Zinc in PDB 5m8t: Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone, PDB code: 5m8t 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)	48.75 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.732, 140.605, 191.253, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.5

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone (pdb code 5m8t). 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 (T391V-R374S- Y362F) in Complex with Tropolone, PDB code: 5m8t:
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 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:33.4 occ:1.00 NE2 A:HIS404 2.0 31.4 1.0 O A:HOH601 2.0 40.9 1.0 NE2 A:HIS377 2.1 35.0 1.0 NE2 A:HIS381 2.2 40.2 1.0 CE1 A:HIS404 2.8 31.7 1.0 CD2 A:HIS377 3.0 31.6 1.0 CE1 A:HIS377 3.1 33.5 1.0 CD2 A:HIS381 3.1 38.4 1.0 CD2 A:HIS404 3.1 31.0 1.0 CE1 A:HIS381 3.1 39.9 1.0 OA1 A:0TR513 3.3 52.6 1.0 ZN A:ZN512 3.3 47.4 1.0 OA2 A:0TR513 3.5 52.5 1.0 CE2 A:PHE400 3.8 34.9 1.0 ND1 A:HIS404 4.0 29.1 1.0 CA1 A:0TR513 4.0 52.7 1.0 CA2 A:0TR513 4.1 53.7 1.0 NE2 A:HIS224 4.1 37.4 1.0 CG A:HIS404 4.1 36.6 1.0 ND1 A:HIS377 4.2 33.6 1.0 CG A:HIS377 4.2 33.3 1.0 CG A:HIS381 4.2 42.3 1.0 ND1 A:HIS381 4.2 41.0 1.0 CZ A:PHE400 4.2 29.6 1.0 CD2 A:HIS224 4.4 32.5 1.0 CD2 A:PHE400 4.6 32.2 1.0 CE1 A:PHE220 4.6 35.5 1.0 CD2 A:LEU403 4.7 34.0 1.0 NE2 A:HIS215 4.8 42.7 1.0 CE1 A:HIS224 4.9 34.0 1.0 CZ A:PHE220 4.9 33.5 1.0 CA6 A:0TR513 5.0 52.8 1.0 NE2 A:HIS192 5.0 36.1 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:47.4 occ:1.00 NE2 A:HIS192 2.1 36.1 1.0 O A:HOH601 2.1 40.9 1.0 NE2 A:HIS215 2.1 42.7 1.0 NE2 A:HIS224 2.3 37.4 1.0 OA2 A:0TR513 2.9 52.5 1.0 CE1 A:HIS224 3.0 34.0 1.0 CD2 A:HIS192 3.0 33.1 1.0 CE1 A:HIS215 3.0 33.8 1.0 CE1 A:HIS192 3.2 32.9 1.0 CD2 A:HIS215 3.2 38.5 1.0 ZN A:ZN511 3.3 33.4 1.0 CD2 A:HIS224 3.5 32.5 1.0 OA1 A:0TR513 3.6 52.6 1.0 CZ A:PHE400 3.9 29.6 1.0 CE2 A:PHE400 4.0 34.9 1.0 NE2 A:HIS404 4.0 31.4 1.0 CA2 A:0TR513 4.2 53.7 1.0 ND1 A:HIS215 4.2 40.8 1.0 CG A:HIS192 4.2 31.8 1.0 ND1 A:HIS224 4.2 33.5 1.0 ND1 A:HIS192 4.2 33.2 1.0 CG A:HIS215 4.3 42.6 1.0 CE1 A:HIS404 4.3 31.7 1.0 CG A:HIS224 4.5 32.2 1.0 CA1 A:0TR513 4.5 52.7 1.0 NE2 A:HIS377 4.7 35.0 1.0 NE2 A:HIS381 4.9 40.2 1.0 CE1 A:PHE220 4.9 35.5 1.0 OG A:SER394 5.0 42.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn515 b:40.2 occ:1.00 NE2 B:HIS192 2.1 29.9 1.0 NE2 B:HIS224 2.1 31.0 1.0 O B:HOH601 2.1 36.5 1.0 NE2 B:HIS215 2.2 36.0 1.0 CD2 B:HIS192 2.9 25.1 1.0 CE1 B:HIS224 2.9 31.2 1.0 CE1 B:HIS215 3.0 28.9 1.0 CE1 B:HIS192 3.2 28.6 1.0 CD2 B:HIS224 3.2 27.7 1.0 OA2 B:0TR517 3.2 52.5 1.0 CD2 B:HIS215 3.3 30.9 1.0 ZN B:ZN516 3.4 32.3 1.0 CZ B:PHE400 3.8 28.0 1.0 CE2 B:PHE400 3.9 32.9 1.0 OA1 B:0TR517 4.0 52.6 1.0 NE2 B:HIS404 4.0 29.9 1.0 ND1 B:HIS224 4.1 29.3 1.0 CG B:HIS192 4.1 29.0 1.0 ND1 B:HIS215 4.1 32.3 1.0 ND1 B:HIS192 4.2 29.8 1.0 CE1 B:HIS404 4.2 29.4 1.0 CG B:HIS224 4.3 32.3 1.0 CG B:HIS215 4.3 31.6 1.0 CA2 B:0TR517 4.5 52.6 1.0 CE1 B:PHE220 4.8 29.8 1.0 NE2 B:HIS377 4.8 29.7 1.0 CA1 B:0TR517 4.8 52.7 1.0 OG B:SER394 5.0 36.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn516 b:32.3 occ:1.00 NE2 B:HIS404 2.0 29.9 1.0 O B:HOH601 2.0 36.5 1.0 NE2 B:HIS381 2.1 34.0 1.0 NE2 B:HIS377 2.1 29.7 1.0 CE1 B:HIS404 2.7 29.4 1.0 CE1 B:HIS381 3.0 35.4 1.0 CE1 B:HIS377 3.0 29.9 1.0 CD2 B:HIS381 3.1 35.1 1.0 CD2 B:HIS377 3.1 30.8 1.0 CD2 B:HIS404 3.2 26.4 1.0 ZN B:ZN515 3.4 40.2 1.0 OA1 B:0TR517 3.6 52.6 1.0 OA2 B:0TR517 3.6 52.5 1.0 CE2 B:PHE400 3.8 32.9 1.0 ND1 B:HIS404 3.9 28.4 1.0 CA1 B:0TR517 4.1 52.7 1.0 CA2 B:0TR517 4.1 52.6 1.0 ND1 B:HIS381 4.1 33.5 1.0 NE2 B:HIS224 4.1 31.0 1.0 ND1 B:HIS377 4.2 23.9 1.0 CG B:HIS404 4.2 27.2 1.0 CG B:HIS381 4.2 36.7 1.0 CZ B:PHE400 4.2 28.0 1.0 CG B:HIS377 4.2 27.6 1.0 CD2 B:HIS224 4.4 27.7 1.0 CD2 B:LEU403 4.4 31.9 1.0 CD2 B:PHE400 4.5 31.0 1.0 CE1 B:PHE220 4.6 29.8 1.0 NE2 B:HIS215 4.8 36.0 1.0 NE2 B:HIS192 4.9 29.9 1.0 CZ B:PHE220 4.9 31.0 1.0 CE1 B:HIS224 5.0 31.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn514 b:47.2 occ:1.00 NE2 C:HIS215 2.1 43.0 1.0 NE2 C:HIS192 2.1 42.4 1.0 O C:HOH601 2.1 39.0 1.0 NE2 C:HIS224 2.4 36.7 1.0 CE1 C:HIS215 2.8 39.0 1.0 CE1 C:HIS192 3.0 38.1 1.0 CD2 C:HIS192 3.1 36.1 1.0 CD2 C:HIS215 3.2 37.8 1.0 CE1 C:HIS224 3.2 38.2 1.0 OA2 C:0TR516 3.3 52.5 1.0 ZN C:ZN515 3.4 34.1 1.0 CD2 C:HIS224 3.6 35.2 1.0 OA1 C:0TR516 3.6 53.5 1.0 CE2 C:PHE400 4.0 36.0 1.0 ND1 C:HIS215 4.0 39.3 1.0 CZ C:PHE400 4.1 34.4 1.0 NE2 C:HIS404 4.1 37.7 1.0 ND1 C:HIS192 4.1 39.3 1.0 CG C:HIS215 4.2 39.9 1.0 CG C:HIS192 4.2 39.1 1.0 CA2 C:0TR516 4.4 52.6 1.0 ND1 C:HIS224 4.4 31.5 1.0 CA1 C:0TR516 4.5 54.1 1.0 CG C:HIS224 4.6 31.4 1.0 CE1 C:HIS404 4.6 35.5 1.0 NE2 C:HIS377 4.7 40.2 1.0 OG C:SER394 4.9 40.5 1.0 NE2 C:HIS381 5.0 41.1 1.0 CE1 C:PHE220 5.0 36.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn515 b:34.1 occ:1.00 NE2 C:HIS377 2.0 40.2 1.0 NE2 C:HIS404 2.0 37.7 1.0 NE2 C:HIS381 2.0 41.1 1.0 O C:HOH601 2.1 39.0 1.0 CE1 C:HIS404 2.8 35.5 1.0 CE1 C:HIS381 2.9 43.9 1.0 CD2 C:HIS377 3.0 32.3 1.0 CD2 C:HIS381 3.0 41.9 1.0 CE1 C:HIS377 3.1 35.3 1.0 CD2 C:HIS404 3.2 35.2 1.0 OA1 C:0TR516 3.4 53.5 1.0 ZN C:ZN514 3.4 47.2 1.0 CE2 C:PHE400 3.9 36.0 1.0 ND1 C:HIS404 4.0 30.6 1.0 ND1 C:HIS381 4.0 44.6 1.0 OA2 C:0TR516 4.0 52.5 1.0 CG C:HIS381 4.1 45.3 1.0 CA1 C:0TR516 4.1 54.1 1.0 CG C:HIS377 4.1 33.8 1.0 ND1 C:HIS377 4.2 37.0 1.0 NE2 C:HIS224 4.2 36.7 1.0 CG C:HIS404 4.2 38.6 1.0 CZ C:PHE400 4.4 34.4 1.0 CA2 C:0TR516 4.4 52.6 1.0 CD2 C:HIS224 4.4 35.2 1.0 CD2 C:LEU403 4.5 35.5 1.0 CD2 C:PHE400 4.6 34.0 1.0 CE1 C:PHE220 4.7 36.0 1.0 NE2 C:HIS215 4.8 43.0 1.0 CA6 C:0TR516 4.9 52.8 1.0 CZ C:PHE220 5.0 31.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn516 b:41.2 occ:1.00 NE2 D:HIS224 2.2 27.4 1.0 O D:HOH601 2.2 34.9 1.0 NE2 D:HIS215 2.2 34.7 1.0 NE2 D:HIS192 2.3 24.5 1.0 CE1 D:HIS224 3.0 28.2 1.0 CE1 D:HIS215 3.0 34.5 1.0 CD2 D:HIS192 3.1 24.8 1.0 CD2 D:HIS224 3.3 27.4 1.0 CD2 D:HIS215 3.3 36.1 1.0 ZN D:ZN517 3.4 31.1 1.0 CE1 D:HIS192 3.4 31.4 1.0 OA2 D:0TR518 3.5 52.6 0.8 OA1 D:0TR518 3.7 52.5 0.8 CE2 D:PHE400 4.0 28.4 1.0 CZ D:PHE400 4.0 27.5 1.0 NE2 D:HIS404 4.1 27.9 1.0 ND1 D:HIS215 4.1 34.9 1.0 ND1 D:HIS224 4.2 27.8 1.0 CG D:HIS215 4.3 34.4 1.0 CG D:HIS224 4.3 26.2 1.0 CG D:HIS192 4.3 27.5 1.0 CE1 D:HIS404 4.4 28.7 1.0 ND1 D:HIS192 4.5 28.8 1.0 CA2 D:0TR518 4.6 52.7 0.8 CA1 D:0TR518 4.7 52.6 0.8 NE2 D:HIS377 4.7 32.1 1.0 CE1 D:PHE220 4.8 32.5 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) 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 (T391V-R374S- Y362F) in Complex with Tropolone within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn517 b:31.1 occ:1.00 NE2 D:HIS404 2.0 27.9 1.0 NE2 D:HIS377 2.1 32.1 1.0 O D:HOH601 2.2 34.9 1.0 NE2 D:HIS381 2.2 34.9 1.0 CE1 D:HIS404 2.8 28.7 1.0 CE1 D:HIS377 3.0 35.0 1.0 CD2 D:HIS404 3.1 27.6 1.0 CD2 D:HIS377 3.1 29.9 1.0 CD2 D:HIS381 3.1 35.1 1.0 CE1 D:HIS381 3.2 35.0 1.0 ZN D:ZN516 3.4 41.2 1.0 OA1 D:0TR518 3.5 52.5 0.8 CE2 D:PHE400 3.8 28.4 1.0 OA2 D:0TR518 3.9 52.6 0.8 ND1 D:HIS404 4.0 26.9 1.0 ND1 D:HIS377 4.1 30.1 1.0 CA1 D:0TR518 4.1 52.6 0.8 CG D:HIS404 4.1 28.8 1.0 NE2 D:HIS224 4.2 27.4 1.0 CG D:HIS377 4.2 29.0 1.0 CG D:HIS381 4.2 36.8 1.0 ND1 D:HIS381 4.3 36.6 1.0 CA2 D:0TR518 4.3 52.7 0.8 CZ D:PHE400 4.3 27.5 1.0 CD2 D:HIS224 4.4 27.4 1.0 CD2 D:PHE400 4.5 31.9 1.0 CD2 D:LEU403 4.5 32.8 1.0 CE1 D:PHE220 4.7 32.5 1.0 NE2 D:HIS215 4.8 34.7 1.0 CE1 D:HIS224 5.0 28.2 1.0 CZ D:PHE220 5.0 31.8 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