Copper in PDB 5ehf: Laccase From Antrodiella Faginea

All present enzymatic activity of Laccase From Antrodiella Faginea:
1.10.3.2;

The structure of Laccase From Antrodiella Faginea, PDB code: 5ehf was solved by K.M.Polyakov, O.A.Glazunova, T.V.Fedorova, P.V.Dorovatovskii, O.V.Koroleva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.91 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.150, 81.540, 78.500, 90.00, 104.75, 90.00
R / Rfree (%)	16 / 19.5

The structure of Laccase From Antrodiella Faginea also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Copper atom in the Laccase From Antrodiella Faginea (pdb code 5ehf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Laccase From Antrodiella Faginea, PDB code: 5ehf:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Laccase From Antrodiella Faginea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Laccase From Antrodiella Faginea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu507 b:14.6 occ:0.80 O A:HOH824 1.9 13.1 0.8 NE2 A:HIS400 2.0 10.5 1.0 NE2 A:HIS450 2.0 15.9 1.0 NE2 A:HIS111 2.1 11.9 1.0 O A:HOH700 2.7 16.9 0.8 CE1 A:HIS400 2.8 11.2 1.0 CE1 A:HIS450 2.9 15.9 1.0 CE1 A:HIS111 3.0 11.6 1.0 CD2 A:HIS450 3.1 15.7 1.0 CD2 A:HIS111 3.1 11.4 1.0 CD2 A:HIS400 3.1 10.5 1.0 CD2 A:HIS398 3.6 16.4 1.0 CU A:CU508 3.7 16.1 0.8 O A:HOH959 3.7 19.1 1.0 CU A:CU509 3.9 14.9 0.8 ND1 A:HIS400 4.0 10.2 1.0 ND1 A:HIS450 4.1 15.8 1.0 CG A:HIS400 4.1 10.5 1.0 CD2 A:HIS64 4.2 13.0 1.0 CG A:HIS450 4.2 15.2 1.0 ND1 A:HIS111 4.2 12.8 1.0 NE2 A:HIS398 4.2 16.5 1.0 CG A:HIS111 4.2 12.1 1.0 CE1 A:HIS109 4.2 13.6 1.0 NE2 A:HIS64 4.2 14.1 1.0 NE2 A:HIS109 4.5 13.2 1.0 NE2 A:HIS452 4.6 11.2 1.0 CG A:HIS398 4.7 15.2 1.0 CD2 A:HIS452 4.8 12.6 1.0 CG A:HIS64 4.9 12.5 1.0 CD2 A:PHE448 4.9 15.2 1.0 CE1 A:HIS64 5.0 12.5 1.0

Copper binding site 2 out of 4 in the Laccase From Antrodiella Faginea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Laccase From Antrodiella Faginea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu508 b:16.1 occ:0.80 O A:HOH700 1.9 16.9 0.8 NE2 A:HIS452 2.0 11.2 1.0 ND1 A:HIS66 2.1 16.9 1.0 NE2 A:HIS109 2.1 13.2 1.0 O A:HOH824 2.2 13.1 0.8 CE1 A:HIS66 2.9 14.4 1.0 CD2 A:HIS452 3.0 12.6 1.0 CE1 A:HIS109 3.0 13.6 1.0 CE1 A:HIS452 3.0 12.2 1.0 CD2 A:HIS109 3.2 12.6 1.0 CG A:HIS66 3.2 15.3 1.0 CU A:CU507 3.7 14.6 0.8 CB A:HIS66 3.7 14.0 1.0 CU A:CU509 3.8 14.9 0.8 CD2 A:HIS398 3.8 16.4 1.0 CD2 A:HIS64 3.9 13.0 1.0 CZ2 A:TRP107 4.0 11.5 1.0 NE2 A:HIS398 4.0 16.5 1.0 O A:HOH959 4.1 19.1 1.0 NE2 A:HIS66 4.1 13.8 1.0 ND1 A:HIS452 4.1 12.3 1.0 CG A:HIS452 4.2 13.6 1.0 ND1 A:HIS109 4.2 13.4 1.0 NE2 A:HIS64 4.2 14.1 1.0 CD2 A:HIS66 4.2 13.8 1.0 CG A:HIS109 4.3 12.3 1.0 CE2 A:TRP107 4.4 11.6 1.0 NE1 A:TRP107 4.6 10.8 1.0 CG A:HIS398 4.7 15.2 1.0 CA A:HIS66 4.7 13.8 1.0 CH2 A:TRP107 4.7 10.9 1.0 NE2 A:HIS111 4.8 11.9 1.0 NE2 A:HIS450 4.8 15.9 1.0 CE1 A:HIS450 4.8 15.9 1.0 CD2 A:HIS111 4.9 11.4 1.0 NE2 A:HIS400 4.9 10.5 1.0 CE1 A:HIS398 4.9 16.7 1.0

Copper binding site 3 out of 4 in the Laccase From Antrodiella Faginea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Laccase From Antrodiella Faginea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu509 b:14.9 occ:0.80 NE2 A:HIS398 2.0 16.5 1.0 NE2 A:HIS64 2.0 14.1 1.0 O A:HOH700 2.0 16.9 0.8 O A:HOH888 2.2 9.5 1.0 CD2 A:HIS398 2.9 16.4 1.0 CE1 A:HIS64 2.9 12.5 1.0 CE1 A:HIS398 3.0 16.7 1.0 CD2 A:HIS64 3.0 13.0 1.0 NE2 A:HIS400 3.3 10.5 1.0 CE1 A:HIS400 3.5 11.2 1.0 CD2 A:HIS400 3.5 10.5 1.0 ND1 A:HIS66 3.5 16.9 1.0 CG A:HIS66 3.7 15.3 1.0 CA A:HIS66 3.7 13.8 1.0 CG A:HIS400 3.7 10.5 1.0 CU A:CU508 3.8 16.1 0.8 ND1 A:HIS400 3.8 10.2 1.0 N A:GLY67 3.9 12.4 1.0 CU A:CU507 3.9 14.6 0.8 CE1 A:HIS66 4.0 14.4 1.0 CB A:HIS66 4.0 14.0 1.0 ND1 A:HIS64 4.0 11.7 1.0 CG A:HIS398 4.0 15.2 1.0 ND1 A:HIS398 4.1 15.5 1.0 CG A:HIS64 4.1 12.5 1.0 CD2 A:HIS66 4.1 13.8 1.0 O A:HOH824 4.2 13.1 0.8 C A:HIS66 4.3 13.5 1.0 NE2 A:HIS66 4.3 13.8 1.0 O A:HOH796 4.5 15.5 1.0 CA A:HIS400 4.5 11.1 1.0 O A:HOH641 4.7 17.8 1.0 CB A:HIS400 4.7 10.9 1.0 N A:HIS66 4.8 13.5 1.0 O A:LEU399 4.9 12.6 1.0 CA A:GLY67 4.9 12.8 1.0 O A:TRP65 4.9 12.9 1.0

Copper binding site 4 out of 4 in the Laccase From Antrodiella Faginea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Laccase From Antrodiella Faginea within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu510 b:15.7 occ:0.80 ND1 A:HIS456 2.0 15.7 1.0 ND1 A:HIS395 2.1 21.1 1.0 SG A:CYS451 2.1 16.4 1.0 CE1 A:HIS395 3.0 24.4 1.0 CG A:HIS456 3.0 15.5 1.0 CE1 A:HIS456 3.0 16.1 1.0 CG A:HIS395 3.2 19.9 1.0 CB A:CYS451 3.3 15.4 1.0 CB A:HIS456 3.3 15.1 1.0 CB A:HIS395 3.6 19.4 1.0 CD1 A:ILE453 3.6 14.9 1.0 CD2 A:PHE461 3.7 15.5 1.0 CE2 A:PHE461 3.7 15.0 1.0 CB A:ILE453 3.8 14.4 1.0 CA A:HIS395 4.1 18.6 1.0 CG1 A:ILE453 4.1 14.7 1.0 NE2 A:HIS456 4.1 16.7 1.0 CD2 A:HIS456 4.1 17.4 1.0 NE2 A:HIS395 4.1 22.6 1.0 CD2 A:HIS395 4.2 21.7 1.0 CA A:CYS451 4.6 13.1 1.0 CD A:PRO396 4.6 14.8 1.0 CG2 A:ILE453 4.7 14.1 1.0 O A:GLY392 4.7 27.2 1.0 N A:ILE453 4.7 13.4 1.0 CG A:PHE461 4.7 13.9 1.0 CZ A:PHE461 4.8 15.3 1.0 CA A:ILE453 4.8 14.2 1.0 CA A:HIS456 4.8 16.5 1.0 O A:ILE453 4.9 17.8 1.0

O.A.Glazunova, K.M.Polyakov, K.V.Moiseenko, S.A.Kurzeev, T.V.Fedorova. Structure-Function Study of Two New Middle-Redox Potential Laccases From Basidiomycetes Antrodiella Faginea and Steccherinum Murashkinskyi. Int. J. Biol. Macromol. V. 118 406 2018.
ISSN: ISSN 1879-0003
PubMed: 29890251
DOI: 10.1016/J.IJBIOMAC.2018.06.038