Copper in PDB 6z0j: Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5)

The structure of Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5), PDB code: 6z0j 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)	67.80 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.797, 94.294, 97.564, 90, 90, 90
R / Rfree (%)	22 / 26.8

The binding sites of Copper atom in the Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5) (pdb code 6z0j). 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 PA5930 (Tris-Hcl pH 8.5), PDB code: 6z0j:
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 PA5930 (Tris-Hcl pH 8.5)


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 PA5930 (Tris-Hcl pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:64.2 occ:1.00 ND1 A:HIS448 2.2 49.3 1.0 SG A:CYS443 2.3 57.4 1.0 ND1 A:HIS389 2.6 55.8 1.0 CE1 A:HIS448 3.1 48.0 1.0 SD A:MET453 3.1 53.1 1.0 CB A:CYS443 3.2 51.4 1.0 CG A:HIS389 3.2 52.1 1.0 CE1 A:HIS389 3.2 55.5 1.0 CG A:HIS448 3.3 48.0 1.0 CB A:HIS389 3.6 49.7 1.0 CB A:HIS448 3.6 46.7 1.0 CE A:MET453 3.9 53.2 1.0 CD1 A:ILE445 4.0 45.8 1.0 CD2 A:HIS389 4.0 54.2 1.0 NE2 A:HIS389 4.0 55.4 1.0 CA A:HIS389 4.2 48.7 1.0 NE2 A:HIS448 4.2 47.6 1.0 CD2 A:HIS448 4.4 47.7 1.0 CE A:MET344 4.4 54.0 1.0 CB A:ILE445 4.5 44.5 1.0 CG1 A:VAL351 4.5 69.4 1.0 CA A:CYS443 4.6 49.6 1.0 CG1 A:ILE445 4.6 45.1 1.0 CG A:MET453 4.9 50.6 1.0 CD A:PRO390 5.0 46.7 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5)


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 PA5930 (Tris-Hcl pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:41.6 occ:1.00 ND1 A:HIS106 2.1 37.5 1.0 NE2 A:HIS145 2.1 40.2 1.0 NE2 A:HIS444 2.2 43.2 1.0 O A:HOH639 2.3 55.6 1.0 CE1 A:HIS444 3.0 44.7 1.0 CD2 A:HIS145 3.0 40.5 1.0 CE1 A:HIS106 3.1 37.3 1.0 CG A:HIS106 3.1 37.8 1.0 CE1 A:HIS145 3.1 39.9 1.0 CD2 A:HIS444 3.2 43.5 1.0 CB A:HIS106 3.4 38.3 1.0 CU A:CU504 3.7 70.3 1.0 CZ2 A:TRP143 3.8 43.4 1.0 ND1 A:HIS145 4.1 40.5 1.0 ND1 A:HIS444 4.1 45.4 1.0 CG A:HIS145 4.1 40.2 1.0 NE2 A:HIS106 4.2 36.6 1.0 CD2 A:HIS106 4.2 37.5 1.0 CE2 A:TRP143 4.2 42.9 1.0 CD2 A:HIS104 4.2 38.3 1.0 CG A:HIS444 4.3 44.4 1.0 NE2 A:HIS392 4.3 41.1 1.0 CH2 A:TRP143 4.4 43.1 1.0 CD2 A:HIS392 4.4 40.9 1.0 NE1 A:TRP143 4.4 42.8 1.0 CA A:HIS106 4.6 38.8 1.0 CU A:CU503 4.6 62.1 1.0 NE2 A:HIS104 4.7 38.0 1.0 CB A:ALA279 4.8 38.5 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5)


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 PA5930 (Tris-Hcl pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:62.1 occ:1.00 NE2 A:HIS394 2.1 38.3 1.0 NE2 A:HIS147 2.1 43.2 1.0 NE2 A:HIS442 2.3 49.3 1.0 O A:HOH639 2.3 55.6 1.0 CD2 A:HIS147 2.6 42.2 1.0 CE1 A:HIS394 2.9 37.5 1.0 CE1 A:HIS442 3.0 49.4 1.0 CD2 A:HIS394 3.2 38.7 1.0 CD2 A:HIS442 3.3 48.6 1.0 CE1 A:HIS147 3.4 43.6 1.0 CU A:CU504 3.6 70.3 1.0 CG A:HIS147 3.9 42.4 1.0 CD2 A:HIS392 3.9 40.9 1.0 ND1 A:HIS394 4.1 37.4 1.0 ND1 A:HIS442 4.2 50.2 1.0 NE2 A:HIS392 4.2 41.1 1.0 ND1 A:HIS147 4.2 43.5 1.0 NE2 A:HIS104 4.2 38.0 1.0 CG A:HIS394 4.3 38.7 1.0 CD2 A:HIS104 4.3 38.3 1.0 CG A:HIS442 4.4 48.9 1.0 CE A:MET454 4.4 50.9 1.0 CU A:CU502 4.6 41.6 1.0 NE2 A:HIS444 4.8 43.2 1.0 CE1 A:HIS104 4.8 38.5 1.0 OE2 A:GLU449 4.8 62.6 1.0 CD2 A:HIS444 4.9 43.5 1.0 CE1 A:HIS145 4.9 39.9 1.0 CG A:HIS104 4.9 38.5 1.0 NE2 A:HIS145 5.0 40.2 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Laccase From Pediococcus Acidilactici PA5930 (Tris-Hcl pH 8.5)


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 PA5930 (Tris-Hcl pH 8.5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu504 b:70.3 occ:1.00 NE2 A:HIS392 2.0 41.1 1.0 NE2 A:HIS104 2.2 38.0 1.0 O A:HOH639 2.9 55.6 1.0 CD2 A:HIS104 2.9 38.3 1.0 CD2 A:HIS392 3.0 40.9 1.0 CE1 A:HIS392 3.0 40.2 1.0 O A:HOH640 3.0 40.6 1.0 ND1 A:HIS106 3.3 37.5 1.0 CE1 A:HIS104 3.3 38.5 1.0 CD2 A:HIS394 3.4 38.7 1.0 NE2 A:HIS394 3.4 38.3 1.0 CG A:HIS106 3.6 37.8 1.0 CU A:CU503 3.6 62.1 1.0 CU A:CU502 3.7 41.6 1.0 CA A:HIS106 3.7 38.8 1.0 CB A:HIS106 3.8 38.3 1.0 CE1 A:HIS106 3.9 37.3 1.0 CG A:HIS394 4.0 38.7 1.0 CE1 A:HIS394 4.0 37.5 1.0 ND1 A:HIS392 4.0 40.0 1.0 CG A:HIS392 4.1 40.6 1.0 CG A:HIS104 4.1 38.5 1.0 ND1 A:HIS394 4.3 37.4 1.0 ND1 A:HIS104 4.3 38.9 1.0 CD2 A:HIS106 4.4 37.5 1.0 NE2 A:HIS106 4.6 36.6 1.0 N A:HIS106 4.6 39.8 1.0 N A:GLY107 4.6 39.3 1.0 CA A:HIS394 4.6 41.1 1.0 C A:HIS106 4.6 39.6 1.0 NE2 A:HIS145 4.7 40.2 1.0 CB A:HIS394 4.8 40.2 1.0 NE2 A:HIS442 4.9 49.3 1.0 NE2 A:HIS444 5.0 43.2 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