Copper in PDB 6f5k: Crystal Structure of Laccase From Myceliophthora Thermophila

The structure of Crystal Structure of Laccase From Myceliophthora Thermophila, PDB code: 6f5k was solved by H.A.Ernst, L.J.Joergensen, K.Piontek, C.Bukh, L.H.Oestergaard, S.Larsen, M.J.Bjerrum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 1.62
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.449, 128.426, 163.624, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.9

The structure of Crystal Structure of Laccase From Myceliophthora Thermophila also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Copper atom in the Crystal Structure of Laccase From Myceliophthora Thermophila (pdb code 6f5k). 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 Myceliophthora Thermophila, PDB code: 6f5k:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Laccase From Myceliophthora Thermophila


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 Myceliophthora Thermophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:15.5 occ:1.00 ND1 A:HIS431 2.0 12.4 1.0 ND1 A:HIS508 2.0 12.8 1.0 SG A:CYS503 2.2 14.5 1.0 HD12 A:ILE505 2.6 18.1 1.0 HD13 A:LEU513 2.9 17.4 1.0 CE1 A:HIS431 2.9 13.4 1.0 CG A:HIS508 3.0 13.1 1.0 CE1 A:HIS508 3.0 14.7 1.0 HE1 A:HIS431 3.1 16.1 1.0 CG A:HIS431 3.1 12.3 1.0 HB3 A:HIS431 3.1 14.8 1.0 HB2 A:HIS508 3.1 13.6 1.0 HB3 A:HIS508 3.2 13.6 1.0 HB A:ILE505 3.2 16.0 1.0 HB2 A:CYS503 3.2 15.6 1.0 CB A:CYS503 3.2 13.0 1.0 HE1 A:HIS508 3.2 17.7 1.0 CB A:HIS508 3.3 11.3 1.0 HA A:HIS431 3.3 13.4 1.0 HB3 A:CYS503 3.4 15.6 1.0 HD2 A:PRO432 3.5 15.3 1.0 CB A:HIS431 3.5 12.4 1.0 CD1 A:ILE505 3.6 15.1 1.0 CD1 A:LEU513 3.6 14.5 1.0 HD12 A:LEU513 3.7 17.4 1.0 HD11 A:LEU513 3.8 17.4 1.0 CA A:HIS431 3.9 11.1 1.0 CB A:ILE505 4.0 13.3 1.0 HD11 A:ILE505 4.1 18.1 1.0 NE2 A:HIS431 4.1 12.2 1.0 NE2 A:HIS508 4.1 15.8 1.0 CD2 A:HIS508 4.1 14.6 1.0 HD13 A:ILE505 4.1 18.1 1.0 H A:ILE505 4.1 15.9 1.0 HG13 A:ILE505 4.1 18.8 1.0 CD2 A:HIS431 4.2 12.9 1.0 CG1 A:ILE505 4.2 15.6 1.0 O A:PRO430 4.4 14.0 1.0 CD A:PRO432 4.4 12.7 1.0 HB2 A:HIS431 4.4 14.8 1.0 CA A:CYS503 4.6 12.5 1.0 HD3 A:PRO432 4.7 15.3 1.0 HG21 A:ILE505 4.7 17.6 1.0 HA A:CYS503 4.8 15.0 1.0 CA A:HIS508 4.8 13.8 1.0 HE2 A:HIS431 4.8 14.6 1.0 C A:HIS431 4.9 13.3 1.0 HB3 A:LEU513 4.9 16.1 1.0 N A:ILE505 4.9 13.3 1.0 CG2 A:ILE505 4.9 14.7 1.0 HE2 A:HIS508 4.9 19.0 1.0 N A:PRO432 4.9 11.0 1.0 N A:HIS431 4.9 12.7 1.0 CG A:LEU513 4.9 11.3 1.0 HG22 A:ILE505 5.0 17.6 1.0 HD2 A:HIS508 5.0 17.5 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Laccase From Myceliophthora Thermophila


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 Myceliophthora Thermophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:19.3 occ:1.00 NE2 A:HIS434 1.9 13.0 1.0 NE2 A:HIS93 1.9 14.0 1.0 O A:HOH1094 2.6 11.8 1.0 CE1 A:HIS434 2.9 15.2 1.0 CD2 A:HIS93 2.9 14.0 1.0 CD2 A:HIS434 2.9 13.2 1.0 CE1 A:HIS93 2.9 14.3 1.0 HA A:HIS95 3.0 15.8 1.0 HD2 A:HIS93 3.0 16.9 1.0 HE1 A:HIS434 3.1 18.3 1.0 HD2 A:HIS434 3.1 15.8 1.0 HE1 A:HIS93 3.2 17.2 1.0 CD2 A:HIS436 3.3 11.1 1.0 NE2 A:HIS436 3.3 13.2 1.0 HD2 A:HIS436 3.5 13.3 1.0 ND1 A:HIS95 3.6 16.5 1.0 H A:GLY96 3.7 18.1 1.0 CG A:HIS95 3.7 16.7 1.0 O A:OH629 3.7 34.8 1.0 CG A:HIS436 3.7 11.4 1.0 CE1 A:HIS436 3.8 16.0 1.0 HA A:HIS436 3.8 13.9 1.0 HB2 A:HIS95 3.8 16.4 1.0 CA A:HIS95 3.8 13.2 1.0 CU A:CU603 4.0 19.6 1.0 CB A:HIS95 4.0 13.7 1.0 ND1 A:HIS436 4.0 15.0 1.0 ND1 A:HIS434 4.0 14.1 1.0 CU A:CU604 4.0 20.9 1.0 ND1 A:HIS93 4.0 12.7 1.0 CG A:HIS93 4.0 13.7 1.0 CG A:HIS434 4.0 15.0 1.0 CE1 A:HIS95 4.1 14.1 1.0 CD2 A:HIS95 4.2 19.6 1.0 HE1 A:HIS436 4.2 19.2 1.0 N A:GLY96 4.3 15.1 1.0 NE2 A:HIS95 4.4 19.3 1.0 HE1 A:HIS95 4.4 16.9 1.0 CA A:HIS436 4.5 11.6 1.0 HD1 A:HIS436 4.5 18.0 1.0 CB A:HIS436 4.6 11.5 1.0 C A:HIS95 4.6 17.9 1.0 HD2 A:HIS95 4.7 23.5 1.0 HD1 A:HIS434 4.8 16.9 1.0 HB3 A:HIS436 4.8 13.8 1.0 N A:HIS95 4.8 11.5 1.0 HD1 A:HIS93 4.8 15.3 1.0 N A:HIS436 4.8 11.8 1.0 O A:LEU435 4.9 14.6 1.0 HB3 A:HIS95 4.9 16.4 1.0 HE2 A:HIS95 5.0 23.1 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Laccase From Myceliophthora Thermophila


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 Myceliophthora Thermophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:19.6 occ:1.00 NE2 A:HIS436 2.0 13.2 1.0 NE2 A:HIS502 2.1 14.7 1.0 NE2 A:HIS140 2.1 19.5 1.0 O A:OH629 2.1 34.8 1.0 CE1 A:HIS436 2.9 16.0 1.0 HD23 A:LEU500 2.9 19.8 1.0 HD2 A:HIS434 2.9 15.8 1.0 HE1 A:HIS436 3.0 19.2 1.0 CD2 A:HIS502 3.0 13.3 1.0 CE1 A:HIS502 3.0 18.9 1.0 CE1 A:HIS140 3.0 19.1 1.0 CD2 A:HIS140 3.1 13.6 1.0 CD2 A:HIS436 3.1 11.1 1.0 HD2 A:HIS502 3.2 16.0 1.0 HE1 A:HIS140 3.2 22.9 1.0 HE1 A:HIS502 3.3 22.7 1.0 HD2 A:HIS140 3.3 16.3 1.0 HD2 A:HIS436 3.4 13.3 1.0 CD2 A:HIS434 3.8 13.2 1.0 HD2 A:HIS93 3.8 16.9 1.0 CD2 A:LEU500 3.9 16.5 1.0 HE1 A:HIS138 3.9 17.3 1.0 CU A:CU602 4.0 19.3 1.0 ND1 A:HIS436 4.0 15.0 1.0 CD2 A:HIS93 4.0 14.0 1.0 HB3 A:LEU500 4.1 14.5 1.0 O A:HOH1129 4.1 29.9 1.0 ND1 A:HIS502 4.1 13.3 1.0 CG A:HIS502 4.1 16.0 1.0 ND1 A:HIS140 4.2 19.7 1.0 CG A:HIS436 4.2 11.4 1.0 NE2 A:HIS93 4.2 14.0 1.0 CG A:HIS140 4.2 14.2 1.0 HD21 A:LEU500 4.3 19.8 1.0 NE2 A:HIS434 4.3 13.0 1.0 HD22 A:LEU500 4.3 19.8 1.0 HG A:LEU500 4.6 19.1 1.0 CU A:CU604 4.6 20.9 1.0 CG A:LEU500 4.7 15.9 1.0 CE1 A:HIS138 4.7 14.4 1.0 HD1 A:HIS436 4.8 18.0 1.0 CG A:HIS93 4.8 13.7 1.0 CB A:LEU500 4.9 12.1 1.0 HD1 A:HIS502 4.9 15.9 1.0 NE2 A:HIS504 4.9 16.0 1.0 HD2 A:HIS504 4.9 19.5 1.0 HD1 A:HIS140 5.0 23.7 1.0 CG A:HIS434 5.0 15.0 1.0 CE1 A:HIS93 5.0 14.3 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Laccase From Myceliophthora Thermophila


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 Myceliophthora Thermophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:20.9 occ:1.00 ND1 A:HIS95 2.0 16.5 1.0 NE2 A:HIS138 2.0 14.6 1.0 NE2 A:HIS504 2.1 16.0 1.0 O A:OH629 2.6 34.8 1.0 HB2 A:HIS95 2.8 16.4 1.0 CE1 A:HIS95 2.9 14.1 1.0 CD2 A:HIS138 3.0 12.8 1.0 CE1 A:HIS504 3.0 19.1 1.0 CG A:HIS95 3.0 16.7 1.0 CE1 A:HIS138 3.0 14.4 1.0 HE1 A:HIS95 3.1 16.9 1.0 HE1 A:HIS504 3.1 22.9 1.0 HD2 A:HIS138 3.1 15.4 1.0 CD2 A:HIS504 3.2 16.3 1.0 HD2 A:HIS93 3.2 16.9 1.0 HE1 A:HIS138 3.2 17.3 1.0 HZ2 A:TRP136 3.3 16.0 1.0 CB A:HIS95 3.4 13.7 1.0 HD2 A:HIS504 3.4 19.5 1.0 CZ2 A:TRP136 3.6 13.3 1.0 HB3 A:HIS95 3.9 16.4 1.0 CU A:CU602 4.0 19.3 1.0 CE2 A:TRP136 4.0 16.3 1.0 CD2 A:HIS93 4.0 14.0 1.0 HE1 A:TRP136 4.0 22.7 1.0 NE2 A:HIS95 4.0 19.3 1.0 CD2 A:HIS95 4.1 19.6 1.0 ND1 A:HIS138 4.1 15.3 1.0 HD2 A:HIS434 4.1 15.8 1.0 CG A:HIS138 4.1 16.0 1.0 ND1 A:HIS504 4.1 14.1 1.0 NE1 A:TRP136 4.2 18.9 1.0 NE2 A:HIS434 4.2 13.0 1.0 CD2 A:HIS434 4.2 13.2 1.0 CH2 A:TRP136 4.2 15.8 1.0 CG A:HIS504 4.2 13.1 1.0 HH2 A:TRP136 4.4 18.9 1.0 NE2 A:HIS93 4.5 14.0 1.0 HA A:HIS95 4.5 15.8 1.0 CA A:HIS95 4.6 13.2 1.0 O A:HOH1129 4.6 29.9 1.0 CU A:CU603 4.6 19.6 1.0 HE2 A:HIS95 4.8 23.1 1.0 HA3 A:GLY270 4.9 13.4 1.0 HE1 A:HIS502 4.9 22.7 1.0 HD1 A:HIS138 4.9 18.4 1.0 HD1 A:HIS504 4.9 16.9 1.0 CD2 A:TRP136 4.9 14.8 1.0 HD2 A:HIS95 5.0 23.5 1.0

H.A.Ernst, L.J.Jorgensen, C.Bukh, K.Piontek, D.A.Plattner, L.H.Ostergaard, S.Larsen, M.J.Bjerrum. A Comparative Structural Analysis of the Surface Properties of Asco-Laccases. Plos One V. 13 06589 2018.
ISSN: ESSN 1932-6203
PubMed: 30395580
DOI: 10.1371/JOURNAL.PONE.0206589