Copper in PDB 6z0k: Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5)

The structure of Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5), PDB code: 6z0k was solved by P.Casino, J.Huesa, I.Pardo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.56 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.07, 78.188, 162.493, 90, 90, 90
R / Rfree (%)	19.7 / 21.9

The binding sites of Copper atom in the Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5) (pdb code 6z0k). 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 Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5), PDB code: 6z0k:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5)


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 Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:40.8 occ:1.00 ND1 A:HIS389 2.0 32.2 1.0 SG A:CYS443 2.1 31.1 1.0 ND1 A:HIS448 2.2 29.1 1.0 CE1 A:HIS389 2.8 31.8 1.0 CB A:CYS443 3.1 27.4 1.0 CE1 A:HIS448 3.2 29.1 1.0 CG A:HIS448 3.2 28.4 1.0 CG A:HIS389 3.2 30.6 1.0 SD A:MET453 3.2 32.6 1.0 CB A:HIS448 3.5 28.1 1.0 CB A:HIS389 3.7 29.6 1.0 CD1 A:ILE445 3.9 26.5 1.0 NE2 A:HIS389 4.0 31.9 1.0 CB A:ILE445 4.2 25.6 1.0 CD2 A:HIS389 4.2 32.0 1.0 CA A:HIS389 4.3 28.2 1.0 CE A:MET344 4.3 35.3 1.0 CE A:MET453 4.3 32.3 1.0 NE2 A:HIS448 4.3 29.0 1.0 CD2 A:HIS448 4.3 28.8 1.0 CG1 A:ILE445 4.4 26.1 1.0 CA A:CYS443 4.5 26.6 1.0 CG A:MET453 4.8 30.2 1.0 CD A:PRO390 4.9 25.7 1.0 N A:ILE445 4.9 24.6 1.0 CG1 A:VAL351 4.9 29.8 1.0 CG2 A:ILE445 5.0 25.4 1.0 CA A:HIS448 5.0 27.7 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5)


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 Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:35.6 occ:1.00 ND1 A:HIS106 2.1 25.9 1.0 NE2 A:HIS145 2.2 27.4 1.0 NE2 A:HIS444 2.2 25.0 1.0 O A:HOH858 2.4 12.7 1.0 CG A:HIS106 3.0 26.2 1.0 CE1 A:HIS106 3.1 26.3 1.0 CE1 A:HIS145 3.1 27.4 1.0 CD2 A:HIS444 3.2 24.8 1.0 CE1 A:HIS444 3.2 24.9 1.0 CD2 A:HIS145 3.3 26.8 1.0 CB A:HIS106 3.3 26.0 1.0 CU A:CU504 3.8 47.5 1.0 CZ2 A:TRP143 3.9 24.3 1.0 CD2 A:HIS104 4.1 27.1 1.0 NE2 A:HIS106 4.1 26.8 1.0 CD2 A:HIS106 4.2 26.9 1.0 CE2 A:TRP143 4.3 24.0 1.0 ND1 A:HIS145 4.3 27.6 1.0 ND1 A:HIS444 4.3 24.7 1.0 CG A:HIS444 4.3 24.5 1.0 CG A:HIS145 4.4 26.6 1.0 NE1 A:TRP143 4.4 24.3 1.0 NE2 A:HIS392 4.5 27.2 1.0 CD2 A:HIS392 4.5 26.4 1.0 NE2 A:HIS104 4.6 28.2 1.0 CH2 A:TRP143 4.6 24.1 1.0 CA A:HIS106 4.6 25.5 1.0 CB A:ALA279 4.7 22.4 1.0 CU A:CU503 4.8 46.3 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5)


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 Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:46.3 occ:1.00 NE2 A:HIS394 1.9 31.4 1.0 NE2 A:HIS147 2.0 30.9 1.0 NE2 A:HIS442 2.1 28.7 1.0 O A:HOH858 2.3 12.7 1.0 CE1 A:HIS394 2.8 31.0 1.0 CD2 A:HIS147 2.9 29.7 1.0 CE1 A:HIS442 3.0 28.1 1.0 CD2 A:HIS394 3.0 30.0 1.0 CE1 A:HIS147 3.1 30.1 1.0 CD2 A:HIS442 3.1 28.0 1.0 CU A:CU504 3.8 47.5 1.0 CD2 A:HIS392 3.9 26.4 1.0 ND1 A:HIS394 4.0 31.0 1.0 ND1 A:HIS442 4.0 28.2 1.0 CG A:HIS147 4.1 29.3 1.0 CG A:HIS394 4.1 30.3 1.0 ND1 A:HIS147 4.1 29.6 1.0 CG A:HIS442 4.1 27.7 1.0 NE2 A:HIS104 4.3 28.2 1.0 NE2 A:HIS392 4.4 27.2 1.0 CD2 A:HIS104 4.4 27.1 1.0 CB A:MET440 4.5 34.3 1.0 CU A:CU502 4.8 35.6 1.0 OE2 A:GLU449 4.8 37.8 1.0 CG A:MET440 4.8 36.5 1.0 OE1 A:GLU449 4.9 38.0 1.0 CD A:GLU449 4.9 35.6 1.0 CE1 A:HIS104 4.9 26.9 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5)


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 Laccase From Pediococcus Acidilactici PP5930 (Hepes pH 7.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu504 b:47.5 occ:1.00 NE2 A:HIS392 2.0 27.2 1.0 NE2 A:HIS104 2.1 28.2 1.0 O A:HOH858 2.9 12.7 1.0 CD2 A:HIS392 2.9 26.4 1.0 CD2 A:HIS104 2.9 27.1 1.0 CE1 A:HIS392 3.0 26.5 1.0 CD2 A:HIS394 3.0 30.0 1.0 O A:HOH779 3.0 21.4 1.0 NE2 A:HIS394 3.1 31.4 1.0 CE1 A:HIS104 3.1 26.9 1.0 ND1 A:HIS106 3.3 25.9 1.0 CG A:HIS106 3.6 26.2 1.0 CG A:HIS394 3.7 30.3 1.0 CU A:CU503 3.8 46.3 1.0 CA A:HIS106 3.8 25.5 1.0 CE1 A:HIS394 3.8 31.0 1.0 CU A:CU502 3.8 35.6 1.0 CB A:HIS106 3.8 26.0 1.0 CE1 A:HIS106 3.9 26.3 1.0 CG A:HIS392 4.1 26.0 1.0 ND1 A:HIS392 4.1 27.0 1.0 CG A:HIS104 4.1 26.8 1.0 ND1 A:HIS394 4.1 31.0 1.0 ND1 A:HIS104 4.2 27.3 1.0 CD2 A:HIS106 4.4 26.9 1.0 CA A:HIS394 4.5 28.8 1.0 NE2 A:HIS106 4.6 26.8 1.0 N A:GLY107 4.6 25.9 1.0 CB A:HIS394 4.7 29.5 1.0 C A:HIS106 4.7 25.8 1.0 N A:HIS106 4.7 24.8 1.0 NE2 A:HIS442 4.9 28.7 1.0 N A:HIS394 5.0 27.5 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 J Microbiol Biotechnol. 2021.
ISSN: ESSN 1738-8872
DOI: 10.1111/1751-7915.13751