Copper in PDB 5nq8: Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II

The structure of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II, PDB code: 5nq8 was solved by M.Orlikowska, M.De J.Rostro-Alanis, A.Bujacz, C.Hernandez-Luna, R.Rubio, R.Parra, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 2.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	184.410, 184.410, 184.410, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 17.3

The structure of Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Copper atom in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II (pdb code 5nq8). 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 Laccases From Pycnoporus Sanguineus, Izoform II, PDB code: 5nq8:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II


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 Laccases From Pycnoporus Sanguineus, Izoform II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:28.9 occ:1.00 ND1 A:HIS477 2.0 30.2 1.0 ND1 A:HIS416 2.0 31.1 1.0 SG A:CYS472 2.3 29.1 1.0 CE1 A:HIS416 2.9 30.7 1.0 CE1 A:HIS477 2.9 31.7 1.0 CG A:HIS477 3.1 30.8 1.0 CG A:HIS416 3.1 30.7 1.0 CB A:CYS472 3.3 28.4 1.0 CB A:HIS477 3.4 30.5 1.0 CB A:HIS416 3.5 30.0 1.0 CD1 A:ILE474 3.5 28.3 1.0 CD2 A:PHE482 3.7 32.0 1.0 CE2 A:PHE482 3.8 33.1 1.0 CB A:ILE474 3.9 26.9 1.0 CA A:HIS416 4.0 28.6 1.0 NE2 A:HIS416 4.1 32.2 1.0 NE2 A:HIS477 4.1 31.4 1.0 CG1 A:ILE474 4.1 27.2 1.0 CD2 A:HIS477 4.2 31.1 1.0 CD2 A:HIS416 4.2 32.5 1.0 CG2 A:ILE474 4.6 26.8 1.0 CA A:CYS472 4.7 27.6 1.0 CD A:PRO417 4.7 26.6 1.0 O A:GLY413 4.7 35.7 1.0 N A:ILE474 4.8 26.9 1.0 CA A:ILE474 4.9 27.1 1.0 CA A:HIS477 5.0 30.5 1.0 C A:HIS416 5.0 27.8 1.0 CG A:PHE482 5.0 31.3 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II


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 Laccases From Pycnoporus Sanguineus, Izoform II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:30.5 occ:1.00 NE2 A:HIS419 2.0 26.9 1.0 NE2 A:HIS85 2.0 27.4 1.0 O A:HOH1044 2.5 29.1 1.0 CE1 A:HIS85 2.9 24.7 1.0 CD2 A:HIS419 2.9 25.7 1.0 CD2 A:HIS85 3.0 25.2 1.0 CE1 A:HIS419 3.0 26.5 1.0 O1 A:PER605 3.3 34.2 0.5 NE2 A:HIS421 3.4 27.5 1.0 ND1 A:HIS87 3.4 26.0 1.0 CE1 A:HIS421 3.5 26.5 1.0 CD2 A:HIS421 3.5 26.3 1.0 ND1 A:HIS421 3.7 26.4 1.0 CG A:HIS87 3.7 24.6 1.0 CG A:HIS421 3.7 26.3 1.0 CE1 A:HIS87 3.8 25.7 1.0 CA A:HIS87 3.9 25.4 1.0 ND1 A:HIS85 4.0 24.6 1.0 O2 A:PER605 4.0 29.4 0.5 CG A:HIS419 4.1 26.2 1.0 CU A:CU603 4.1 27.5 1.0 N A:GLY88 4.1 24.6 1.0 CG A:HIS85 4.1 24.7 1.0 ND1 A:HIS419 4.1 26.2 1.0 CB A:HIS87 4.2 25.8 1.0 CD2 A:HIS87 4.3 25.7 1.0 NE2 A:HIS87 4.3 25.8 1.0 CU A:CU604 4.4 29.6 1.0 C A:HIS87 4.5 25.8 1.0 O A:HOH956 4.5 25.6 1.0 CA A:HIS421 4.5 26.6 1.0 O A:HOH771 4.6 25.4 1.0 CB A:HIS421 4.6 26.5 1.0 N A:HIS87 4.9 24.5 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II


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 Laccases From Pycnoporus Sanguineus, Izoform II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:27.5 occ:1.00 O1 A:PER605 1.9 34.2 0.5 ND1 A:HIS87 2.0 26.0 1.0 NE2 A:HIS130 2.0 24.9 1.0 NE2 A:HIS473 2.1 27.2 1.0 CE1 A:HIS87 2.9 25.7 1.0 CE1 A:HIS130 3.0 24.9 1.0 CD2 A:HIS130 3.0 23.9 1.0 CE1 A:HIS473 3.0 26.5 1.0 CG A:HIS87 3.0 24.6 1.0 CD2 A:HIS473 3.1 26.3 1.0 O2 A:PER605 3.3 29.4 0.5 CB A:HIS87 3.5 25.8 1.0 CZ2 A:TRP128 3.6 24.4 1.0 CD2 A:HIS85 3.8 25.2 1.0 CE2 A:TRP128 3.9 23.2 1.0 NE1 A:TRP128 4.0 23.6 1.0 NE2 A:HIS87 4.0 25.8 1.0 CU A:CU602 4.1 30.5 1.0 ND1 A:HIS130 4.1 24.1 1.0 CG A:HIS130 4.1 23.8 1.0 CD2 A:HIS87 4.1 25.7 1.0 ND1 A:HIS473 4.2 25.1 1.0 CG A:HIS473 4.3 26.4 1.0 NE2 A:HIS85 4.3 27.4 1.0 CH2 A:TRP128 4.3 24.4 1.0 CD2 A:HIS419 4.4 25.7 1.0 CB A:ALA262 4.4 25.0 1.0 NE2 A:HIS419 4.5 26.9 1.0 O A:HOH932 4.5 35.5 1.0 CA A:HIS87 4.6 25.4 1.0 CD2 A:TRP128 4.8 23.4 1.0 CD1 A:TRP128 4.9 24.1 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Laccases From Pycnoporus Sanguineus, Izoform II


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 Laccases From Pycnoporus Sanguineus, Izoform II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:29.6 occ:1.00 O2 A:PER605 1.9 29.4 0.5 NE2 A:HIS421 2.0 27.5 1.0 NE2 A:HIS132 2.0 28.1 1.0 NE2 A:HIS471 2.1 30.1 1.0 CE1 A:HIS421 2.9 26.5 1.0 CD2 A:HIS471 3.0 28.2 1.0 CD2 A:HIS132 3.0 25.8 1.0 CE1 A:HIS132 3.0 29.6 1.0 CE1 A:HIS471 3.1 28.9 1.0 CD2 A:HIS421 3.1 26.3 1.0 O1 A:PER605 3.1 34.2 0.5 O A:HOH932 3.9 35.5 1.0 CD2 A:HIS419 4.0 25.7 1.0 ND1 A:HIS421 4.1 26.4 1.0 CG A:HIS471 4.1 28.8 1.0 ND1 A:HIS132 4.1 27.6 1.0 ND1 A:HIS471 4.2 28.7 1.0 CG A:HIS132 4.2 26.5 1.0 CD2 A:PHE469 4.2 26.9 1.0 CG A:HIS421 4.2 26.3 1.0 CU A:CU602 4.4 30.5 1.0 CB A:PHE469 4.4 27.3 1.0 CD2 A:HIS85 4.6 25.2 1.0 CG A:PRO100 4.6 27.0 1.0 NE2 A:HIS419 4.7 26.9 1.0 NE2 A:HIS85 4.7 27.4 1.0 CG A:PHE469 4.8 27.3 1.0 NE2 A:HIS473 5.0 27.2 1.0 CD2 A:HIS473 5.0 26.3 1.0

M.Orlikowska, M.De J Rostro-Alanis, A.Bujacz, C.Hernandez-Luna, R.Rubio, R.Parra, G.Bujacz. Structural Studies of Two Thermostable Laccases From the White-Rot Fungus Pycnoporus Sanguineus. Int. J. Biol. Macromol. V. 107 1629 2018.
ISSN: ISSN 1879-0003
PubMed: 29055703
DOI: 10.1016/J.IJBIOMAC.2017.10.024