Copper in PDB 6xj0: Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus

The structure of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus, PDB code: 6xj0 was solved by I.Pardo, A.S.Soares, R.Collins, S.H.Partowmah, E.A.Coler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	110.31 / 2.34
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.37, 127.37, 75.27, 90, 90, 120
R / Rfree (%)	18.2 / 22.3

The structure of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Copper atom in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus (pdb code 6xj0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus, PDB code: 6xj0:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:24.6 occ:1.00 CU2 A:C2O601 0.0 24.6 1.0 NE2 A:HIS147 2.0 20.2 1.0 ND1 A:HIS108 2.1 21.5 1.0 NE2 A:HIS446 2.1 22.5 1.0 O1 A:C2O601 2.3 19.2 1.0 CE1 A:HIS147 2.9 19.9 1.0 CE1 A:HIS108 2.9 20.0 1.0 CD2 A:HIS446 3.1 19.9 1.0 CE1 A:HIS446 3.1 21.8 1.0 CD2 A:HIS147 3.1 20.4 1.0 CG A:HIS108 3.2 20.8 1.0 CB A:HIS108 3.6 21.1 1.0 CZ2 A:TRP145 3.8 18.3 1.0 CU A:CU602 3.8 27.0 1.0 CD2 A:HIS106 4.0 22.7 1.0 ND1 A:HIS147 4.1 21.0 1.0 NE2 A:HIS108 4.1 19.3 1.0 CE2 A:TRP145 4.2 19.3 1.0 CG A:HIS147 4.2 20.1 1.0 ND1 A:HIS446 4.2 21.8 1.0 CG A:HIS446 4.2 20.6 1.0 CD2 A:HIS108 4.2 20.4 1.0 NE2 A:HIS106 4.3 24.4 1.0 NE2 A:HIS394 4.3 22.3 1.0 NE1 A:TRP145 4.4 21.0 1.0 CD2 A:HIS394 4.4 18.4 1.0 CH2 A:TRP145 4.4 17.2 1.0 CU3 A:C2O601 4.5 26.8 1.0 CA A:HIS108 4.7 21.5 1.0 CB A:ALA282 4.8 17.3 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:26.8 occ:1.00 CU3 A:C2O601 0.0 26.8 1.0 NE2 A:HIS396 2.1 20.9 1.0 NE2 A:HIS444 2.1 21.2 1.0 NE2 A:HIS149 2.1 24.7 1.0 O1 A:C2O601 2.3 19.2 1.0 CD2 A:HIS149 2.9 21.8 1.0 CE1 A:HIS396 3.0 19.2 1.0 CE1 A:HIS444 3.0 19.1 1.0 CD2 A:HIS444 3.2 19.6 1.0 CD2 A:HIS396 3.2 20.6 1.0 CE1 A:HIS149 3.2 23.7 1.0 CU A:CU602 3.6 27.0 1.0 CD2 A:HIS394 3.8 18.4 1.0 OE2 A:GLU451 4.0 46.0 1.0 ND1 A:HIS396 4.1 16.7 1.0 ND1 A:HIS444 4.1 20.6 1.0 CG A:HIS149 4.1 22.7 1.0 ND1 A:HIS149 4.2 22.7 1.0 CG A:HIS396 4.2 19.0 1.0 CG A:HIS444 4.3 20.7 1.0 NE2 A:HIS106 4.3 24.4 1.0 NE2 A:HIS394 4.3 22.3 1.0 CE A:MET456 4.3 29.0 1.0 CD2 A:HIS106 4.5 22.7 1.0 CU2 A:C2O601 4.5 24.6 1.0 CD A:GLU451 4.6 37.9 1.0 OE1 A:GLU451 4.7 35.8 1.0 CD2 A:HIS446 4.8 19.9 1.0 NE2 A:HIS446 4.8 22.5 1.0 CB A:MET442 4.9 23.3 1.0 CE1 A:HIS106 4.9 21.2 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:27.0 occ:1.00 NE2 A:HIS106 2.0 24.4 1.0 NE2 A:HIS394 2.0 22.3 1.0 CE1 A:HIS106 2.9 21.2 1.0 CD2 A:HIS394 3.0 18.4 1.0 O A:HOH844 3.0 30.6 1.0 CE1 A:HIS394 3.1 20.2 1.0 CD2 A:HIS106 3.1 22.7 1.0 O1 A:C2O601 3.3 19.2 1.0 NE2 A:HIS396 3.3 20.9 1.0 CD2 A:HIS396 3.4 20.6 1.0 ND1 A:HIS108 3.4 21.5 1.0 CU3 A:C2O601 3.6 26.8 1.0 CE1 A:HIS396 3.7 19.2 1.0 CG A:HIS108 3.8 20.8 1.0 CU2 A:C2O601 3.8 24.6 1.0 CG A:HIS396 3.8 19.0 1.0 CA A:HIS108 3.9 21.5 1.0 CE1 A:HIS108 3.9 20.0 1.0 ND1 A:HIS396 4.0 16.7 1.0 ND1 A:HIS106 4.0 21.3 1.0 CB A:HIS108 4.1 21.1 1.0 CG A:HIS394 4.1 19.1 1.0 CG A:HIS106 4.1 21.8 1.0 ND1 A:HIS394 4.1 20.2 1.0 CD2 A:HIS108 4.4 20.4 1.0 NE2 A:HIS108 4.5 19.3 1.0 CA A:HIS396 4.5 20.6 1.0 N A:GLY109 4.5 22.4 1.0 CB A:HIS396 4.7 20.7 1.0 C A:HIS108 4.7 21.7 1.0 N A:HIS396 4.8 19.6 1.0 N A:HIS108 4.9 21.0 1.0 NE2 A:HIS444 5.0 21.2 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Pentosaceus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:23.0 occ:1.00 ND1 A:HIS391 2.0 24.2 1.0 ND1 A:HIS450 2.1 20.0 1.0 SG A:CYS445 2.2 22.4 1.0 CE1 A:HIS391 2.9 25.1 1.0 CE1 A:HIS450 3.0 19.8 1.0 SD A:MET455 3.0 25.0 1.0 CG A:HIS391 3.1 23.0 1.0 CB A:CYS445 3.1 20.1 1.0 CG A:HIS450 3.2 17.8 1.0 CB A:HIS450 3.5 18.5 1.0 CB A:HIS391 3.6 21.8 1.0 CE A:MET455 4.0 24.3 1.0 NE2 A:HIS391 4.1 27.3 1.0 NE2 A:HIS450 4.1 18.8 1.0 CD1 A:ILE447 4.1 20.8 1.0 CD2 A:HIS391 4.2 25.1 1.0 CA A:HIS391 4.2 19.5 1.0 CD2 A:HIS450 4.2 18.0 1.0 CB A:ILE447 4.2 22.0 1.0 CG1 A:ILE447 4.4 21.3 1.0 CA A:CYS445 4.5 20.3 1.0 CG A:MET455 4.7 23.0 1.0 CD A:PRO392 5.0 18.0 1.0 CG2 A:ILE447 5.0 21.1 1.0

I.Olmeda, P.Casino, R.E.Collins, R.Sendra, S.Callejon, J.Huesa, A.S.Soares, S.Ferrer, I.Pardo. Structural Analysis and Biochemical Properties of Laccase Enzymes From Two Pediococcus Species. Microb Biotechnol 2021.
ISSN: ISSN 1751-7915
PubMed: 33635570
DOI: 10.1111/1751-7915.13751