Zinc in PDB 5m8o: Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone, PDB code: 5m8o was solved by X.Lai, M.Soler-Lopez, H.J.Wichers, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.69 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.688, 140.202, 191.058, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.1

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone (pdb code 5m8o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone, PDB code: 5m8o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:26.4 occ:1.00 OA1 A:0TR512 1.8 19.8 1.0 NE2 A:HIS215 2.1 18.6 1.0 NE2 A:HIS192 2.2 17.6 1.0 OA2 A:0TR512 2.6 20.2 1.0 CE1 A:HIS192 3.0 17.0 1.0 CA1 A:0TR512 3.0 25.0 1.0 CE1 A:HIS215 3.1 14.3 1.0 CD2 A:HIS215 3.1 18.0 1.0 ZN A:ZN514 3.2 19.9 1.0 CD2 A:HIS192 3.4 17.0 1.0 CA2 A:0TR512 3.4 21.4 1.0 NE2 A:HIS224 3.5 18.1 1.0 CE1 A:HIS224 4.0 19.3 1.0 CE2 A:PHE400 4.1 12.8 1.0 OG A:SER394 4.1 19.7 1.0 ND1 A:HIS192 4.2 18.9 1.0 CA6 A:0TR512 4.2 22.9 1.0 ND1 A:HIS215 4.2 15.6 1.0 CG A:HIS215 4.3 17.9 1.0 NE2 A:HIS381 4.3 21.4 1.0 CG A:HIS192 4.4 12.6 1.0 CE1 A:HIS381 4.4 17.7 1.0 NE2 A:HIS404 4.4 20.5 1.0 CZ A:PHE400 4.4 14.9 1.0 NE2 A:HIS377 4.6 19.7 1.0 CD2 A:HIS224 4.7 13.5 1.0 CA3 A:0TR512 4.7 20.3 1.0 CE1 A:HIS377 4.8 19.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn514 b:19.9 occ:1.00 NE2 A:HIS404 1.9 20.5 1.0 NE2 A:HIS377 2.1 19.7 1.0 NE2 A:HIS381 2.2 21.4 1.0 CE1 A:HIS404 2.7 18.1 1.0 CE1 A:HIS377 3.0 19.4 1.0 CD2 A:HIS404 3.0 17.6 1.0 CD2 A:HIS377 3.1 21.8 1.0 OA2 A:0TR512 3.1 20.2 1.0 CD2 A:HIS381 3.1 18.5 1.0 CE1 A:HIS381 3.1 17.7 1.0 ZN A:ZN513 3.2 26.4 1.0 OA1 A:0TR512 3.8 19.8 1.0 CE2 A:PHE400 3.8 12.8 1.0 NE2 A:HIS224 3.8 18.1 1.0 ND1 A:HIS404 3.9 15.5 1.0 CA2 A:0TR512 3.9 21.4 1.0 CG A:HIS404 4.1 18.1 1.0 ND1 A:HIS377 4.1 21.1 1.0 CG A:HIS377 4.2 20.4 1.0 ND1 A:HIS381 4.2 17.7 1.0 CA1 A:0TR512 4.2 25.0 1.0 CZ A:PHE400 4.2 14.9 1.0 CG A:HIS381 4.2 22.1 1.0 CD2 A:HIS224 4.2 13.5 1.0 CD2 A:LEU403 4.5 18.1 1.0 CD2 A:PHE400 4.6 16.9 1.0 CE1 A:HIS224 4.7 19.3 1.0 CE1 A:PHE220 4.7 14.5 1.0 NE2 A:HIS215 4.7 18.6 1.0 CA3 A:0TR512 4.7 20.3 1.0 NE2 A:HIS192 5.0 17.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn517 b:23.8 occ:1.00 OA1 B:0TR516 1.9 13.9 1.0 NE2 B:HIS215 2.1 19.8 1.0 NE2 B:HIS192 2.2 20.0 1.0 OA2 B:0TR516 2.5 20.9 1.0 CE1 B:HIS215 2.9 14.6 1.0 CE1 B:HIS192 3.0 14.4 1.0 CA1 B:0TR516 3.1 16.7 1.0 CD2 B:HIS215 3.1 16.6 1.0 ZN B:ZN518 3.2 18.4 1.0 NE2 B:HIS224 3.2 18.6 1.0 CA2 B:0TR516 3.3 19.3 1.0 CD2 B:HIS192 3.3 13.2 1.0 CE1 B:HIS224 3.7 18.7 1.0 CE2 B:PHE400 4.0 14.5 1.0 ND1 B:HIS215 4.1 14.0 1.0 OG B:SER394 4.1 13.8 1.0 ND1 B:HIS192 4.2 14.3 1.0 CG B:HIS215 4.2 13.1 1.0 CA6 B:0TR516 4.3 16.7 1.0 NE2 B:HIS404 4.3 19.0 1.0 CG B:HIS192 4.4 12.4 1.0 CZ B:PHE400 4.4 13.9 1.0 NE2 B:HIS381 4.4 14.4 1.0 CD2 B:HIS224 4.4 15.6 1.0 CE1 B:HIS381 4.6 11.9 1.0 CA3 B:0TR516 4.6 18.9 1.0 NE2 B:HIS377 4.6 16.4 1.0 CE1 B:HIS377 4.8 14.1 1.0 ND1 B:HIS224 4.9 22.4 1.0 CE1 B:HIS404 5.0 18.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn518 b:18.4 occ:1.00 NE2 B:HIS377 2.0 16.4 1.0 NE2 B:HIS404 2.1 19.0 1.0 NE2 B:HIS381 2.1 14.4 1.0 CE1 B:HIS377 2.9 14.1 1.0 OA2 B:0TR516 2.9 20.9 1.0 CE1 B:HIS404 2.9 18.5 1.0 CD2 B:HIS381 3.0 16.7 1.0 CE1 B:HIS381 3.1 11.9 1.0 CD2 B:HIS377 3.1 20.2 1.0 ZN B:ZN517 3.2 23.8 1.0 CD2 B:HIS404 3.2 16.0 1.0 CA2 B:0TR516 3.7 19.3 1.0 OA1 B:0TR516 3.7 13.9 1.0 NE2 B:HIS224 3.9 18.6 1.0 CE2 B:PHE400 3.9 14.5 1.0 ND1 B:HIS377 4.0 15.1 1.0 CA1 B:0TR516 4.1 16.7 1.0 ND1 B:HIS404 4.1 14.3 1.0 ND1 B:HIS381 4.1 13.9 1.0 CG B:HIS381 4.1 17.4 1.0 CG B:HIS377 4.2 20.1 1.0 CG B:HIS404 4.2 15.6 1.0 CD2 B:HIS224 4.3 15.6 1.0 CZ B:PHE400 4.4 13.9 1.0 CA3 B:0TR516 4.5 18.9 1.0 CD2 B:LEU403 4.5 11.1 1.0 CD2 B:PHE400 4.5 12.5 1.0 CE1 B:PHE220 4.5 15.1 1.0 CE1 B:HIS224 4.6 18.7 1.0 NE2 B:HIS215 4.6 19.8 1.0 CZ B:PHE220 4.9 15.3 1.0 NE2 B:HIS192 5.0 20.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn517 b:18.0 occ:1.00 NE2 C:HIS404 1.9 28.4 1.0 NE2 C:HIS377 1.9 18.7 1.0 NE2 C:HIS381 2.2 25.4 1.0 OA2 C:0TR516 2.7 24.8 1.0 CE1 C:HIS404 2.7 23.7 1.0 CE1 C:HIS377 2.8 21.9 1.0 CE1 C:HIS381 3.0 24.3 1.0 CD2 C:HIS377 3.1 20.6 1.0 CD2 C:HIS381 3.1 21.9 1.0 ZN C:ZN518 3.1 71.3 1.0 CD2 C:HIS404 3.1 25.3 1.0 CA2 C:0TR516 3.5 26.8 1.0 ND1 C:HIS404 3.9 22.4 1.0 OA1 C:0TR516 3.9 27.4 1.0 CE2 C:PHE400 3.9 23.2 1.0 ND1 C:HIS377 4.0 18.9 1.0 CE1 C:HIS224 4.0 27.2 1.0 ND1 C:HIS381 4.0 23.2 1.0 CG C:HIS381 4.1 22.5 1.0 CG C:HIS404 4.1 26.4 1.0 CG C:HIS377 4.1 18.4 1.0 CA1 C:0TR516 4.2 24.2 1.0 CA3 C:0TR516 4.2 26.1 1.0 CZ C:PHE400 4.3 18.6 1.0 ND1 C:HIS224 4.4 33.5 1.0 CD2 C:LEU403 4.6 17.6 1.0 CE1 C:PHE220 4.6 16.3 1.0 CD2 C:PHE400 4.6 21.3 1.0 NE2 C:HIS224 4.6 27.0 1.0 NE2 C:HIS215 4.7 26.5 1.0 NE2 C:HIS192 4.9 26.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn518 b:71.3 occ:1.00 OA1 C:0TR516 1.9 27.4 1.0 OA2 C:0TR516 2.0 24.8 1.0 NE2 C:HIS215 2.2 26.5 1.0 NE2 C:HIS192 2.3 26.4 1.0 CA1 C:0TR516 3.0 24.2 1.0 CE1 C:HIS192 3.0 23.5 1.0 CA2 C:0TR516 3.0 26.8 1.0 CE1 C:HIS215 3.1 28.0 1.0 ZN C:ZN517 3.1 18.0 1.0 CD2 C:HIS215 3.2 22.2 1.0 CD2 C:HIS192 3.4 24.4 1.0 CE1 C:HIS224 3.4 27.2 1.0 NE2 C:HIS224 3.8 27.0 1.0 CE2 C:PHE400 4.0 23.2 1.0 ND1 C:HIS192 4.2 20.1 1.0 OG C:SER394 4.2 25.0 1.0 ND1 C:HIS215 4.2 25.2 1.0 CA6 C:0TR516 4.3 22.0 1.0 CG C:HIS215 4.3 20.5 1.0 NE2 C:HIS404 4.3 28.4 1.0 CA3 C:0TR516 4.3 26.1 1.0 CE1 C:HIS381 4.4 24.3 1.0 NE2 C:HIS381 4.4 25.4 1.0 CZ C:PHE400 4.4 18.6 1.0 CG C:HIS192 4.4 19.9 1.0 NE2 C:HIS377 4.5 18.7 1.0 ND1 C:HIS224 4.6 33.5 1.0 CE1 C:HIS377 4.6 21.9 1.0 CE1 C:HIS404 4.9 23.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn519 b:27.2 occ:1.00 OA1 D:0TR518 1.8 10.7 1.0 NE2 D:HIS215 2.1 16.6 1.0 NE2 D:HIS192 2.2 16.4 1.0 CE1 D:HIS192 2.9 13.2 1.0 OA2 D:0TR518 2.9 27.6 1.0 CE1 D:HIS215 3.0 16.4 1.0 CA1 D:0TR518 3.1 17.1 1.0 NE2 D:HIS224 3.1 16.4 1.0 ZN D:ZN520 3.2 9.0 1.0 CD2 D:HIS215 3.2 14.8 1.0 CD2 D:HIS192 3.3 13.0 1.0 CA2 D:0TR518 3.5 17.6 1.0 CE1 D:HIS224 3.7 17.1 1.0 CE2 D:PHE400 4.1 10.5 1.0 ND1 D:HIS192 4.1 15.9 1.0 ND1 D:HIS215 4.1 18.9 1.0 CA6 D:0TR518 4.2 19.6 1.0 CG D:HIS215 4.3 13.5 1.0 CD2 D:HIS224 4.3 13.7 1.0 OG D:SER394 4.3 15.1 1.0 NE2 D:HIS404 4.3 15.2 1.0 CG D:HIS192 4.3 13.5 1.0 NE2 D:HIS381 4.4 25.4 1.0 CZ D:PHE400 4.5 11.8 1.0 CE1 D:HIS381 4.5 16.2 1.0 NE2 D:HIS377 4.6 21.4 1.0 CE1 D:HIS377 4.7 21.0 1.0 CE1 D:HIS404 4.8 17.9 1.0 CA3 D:0TR518 4.9 17.5 1.0 ND1 D:HIS224 4.9 21.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn520 b:9.0 occ:1.00 NE2 D:HIS404 1.9 15.2 1.0 NE2 D:HIS377 2.0 21.4 1.0 NE2 D:HIS381 2.2 25.4 1.0 CE1 D:HIS404 2.7 17.9 1.0 CE1 D:HIS377 2.8 21.0 1.0 CD2 D:HIS404 3.1 13.5 1.0 CE1 D:HIS381 3.1 16.2 1.0 CD2 D:HIS381 3.1 15.2 1.0 OA2 D:0TR518 3.1 27.6 1.0 CD2 D:HIS377 3.1 17.1 1.0 ZN D:ZN519 3.2 27.2 1.0 OA1 D:0TR518 3.6 10.7 1.0 CA2 D:0TR518 3.8 17.6 1.0 ND1 D:HIS404 3.9 13.9 1.0 CE2 D:PHE400 3.9 10.5 1.0 NE2 D:HIS224 4.0 16.4 1.0 ND1 D:HIS377 4.0 17.9 1.0 CA1 D:0TR518 4.0 17.1 1.0 CG D:HIS404 4.1 12.5 1.0 ND1 D:HIS381 4.1 13.1 1.0 CG D:HIS381 4.2 14.5 1.0 CG D:HIS377 4.2 17.9 1.0 CD2 D:HIS224 4.3 13.7 1.0 CZ D:PHE400 4.4 11.8 1.0 CE1 D:PHE220 4.5 16.9 1.0 CD2 D:PHE400 4.6 16.2 1.0 CD2 D:LEU403 4.6 11.3 1.0 CA3 D:0TR518 4.7 17.5 1.0 NE2 D:HIS215 4.8 16.6 1.0 CE1 D:HIS224 4.8 17.1 1.0 CZ D:PHE220 4.8 18.4 1.0 NE2 D:HIS192 4.9 16.4 1.0

X.Lai, H.J.Wichers, M.Soler-Lopez, B.W.Dijkstra. Structure of Human Tyrosinase Related Protein 1 Reveals A Binuclear Zinc Active Site Important For Melanogenesis. Angew. Chem. Int. Ed. Engl. V. 56 9812 2017.
ISSN: ESSN 1521-3773
PubMed: 28661582
DOI: 10.1002/ANIE.201704616