Zinc in PDB 5m8p: Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine, PDB code: 5m8p 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)	47.92 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.516, 140.322, 191.676, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.2

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine (pdb code 5m8p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine, PDB code: 5m8p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn514 b:38.7 occ:1.00 NE2 A:HIS215 1.9 34.4 1.0 NE2 A:HIS192 1.9 34.0 1.0 O A:HOH605 2.1 36.3 1.0 NE2 A:HIS224 2.2 36.3 1.0 CE1 A:HIS215 2.8 37.8 1.0 CE1 A:HIS192 2.9 34.0 1.0 CE1 A:HIS224 2.9 38.7 1.0 CD2 A:HIS192 3.0 34.2 1.0 CD2 A:HIS215 3.0 32.7 1.0 CD2 A:HIS224 3.4 40.7 1.0 ZN A:ZN515 3.5 36.1 1.0 OH A:TYR513 3.7 41.6 1.0 ND1 A:HIS215 4.0 33.9 1.0 ND1 A:HIS192 4.0 27.3 1.0 NE2 A:HIS404 4.0 34.2 1.0 CZ A:PHE400 4.0 33.4 1.0 CG A:HIS192 4.1 31.2 1.0 CE2 A:PHE400 4.1 31.5 1.0 CG A:HIS215 4.1 34.7 1.0 ND1 A:HIS224 4.1 32.0 1.0 CE1 A:TYR513 4.2 43.7 1.0 CG A:HIS224 4.4 35.5 1.0 CZ A:TYR513 4.4 45.1 1.0 CE1 A:HIS404 4.5 46.7 1.0 NE2 A:HIS377 4.9 38.4 1.0 CD2 A:HIS404 4.9 36.9 1.0 CE1 A:PHE220 5.0 33.5 1.0 CE1 A:HIS377 5.0 33.6 1.0 OG A:SER394 5.0 35.2 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn515 b:36.1 occ:1.00 NE2 A:HIS377 1.8 38.4 1.0 NE2 A:HIS404 2.1 34.2 1.0 NE2 A:HIS381 2.1 54.2 1.0 O A:HOH605 2.1 36.3 1.0 CE1 A:HIS377 2.6 33.6 1.0 CE1 A:HIS404 2.8 46.7 1.0 CD2 A:HIS381 3.0 37.3 1.0 CD2 A:HIS377 3.0 50.4 1.0 CE1 A:HIS381 3.0 45.8 1.0 CD2 A:HIS404 3.2 36.9 1.0 ZN A:ZN514 3.5 38.7 1.0 ND1 A:HIS377 3.8 34.0 1.0 CE1 A:TYR513 3.8 43.7 1.0 ND1 A:HIS404 4.0 34.2 1.0 CE2 A:PHE400 4.0 31.5 1.0 CG A:HIS377 4.0 37.4 1.0 ND1 A:HIS381 4.1 39.5 1.0 CG A:HIS381 4.1 38.6 1.0 NE2 A:HIS224 4.2 36.3 1.0 OH A:TYR513 4.2 41.6 1.0 CG A:HIS404 4.2 32.6 1.0 CZ A:TYR513 4.3 45.1 1.0 CZ A:PHE400 4.5 33.4 1.0 CE1 A:PHE220 4.6 33.5 1.0 CD1 A:TYR513 4.6 39.9 1.0 CD2 A:HIS224 4.6 40.7 1.0 CD2 A:PHE400 4.6 30.1 1.0 NE2 A:HIS215 4.7 34.4 1.0 CD2 A:LEU403 4.7 36.0 1.0 CE1 A:HIS224 4.7 38.7 1.0 CD2 A:HIS215 4.9 32.7 1.0 CZ A:PHE220 4.9 34.3 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn516 b:62.2 occ:1.00 OE2 A:GLU66 1.8 56.2 1.0 OE1 B:GLU66 2.0 51.3 1.0 ND1 B:HIS100 2.1 57.6 1.0 ND1 A:HIS100 2.2 55.3 1.0 OE2 B:GLU66 2.2 60.5 1.0 CD B:GLU66 2.3 56.3 1.0 CD A:GLU66 2.5 48.0 1.0 CE1 B:HIS100 2.7 56.0 1.0 OE1 A:GLU66 2.8 53.3 1.0 CE1 A:HIS100 3.0 54.7 1.0 CG A:HIS100 3.3 46.6 1.0 CG B:HIS100 3.3 51.0 1.0 CG B:GLU66 3.7 55.8 1.0 CB A:HIS100 3.8 44.2 1.0 CG A:GLU66 3.8 46.3 1.0 NE B:ARG64 3.9 51.0 1.0 NE2 B:HIS100 3.9 50.1 1.0 CB B:HIS100 4.0 46.4 1.0 NH2 A:ARG64 4.0 51.7 1.0 NH2 B:ARG64 4.0 47.0 1.0 NE A:ARG64 4.1 48.8 1.0 NE2 A:HIS100 4.2 53.0 1.0 CD2 B:HIS100 4.3 47.7 1.0 CD2 A:HIS100 4.3 43.6 1.0 CZ B:ARG64 4.4 55.9 1.0 CZ A:ARG64 4.5 51.3 1.0 CB B:GLU66 4.6 44.4 1.0 CB A:GLU66 4.8 39.0 1.0 CD B:ARG64 4.9 47.8 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn517 b:46.4 occ:1.00 NE2 B:HIS215 1.8 35.5 1.0 NE2 B:HIS192 1.8 32.7 1.0 NE2 B:HIS224 2.0 33.2 1.0 O B:HOH605 2.3 37.4 1.0 CE1 B:HIS215 2.5 34.1 1.0 CE1 B:HIS192 2.6 35.3 1.0 CE1 B:HIS224 2.8 33.2 1.0 CD2 B:HIS215 3.0 32.7 1.0 CD2 B:HIS192 3.1 36.2 1.0 CD2 B:HIS224 3.2 34.2 1.0 ZN B:ZN518 3.7 47.8 1.0 ND1 B:HIS215 3.7 30.3 1.0 ND1 B:HIS192 3.8 34.3 1.0 CG B:HIS215 4.0 30.2 1.0 CZ B:PHE400 4.0 35.2 1.0 ND1 B:HIS224 4.0 33.4 1.0 CE1 B:PHE400 4.0 38.6 1.0 CG B:HIS192 4.0 36.2 1.0 NE2 B:HIS404 4.2 32.9 1.0 OH B:TYR516 4.2 49.4 1.0 CG B:HIS224 4.2 32.6 1.0 CE1 B:TYR516 4.4 48.3 1.0 CE1 B:HIS404 4.5 32.9 1.0 NE2 B:HIS381 4.8 39.1 1.0 CZ B:TYR516 4.8 46.7 1.0 OG B:SER394 4.9 40.2 1.0 NE2 B:HIS377 5.0 34.9 1.0 OG B:SER214 5.0 30.7 1.0 CE1 B:PHE220 5.0 34.2 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn518 b:47.8 occ:1.00 NE2 B:HIS381 1.4 39.1 1.0 NE2 B:HIS404 1.9 32.9 1.0 NE2 B:HIS377 2.0 34.9 1.0 O B:HOH605 2.2 37.4 1.0 CE1 B:HIS381 2.3 34.7 1.0 CD2 B:HIS381 2.6 36.2 1.0 CE1 B:HIS404 2.6 32.9 1.0 CE1 B:HIS377 3.0 35.8 1.0 CD2 B:HIS377 3.0 35.1 1.0 CD2 B:HIS404 3.1 33.5 1.0 ND1 B:HIS381 3.5 32.1 1.0 CG B:HIS381 3.6 37.4 1.0 ZN B:ZN517 3.7 46.4 1.0 CE1 B:PHE400 3.8 38.6 1.0 ND1 B:HIS404 3.8 32.9 1.0 CG B:HIS404 4.1 34.0 1.0 ND1 B:HIS377 4.1 35.9 1.0 CE1 B:TYR516 4.1 48.3 1.0 NE2 B:HIS224 4.1 33.2 1.0 CG B:HIS377 4.1 34.8 1.0 OH B:TYR516 4.3 49.4 1.0 CZ B:PHE400 4.4 35.2 1.0 CZ B:TYR516 4.4 46.7 1.0 CD1 B:PHE400 4.4 34.7 1.0 CD2 B:HIS224 4.4 34.2 1.0 CD2 B:LEU403 4.5 30.3 1.0 NE2 B:HIS215 4.6 35.5 1.0 CE1 B:PHE220 4.7 34.2 1.0 CE1 B:HIS224 4.9 33.2 1.0 CD1 B:TYR516 4.9 48.6 1.0 CZ B:PHE220 4.9 34.7 1.0 CD2 B:HIS215 5.0 32.7 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn517 b:50.4 occ:1.00 NE2 C:HIS404 2.0 55.9 1.0 NE2 C:HIS377 2.0 61.8 1.0 O C:HOH608 2.1 54.9 1.0 NE2 C:HIS381 2.1 68.8 1.0 CE1 C:HIS404 2.3 55.1 1.0 CE1 C:HIS377 2.7 66.7 1.0 CE1 C:HIS381 3.1 68.8 1.0 CD2 C:HIS381 3.1 67.4 1.0 CD2 C:HIS404 3.3 56.1 1.0 CD2 C:HIS377 3.3 64.0 1.0 ND1 C:HIS404 3.5 54.6 1.0 ZN C:ZN518 3.6 63.2 1.0 CE1 C:PHE400 3.8 52.0 1.0 CE2 C:TYR516 3.8 94.1 1.0 ND1 C:HIS377 3.9 67.5 1.0 CG C:HIS404 4.0 52.7 1.0 ND1 C:HIS381 4.2 69.3 1.0 CG C:HIS381 4.2 69.5 1.0 CG C:HIS377 4.3 62.5 1.0 CZ C:TYR516 4.4 83.4 1.0 CZ C:PHE400 4.4 48.1 1.0 CD2 C:TYR516 4.4 97.5 1.0 NE2 C:HIS224 4.4 55.0 1.0 OH C:TYR516 4.5 75.5 1.0 CD1 C:PHE400 4.5 51.0 1.0 CE1 C:PHE220 4.6 52.9 1.0 NE2 C:HIS215 4.6 62.6 1.0 CD2 C:HIS224 4.8 53.4 1.0 CZ C:PHE220 4.9 55.1 1.0 CD2 C:HIS215 4.9 59.9 1.0 CD2 C:LEU403 4.9 53.5 1.0 CE1 C:HIS224 4.9 55.8 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn518 b:63.2 occ:1.00 NE2 C:HIS215 1.8 62.6 1.0 NE2 C:HIS192 1.9 53.9 1.0 O C:HOH608 2.1 54.9 1.0 NE2 C:HIS224 2.1 55.0 1.0 CE1 C:HIS215 2.6 61.3 1.0 CE1 C:HIS192 2.8 56.5 1.0 CE1 C:HIS224 2.9 55.8 1.0 CD2 C:HIS192 2.9 49.9 1.0 CD2 C:HIS215 3.0 59.9 1.0 CD2 C:HIS224 3.2 53.4 1.0 ZN C:ZN517 3.6 50.4 1.0 ND1 C:HIS215 3.8 58.6 1.0 CE2 C:TYR516 3.9 94.1 1.0 CZ C:PHE400 3.9 48.1 1.0 ND1 C:HIS192 3.9 53.4 1.0 CE1 C:PHE400 4.0 52.0 1.0 CG C:HIS215 4.0 56.0 1.0 CG C:HIS192 4.0 47.3 1.0 ND1 C:HIS224 4.0 54.8 1.0 NE2 C:HIS404 4.1 55.9 1.0 OH C:TYR516 4.1 75.5 1.0 CG C:HIS224 4.2 52.9 1.0 CE1 C:HIS404 4.2 55.1 1.0 CZ C:TYR516 4.5 83.4 1.0 CE1 C:PHE220 4.9 52.9 1.0 CD2 C:TYR516 4.9 97.5 1.0 OG C:SER394 5.0 66.6 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn518 b:48.8 occ:1.00 NE2 D:HIS224 1.8 45.3 1.0 NE2 D:HIS215 2.0 55.7 1.0 O D:HOH604 2.1 62.3 1.0 NE2 D:HIS192 2.1 47.2 1.0 CE1 D:HIS224 2.5 46.0 1.0 CD2 D:HIS215 2.8 53.1 1.0 CE1 D:HIS192 3.0 43.8 1.0 CD2 D:HIS224 3.1 45.3 1.0 CE1 D:HIS215 3.1 53.5 1.0 CD2 D:HIS192 3.1 46.1 1.0 ZN D:ZN519 3.7 58.8 1.0 ND1 D:HIS224 3.7 43.8 1.0 OH D:TYR517 3.8 57.0 1.0 NE2 D:HIS404 4.0 46.6 1.0 CG D:HIS224 4.0 41.9 1.0 CG D:HIS215 4.1 55.4 1.0 CZ D:PHE400 4.1 45.6 1.0 ND1 D:HIS215 4.1 52.6 1.0 ND1 D:HIS192 4.2 44.4 1.0 CE2 D:PHE400 4.2 42.6 1.0 CG D:HIS192 4.3 42.1 1.0 CE1 D:TYR517 4.4 60.4 1.0 CE1 D:HIS404 4.4 47.1 1.0 CZ D:TYR517 4.6 59.7 1.0 OG D:SER214 4.6 51.5 1.0 CE1 D:PHE220 4.8 50.7 1.0 NE2 D:HIS377 4.9 53.0 1.0 CD2 D:HIS404 4.9 46.8 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn519 b:58.8 occ:1.00 NE2 D:HIS381 1.8 55.3 1.0 NE2 D:HIS377 2.0 53.0 1.0 NE2 D:HIS404 2.1 46.6 1.0 O D:HOH604 2.1 62.3 1.0 CE1 D:HIS381 2.7 55.6 1.0 CE1 D:HIS404 2.8 47.1 1.0 CD2 D:HIS377 2.9 52.6 1.0 CD2 D:HIS381 2.9 53.8 1.0 CE1 D:HIS377 3.1 55.6 1.0 CD2 D:HIS404 3.2 46.8 1.0 ZN D:ZN518 3.7 48.8 1.0 ND1 D:HIS381 3.8 57.1 1.0 CE1 D:TYR517 3.9 60.4 1.0 CG D:HIS381 3.9 55.3 1.0 OH D:TYR517 3.9 57.0 1.0 ND1 D:HIS404 3.9 44.4 1.0 CG D:HIS377 4.0 52.6 1.0 ND1 D:HIS377 4.1 54.1 1.0 CG D:HIS404 4.2 43.5 1.0 CZ D:TYR517 4.2 59.7 1.0 NE2 D:HIS224 4.2 45.3 1.0 CE2 D:PHE400 4.2 42.6 1.0 CZ D:PHE400 4.6 45.6 1.0 CE1 D:HIS224 4.6 46.0 1.0 CE1 D:PHE220 4.6 50.7 1.0 CD2 D:HIS224 4.7 45.3 1.0 CD2 D:LEU403 4.7 46.5 1.0 CZ D:PHE220 4.8 45.7 1.0 CD1 D:TYR517 4.8 69.2 1.0 CD2 D:PHE400 4.8 39.2 1.0 NE2 D:HIS215 4.9 55.7 1.0 CD2 D:HIS215 4.9 53.1 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