Copper in PDB 6xiz: Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici

The structure of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici, PDB code: 6xiz 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)	73.65 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.06, 147.3, 65.46, 90, 98.55, 90
R / Rfree (%)	11.4 / 16.1

The structure of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici 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 Acidilactici (pdb code 6xiz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici, PDB code: 6xiz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


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 Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:37.7 occ:1.00 ND1 A:HIS448 2.0 32.4 1.0 ND1 A:HIS389 2.1 36.4 1.0 SG A:CYS443 2.2 35.2 1.0 CE1 A:HIS389 2.9 33.0 1.0 CE1 A:HIS448 2.9 33.0 1.0 CG A:HIS448 3.1 31.9 1.0 SD A:MET453 3.2 40.0 1.0 CG A:HIS389 3.2 30.2 1.0 CB A:CYS443 3.2 35.1 1.0 CB A:HIS448 3.6 33.9 1.0 CB A:HIS389 3.6 29.5 1.0 CD1 A:ILE445 3.9 34.9 1.0 NE2 A:HIS389 4.0 32.2 1.0 CE A:MET453 4.0 42.8 1.0 NE2 A:HIS448 4.1 33.1 1.0 CD2 A:HIS448 4.2 32.2 1.0 CD2 A:HIS389 4.2 34.7 1.0 CA A:HIS389 4.2 28.2 1.0 CB A:ILE445 4.2 29.1 1.0 CE A:MET344 4.4 51.2 1.0 CG1 A:ILE445 4.5 31.5 1.0 CA A:CYS443 4.6 36.0 1.0 CG1 A:VAL351 4.7 46.8 1.0 CD A:PRO390 4.8 35.8 1.0 CG A:MET453 4.8 41.8 1.0 N A:ILE445 5.0 34.2 1.0

Copper binding site 2 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


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 Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:42.1 occ:1.00 CU2 A:C2O502 0.0 42.1 1.0 ND1 A:HIS106 2.0 28.3 1.0 NE2 A:HIS145 2.1 33.6 1.0 NE2 A:HIS444 2.3 39.0 1.0 O1 A:C2O502 2.4 26.8 1.0 CE1 A:HIS106 2.9 33.3 1.0 CG A:HIS106 3.0 31.8 1.0 CE1 A:HIS145 3.0 37.6 1.0 CD2 A:HIS145 3.1 35.7 1.0 CD2 A:HIS444 3.2 39.4 1.0 CE1 A:HIS444 3.3 37.5 1.0 CB A:HIS106 3.4 36.3 1.0 O A:HOH610 3.6 49.5 0.5 CU A:CU503 3.8 60.6 1.0 NE2 A:HIS106 4.0 34.6 1.0 CZ2 A:TRP143 4.0 38.8 1.0 CD2 A:HIS106 4.1 34.1 1.0 ND1 A:HIS145 4.2 37.7 1.0 CD2 A:HIS104 4.2 44.1 1.0 CG A:HIS145 4.3 35.4 1.0 CG A:HIS444 4.3 40.7 1.0 CE2 A:TRP143 4.3 31.5 1.0 ND1 A:HIS444 4.4 36.4 1.0 CD2 A:HIS392 4.4 33.9 1.0 NE1 A:TRP143 4.4 34.6 1.0 NE2 A:HIS392 4.5 31.4 1.0 CA A:HIS106 4.6 34.0 1.0 NE2 A:HIS104 4.6 47.0 1.0 CU3 A:C2O502 4.7 58.6 1.0 CB A:ALA279 4.7 34.6 1.0 CH2 A:TRP143 4.7 33.0 1.0

Copper binding site 3 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


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 Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:58.6 occ:1.00 CU3 A:C2O502 0.0 58.6 1.0 NE2 A:HIS394 2.1 41.3 1.0 NE2 A:HIS442 2.2 41.2 1.0 O1 A:C2O502 2.3 26.8 1.0 NE2 A:HIS147 2.4 45.7 1.0 CD2 A:HIS147 2.9 43.0 1.0 CE1 A:HIS442 3.0 42.4 1.0 CE1 A:HIS394 3.0 47.8 1.0 O A:HOH610 3.1 49.5 0.5 CD2 A:HIS394 3.2 47.1 1.0 CD2 A:HIS442 3.3 41.1 1.0 CU A:CU503 3.6 60.6 1.0 CE1 A:HIS147 3.6 53.3 1.0 CD2 A:HIS392 4.0 33.9 1.0 ND1 A:HIS442 4.1 46.5 1.0 ND1 A:HIS394 4.1 43.1 1.0 CG A:HIS147 4.2 47.4 1.0 NE2 A:HIS104 4.3 47.0 1.0 CG A:HIS442 4.3 41.7 1.0 CG A:HIS394 4.3 44.4 1.0 CD2 A:HIS104 4.4 44.1 1.0 ND1 A:HIS147 4.5 58.8 1.0 OE2 A:GLU449 4.6 65.1 1.0 NE2 A:HIS392 4.7 31.4 1.0 CU2 A:C2O502 4.7 42.1 1.0 CD A:GLU449 4.8 66.6 1.0 CB A:MET440 4.8 45.3 1.0 CE1 A:HIS104 4.8 40.0 1.0 OE1 A:GLU449 4.9 113.4 1.0

Copper binding site 4 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


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 Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:60.6 occ:1.00 NE2 A:HIS104 2.2 47.0 1.0 NE2 A:HIS392 2.3 31.4 1.0 O1 A:C2O502 2.8 26.8 1.0 CD2 A:HIS392 2.9 33.9 1.0 CD2 A:HIS104 3.1 44.1 1.0 O A:HOH788 3.1 43.5 1.0 CD2 A:HIS394 3.1 47.1 1.0 CE1 A:HIS104 3.2 40.0 1.0 NE2 A:HIS394 3.2 41.3 1.0 CE1 A:HIS392 3.4 32.3 1.0 ND1 A:HIS106 3.5 28.3 1.0 CU3 A:C2O502 3.6 58.6 1.0 CG A:HIS106 3.7 31.8 1.0 CU2 A:C2O502 3.8 42.1 1.0 CG A:HIS394 3.8 44.4 1.0 CA A:HIS106 3.8 34.0 1.0 CB A:HIS106 3.9 36.3 1.0 CE1 A:HIS394 3.9 47.8 1.0 CE1 A:HIS106 4.1 33.3 1.0 CG A:HIS392 4.1 29.5 1.0 ND1 A:HIS394 4.2 43.1 1.0 CG A:HIS104 4.2 42.0 1.0 ND1 A:HIS104 4.2 51.6 1.0 ND1 A:HIS392 4.3 34.3 1.0 CD2 A:HIS106 4.4 34.1 1.0 NE2 A:HIS106 4.6 34.6 1.0 CA A:HIS394 4.6 39.9 1.0 N A:GLY107 4.6 30.4 1.0 CB A:HIS394 4.7 41.9 1.0 C A:HIS106 4.7 33.3 1.0 N A:HIS106 4.8 35.4 1.0 O A:HOH744 4.8 48.2 1.0 N A:HIS394 4.8 35.1 1.0 NE2 A:HIS442 4.9 41.2 1.0

Copper binding site 5 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:38.6 occ:1.00 ND1 B:HIS448 2.1 38.6 1.0 ND1 B:HIS389 2.1 40.0 1.0 SG B:CYS443 2.2 36.4 1.0 CE1 B:HIS389 3.0 40.7 1.0 CE1 B:HIS448 3.0 41.5 1.0 CG B:HIS448 3.1 36.6 1.0 SD B:MET453 3.2 43.6 1.0 CB B:CYS443 3.2 39.5 1.0 CG B:HIS389 3.2 40.3 1.0 CB B:HIS448 3.5 40.3 1.0 CB B:HIS389 3.6 36.8 1.0 CD1 B:ILE445 3.8 38.4 1.0 CE B:MET453 4.0 49.8 1.0 CB B:ILE445 4.2 34.3 1.0 NE2 B:HIS389 4.2 38.5 1.0 CA B:HIS389 4.2 30.6 1.0 NE2 B:HIS448 4.2 38.1 1.0 CD2 B:HIS448 4.2 38.6 1.0 CD2 B:HIS389 4.3 42.8 1.0 CG1 B:ILE445 4.4 33.8 1.0 CA B:CYS443 4.6 34.5 1.0 CD B:PRO390 4.8 34.5 1.0 CG1 B:VAL351 4.8 41.6 1.0 CG B:MET453 4.8 44.3 1.0 CE B:MET344 4.9 35.3 1.0 N B:ILE445 4.9 28.8 1.0 CG2 B:ILE445 5.0 32.8 1.0

Copper binding site 6 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:42.9 occ:1.00 CU2 B:C2O502 0.0 42.9 1.0 ND1 B:HIS106 2.0 38.0 1.0 NE2 B:HIS145 2.2 37.2 1.0 O1 B:C2O502 2.3 28.8 1.0 NE2 B:HIS444 2.3 34.9 1.0 CE1 B:HIS106 2.9 36.1 1.0 CG B:HIS106 3.0 35.1 1.0 CD2 B:HIS145 3.1 33.4 1.0 CD2 B:HIS444 3.2 40.9 1.0 CE1 B:HIS145 3.2 37.9 1.0 CE1 B:HIS444 3.2 41.4 1.0 CB B:HIS106 3.4 37.1 1.0 O B:HOH609 3.4 60.1 0.5 CU B:CU503 3.7 64.2 1.0 CZ2 B:TRP143 4.0 33.1 1.0 NE2 B:HIS106 4.0 33.0 1.0 CD2 B:HIS106 4.1 34.4 1.0 CD2 B:HIS104 4.2 48.2 1.0 CG B:HIS145 4.3 32.9 1.0 ND1 B:HIS145 4.3 36.0 1.0 CE2 B:TRP143 4.3 33.8 1.0 ND1 B:HIS444 4.4 40.6 1.0 CG B:HIS444 4.4 38.2 1.0 NE1 B:TRP143 4.4 36.4 1.0 NE2 B:HIS392 4.4 34.4 1.0 CD2 B:HIS392 4.5 33.8 1.0 CU3 B:C2O502 4.5 60.3 1.0 NE2 B:HIS104 4.6 54.5 1.0 CA B:HIS106 4.6 35.4 1.0 CH2 B:TRP143 4.7 37.5 1.0 CB B:ALA279 4.8 34.3 1.0

Copper binding site 7 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:60.3 occ:1.00 CU3 B:C2O502 0.0 60.3 1.0 NE2 B:HIS394 2.1 49.3 1.0 NE2 B:HIS442 2.1 39.4 1.0 O1 B:C2O502 2.3 28.8 1.0 NE2 B:HIS147 2.4 50.7 1.0 CE1 B:HIS442 2.8 33.4 1.0 CD2 B:HIS147 3.0 45.8 1.0 CE1 B:HIS394 3.1 46.2 1.0 CD2 B:HIS394 3.1 42.4 1.0 O B:HOH609 3.2 60.1 0.5 CD2 B:HIS442 3.3 36.3 1.0 CU B:CU503 3.5 64.2 1.0 CE1 B:HIS147 3.6 45.9 1.0 CD2 B:HIS392 4.0 33.8 1.0 ND1 B:HIS442 4.0 38.2 1.0 ND1 B:HIS394 4.2 54.8 1.0 CG B:HIS442 4.2 32.8 1.0 CG B:HIS394 4.2 45.3 1.0 NE2 B:HIS104 4.3 54.5 1.0 CG B:HIS147 4.3 40.5 1.0 CD2 B:HIS104 4.4 48.2 1.0 NE2 B:HIS392 4.5 34.4 1.0 ND1 B:HIS147 4.5 54.2 1.0 CU2 B:C2O502 4.5 42.9 1.0 OE2 B:GLU449 4.6 56.2 1.0 OE1 B:GLU449 4.8 104.6 1.0 CB B:MET440 4.8 43.1 1.0 CD B:GLU449 4.8 72.2 1.0 CE1 B:HIS104 4.9 47.7 1.0 CD2 B:HIS444 4.9 40.9 1.0

Copper binding site 8 out of 8 in the Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Multi-Copper Oxidase From Pediococcus Acidilactici within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu503 b:64.2 occ:1.00 NE2 B:HIS104 2.2 54.5 1.0 NE2 B:HIS392 2.3 34.4 1.0 O1 B:C2O502 2.7 28.8 1.0 CD2 B:HIS392 3.0 33.8 1.0 O B:HOH783 3.1 41.8 1.0 CD2 B:HIS104 3.1 48.2 1.0 NE2 B:HIS394 3.1 49.3 1.0 CD2 B:HIS394 3.1 42.4 1.0 CE1 B:HIS104 3.2 47.7 1.0 CE1 B:HIS392 3.3 30.7 1.0 ND1 B:HIS106 3.4 38.0 1.0 CU3 B:C2O502 3.5 60.3 1.0 CU2 B:C2O502 3.7 42.9 1.0 CG B:HIS106 3.7 35.1 1.0 CA B:HIS106 3.7 35.4 1.0 CG B:HIS394 3.8 45.3 1.0 CE1 B:HIS394 3.8 46.2 1.0 CB B:HIS106 3.8 37.1 1.0 CE1 B:HIS106 4.0 36.1 1.0 ND1 B:HIS394 4.1 54.8 1.0 CG B:HIS392 4.2 28.4 1.0 CG B:HIS104 4.2 49.6 1.0 ND1 B:HIS104 4.3 63.6 1.0 ND1 B:HIS392 4.3 36.0 1.0 CD2 B:HIS106 4.4 34.4 1.0 CA B:HIS394 4.6 38.2 1.0 NE2 B:HIS106 4.6 33.0 1.0 N B:HIS106 4.7 35.5 1.0 CB B:HIS394 4.7 42.2 1.0 N B:GLY107 4.8 36.3 1.0 C B:HIS106 4.8 34.3 1.0 NE2 B:HIS442 4.8 39.4 1.0 O B:HOH664 4.9 51.0 1.0 NE2 B:HIS145 4.9 37.2 1.0 N B:HIS394 5.0 31.5 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