 CD2 B:HIS103 4.4 67.4 1.0 CG B:HIS151 4.4 73.5 1.0 CH2 B:TRP149 4.6 67.8 1.0 CU B:CU603 4.7 96.6 1.0 NE2 B:HIS103 4.8 69.0 1.0 CG B:HIS422 5.0 72.8 1.0 CE1 B:HIS422 5.0 83.1 1.0

Copper binding site 7 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:96.6 occ:1.00 NE2 B:HIS491 2.0 67.7 1.0 CE1 B:HIS424 2.3 80.5 1.0 NE2 B:HIS153 2.4 72.7 1.0 NE2 B:HIS424 2.6 78.3 1.0 CD2 B:HIS491 2.8 67.8 1.0 CE1 B:HIS491 3.1 69.8 1.0 ND1 B:HIS424 3.2 77.3 1.0 CD2 B:HIS153 3.3 74.6 1.0 CD2 B:HIS422 3.4 79.0 1.0 CE1 B:HIS153 3.5 75.6 1.0 CD2 B:HIS424 3.6 75.7 1.0 CU B:CU601 3.7 114.6 1.0 NE2 B:HIS422 3.9 79.4 1.0 CG B:HIS424 3.9 77.4 1.0 CG B:HIS491 4.0 73.6 1.0 ND1 B:HIS491 4.1 70.1 1.0 NE2 B:HIS103 4.4 69.0 1.0 CG B:HIS153 4.5 74.2 1.0 ND1 B:HIS153 4.5 74.7 1.0 CD2 B:HIS103 4.6 67.4 1.0 CU B:CU602 4.7 96.6 1.0 CG B:HIS422 4.7 72.8 1.0 CE1 B:HIS103 4.8 72.6 1.0 OE2 B:GLU498 4.9 73.3 1.0 CG B:HIS103 5.0 68.9 1.0

Copper binding site 8 out of 8 in the Bilirubin Oxidase From Bacillus Pumilus


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 Bacillus Pumilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:107.9 occ:1.00 ND1 B:HIS419 2.3 88.0 1.0 SG B:CYS492 2.4 81.3 1.0 ND1 B:HIS497 2.4 86.7 1.0 CB B:CYS492 3.0 73.7 1.0 CE1 B:HIS419 3.1 88.1 1.0 SD B:MET502 3.1 81.4 1.0 CG B:HIS497 3.2 87.3 1.0 CB B:HIS497 3.2 84.5 1.0 CG B:HIS419 3.4 82.9 1.0 CE1 B:HIS497 3.5 87.8 1.0 CB B:ILE494 3.8 77.8 1.0 CG1 B:ILE494 3.8 76.8 1.0 CB B:HIS419 3.9 77.5 1.0 CE B:MET502 4.2 82.8 1.0 NE2 B:HIS419 4.3 85.1 1.0 CD1 B:ILE494 4.3 88.4 1.0 CA B:HIS419 4.3 76.8 1.0 CA B:CYS492 4.4 69.5 1.0 CD2 B:HIS497 4.4 88.3 1.0 CD2 B:HIS419 4.5 82.1 1.0 CG B:MET502 4.5 79.3 1.0 NE2 B:HIS497 4.6 89.6 1.0 N B:ILE494 4.6 73.8 1.0 CG2 B:ILE494 4.6 78.8 1.0 CA B:HIS497 4.7 84.2 1.0 C B:CYS492 4.8 69.9 1.0 CA B:ILE494 4.8 77.6 1.0 CB B:MET502 4.8 82.6 1.0 O B:ILE494 4.8 81.5 1.0

S.Gihaz, N.S.Herzallh, Y.Cohen, O.Bachar, A.Fishman, O.Yehezkeli. The Structure of Bilirubin Oxidase From Bacillus Pumilus Reveals A Unique Disulfide Bond For Site-Specific Direct Electron Transfer. Biosensors (Basel) V. 12 2022.
ISSN: ISSN 2079-6374
PubMed: 35624560
DOI: 10.3390/BIOS12050258