Zinc in PDB 5m8l: Crystal Structure of Human Tyrosinase Related Protein 1

The structure of Crystal Structure of Human Tyrosinase Related Protein 1, PDB code: 5m8l 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)	47.47 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.424, 141.758, 191.741, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 (pdb code 5m8l). 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, PDB code: 5m8l:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:30.9 occ:1.00 NE2 A:HIS192 2.0 21.2 1.0 NE2 A:HIS224 2.1 23.5 1.0 O A:HOH671 2.1 23.9 1.0 NE2 A:HIS215 2.2 24.1 1.0 CE1 A:HIS192 2.9 19.0 1.0 CE1 A:HIS224 2.9 22.8 1.0 CE1 A:HIS215 3.1 23.8 1.0 CD2 A:HIS192 3.1 19.6 1.0 CD2 A:HIS215 3.2 24.1 1.0 CD2 A:HIS224 3.2 23.4 1.0 ZN A:ZN513 3.6 28.0 1.0 NE2 A:HIS404 3.9 24.5 1.0 CE2 A:PHE400 4.0 20.8 1.0 O A:HOH663 4.0 31.1 1.0 ND1 A:HIS192 4.1 19.1 1.0 CZ A:PHE400 4.1 21.8 1.0 ND1 A:HIS224 4.1 24.3 1.0 CG A:HIS192 4.2 16.9 1.0 ND1 A:HIS215 4.2 23.6 1.0 CG A:HIS224 4.2 25.5 1.0 CG A:HIS215 4.3 26.6 1.0 CE1 A:HIS404 4.4 25.4 1.0 NE2 A:HIS377 4.8 28.9 1.0 CD2 A:HIS404 4.9 20.7 1.0 CE1 A:PHE220 5.0 23.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:28.0 occ:1.00 NE2 A:HIS377 2.0 28.9 1.0 NE2 A:HIS404 2.0 24.5 1.0 O A:HOH671 2.1 23.9 1.0 NE2 A:HIS381 2.1 27.2 1.0 CE1 A:HIS404 2.8 25.4 1.0 CE1 A:HIS377 2.9 24.3 1.0 CD2 A:HIS377 3.0 29.0 1.0 CD2 A:HIS381 3.0 25.9 1.0 CE1 A:HIS381 3.1 25.0 1.0 CD2 A:HIS404 3.1 20.7 1.0 ZN A:ZN512 3.6 30.9 1.0 ND1 A:HIS404 4.0 24.2 1.0 ND1 A:HIS377 4.0 28.5 1.0 CE2 A:PHE400 4.0 20.8 1.0 O A:HOH663 4.1 31.1 1.0 CG A:HIS377 4.1 31.3 1.0 ND1 A:HIS381 4.1 27.5 1.0 CG A:HIS381 4.1 27.3 1.0 CG A:HIS404 4.2 23.0 1.0 NE2 A:HIS224 4.3 23.5 1.0 CD2 A:LEU403 4.5 25.0 1.0 CD2 A:HIS224 4.5 23.4 1.0 CZ A:PHE400 4.6 21.8 1.0 CD2 A:PHE400 4.6 21.2 1.0 CE1 A:PHE220 4.7 23.8 1.0 NE2 A:HIS215 5.0 24.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn514 b:83.2 occ:1.00 OE1 B:GLU66 1.6 43.5 1.0 OE2 A:GLU66 1.8 39.0 1.0 ND1 B:HIS100 1.9 43.5 1.0 ND1 A:HIS100 2.1 43.5 1.0 CD B:GLU66 2.4 42.9 1.0 CD A:GLU66 2.5 41.1 1.0 CE1 B:HIS100 2.6 37.8 1.0 OE1 A:GLU66 2.6 44.1 1.0 OE2 B:GLU66 2.7 43.6 1.0 CE1 A:HIS100 2.9 38.6 1.0 CG B:HIS100 3.1 39.6 1.0 CG A:HIS100 3.2 36.2 1.0 CB A:HIS100 3.6 34.1 1.0 CB B:HIS100 3.7 37.4 1.0 CG B:GLU66 3.7 37.9 1.0 NH2 A:ARG64 3.7 40.2 1.0 NE2 B:HIS100 3.8 30.9 1.0 NE A:ARG64 3.9 36.6 1.0 NH2 B:ARG64 4.0 35.9 1.0 CG A:GLU66 4.0 35.6 1.0 CD2 B:HIS100 4.1 37.3 1.0 NE2 A:HIS100 4.1 39.1 1.0 NE B:ARG64 4.2 35.2 1.0 CZ A:ARG64 4.2 36.3 1.0 CD2 A:HIS100 4.2 37.8 1.0 CZ B:ARG64 4.6 36.4 1.0 CB B:GLU66 4.7 35.5 1.0 CB A:GLU66 4.7 32.8 1.0 CD A:ARG64 5.0 34.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn516 b:60.9 occ:1.00 NE2 B:HIS192 1.9 26.9 1.0 NE2 B:HIS215 2.0 34.9 1.0 O B:HOH652 2.1 33.9 1.0 NE2 B:HIS224 2.1 36.5 1.0 CE1 B:HIS192 2.7 30.4 1.0 CE1 B:HIS215 2.9 29.8 1.0 CE1 B:HIS224 3.0 33.9 1.0 CD2 B:HIS192 3.0 27.6 1.0 CD2 B:HIS215 3.1 30.3 1.0 CD2 B:HIS224 3.2 27.4 1.0 ZN B:ZN517 3.6 27.7 1.0 ND1 B:HIS192 3.9 24.8 1.0 ND1 B:HIS215 4.0 28.1 1.0 CE2 B:PHE400 4.0 27.4 1.0 NE2 B:HIS404 4.0 26.9 1.0 CZ B:PHE400 4.0 22.8 1.0 CG B:HIS192 4.1 23.2 1.0 ND1 B:HIS224 4.1 31.5 1.0 CG B:HIS215 4.2 27.5 1.0 O B:HOH650 4.3 37.7 1.0 CG B:HIS224 4.3 28.1 1.0 CE1 B:HIS404 4.4 27.6 1.0 CE1 B:PHE220 4.8 24.6 1.0 NE2 B:HIS377 4.9 22.4 1.0 OG B:SER394 5.0 31.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn517 b:27.7 occ:1.00 NE2 B:HIS381 1.9 35.5 1.0 NE2 B:HIS377 2.0 22.4 1.0 NE2 B:HIS404 2.0 26.9 1.0 O B:HOH652 2.0 33.9 1.0 CE1 B:HIS404 2.8 27.6 1.0 CE1 B:HIS381 2.9 28.3 1.0 CE1 B:HIS377 2.9 21.4 1.0 CD2 B:HIS381 2.9 28.9 1.0 CD2 B:HIS377 3.0 31.9 1.0 CD2 B:HIS404 3.2 25.7 1.0 ZN B:ZN516 3.6 60.9 1.0 ND1 B:HIS381 3.9 28.6 1.0 ND1 B:HIS404 3.9 25.6 1.0 CE2 B:PHE400 4.0 27.4 1.0 CG B:HIS381 4.0 28.8 1.0 ND1 B:HIS377 4.0 22.3 1.0 O B:HOH650 4.1 37.7 1.0 CG B:HIS377 4.1 26.4 1.0 CG B:HIS404 4.2 24.5 1.0 NE2 B:HIS224 4.3 36.5 1.0 CZ B:PHE400 4.5 22.8 1.0 CD2 B:HIS224 4.5 27.4 1.0 CD2 B:PHE400 4.6 26.9 1.0 CD2 B:LEU403 4.7 24.9 1.0 CE1 B:PHE220 4.7 24.6 1.0 NE2 B:HIS215 4.8 34.9 1.0 CZ B:PHE220 4.9 21.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn512 b:44.2 occ:1.00 NE2 C:HIS192 1.9 38.8 1.0 NE2 C:HIS215 1.9 45.9 1.0 O C:HOH615 2.1 40.8 1.0 NE2 C:HIS224 2.2 42.3 1.0 CE1 C:HIS192 2.8 41.4 1.0 CE1 C:HIS215 2.9 44.8 1.0 CE1 C:HIS224 2.9 43.1 1.0 CD2 C:HIS215 3.0 43.9 1.0 CD2 C:HIS192 3.0 35.4 1.0 CD2 C:HIS224 3.3 43.1 1.0 ZN C:ZN513 3.5 44.2 1.0 NE2 C:HIS404 3.9 43.6 1.0 ND1 C:HIS192 3.9 39.6 1.0 ND1 C:HIS215 4.0 44.8 1.0 CE2 C:PHE400 4.0 41.6 1.0 CG C:HIS192 4.1 35.4 1.0 CG C:HIS215 4.1 42.6 1.0 CZ C:PHE400 4.1 39.7 1.0 ND1 C:HIS224 4.1 43.1 1.0 CE1 C:HIS404 4.3 40.5 1.0 CG C:HIS224 4.3 39.6 1.0 O C:HOH610 4.4 38.4 1.0 NE2 C:HIS377 4.8 44.3 1.0 OG C:SER394 4.9 41.0 1.0 CE1 C:HIS377 4.9 47.9 1.0 CD2 C:HIS404 5.0 43.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn513 b:44.2 occ:1.00 NE2 C:HIS377 1.8 44.3 1.0 NE2 C:HIS404 2.1 43.6 1.0 O C:HOH615 2.1 40.8 1.0 NE2 C:HIS381 2.3 49.7 1.0 CE1 C:HIS377 2.5 47.9 1.0 CE1 C:HIS404 2.7 40.5 1.0 CD2 C:HIS377 3.0 42.0 1.0 CD2 C:HIS381 3.1 48.0 1.0 CE1 C:HIS381 3.1 49.1 1.0 CD2 C:HIS404 3.2 43.8 1.0 ZN C:ZN512 3.5 44.2 1.0 ND1 C:HIS377 3.7 45.9 1.0 ND1 C:HIS404 3.9 38.2 1.0 CG C:HIS377 4.0 41.7 1.0 CE2 C:PHE400 4.0 41.6 1.0 ND1 C:HIS381 4.1 50.0 1.0 CG C:HIS381 4.1 49.2 1.0 CG C:HIS404 4.2 42.0 1.0 NE2 C:HIS224 4.3 42.3 1.0 O C:HOH610 4.3 38.4 1.0 CE1 C:PHE220 4.6 40.4 1.0 CZ C:PHE400 4.6 39.7 1.0 CD2 C:PHE400 4.6 44.7 1.0 CD2 C:HIS224 4.7 43.1 1.0 NE2 C:HIS215 4.8 45.9 1.0 CE1 C:HIS224 4.9 43.1 1.0 CD2 C:LEU403 4.9 45.6 1.0 CD2 C:HIS215 4.9 43.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn518 b:31.8 occ:1.00 NE2 D:HIS224 1.8 25.1 1.0 NE2 D:HIS215 2.1 31.5 1.0 NE2 D:HIS192 2.1 20.9 1.0 O D:HOH629 2.3 55.0 1.0 CE1 D:HIS224 2.6 27.3 1.0 CE1 D:HIS215 3.0 28.0 1.0 CD2 D:HIS224 3.0 29.0 1.0 CD2 D:HIS192 3.1 22.4 1.0 CE1 D:HIS192 3.1 21.8 1.0 CD2 D:HIS215 3.1 29.0 1.0 ZN D:ZN519 3.6 42.7 1.0 ND1 D:HIS224 3.8 25.2 1.0 CE2 D:PHE400 4.0 25.2 1.0 CZ D:PHE400 4.0 25.8 1.0 NE2 D:HIS404 4.0 33.9 1.0 CG D:HIS224 4.0 27.2 1.0 ND1 D:HIS215 4.1 30.6 1.0 CG D:HIS215 4.2 30.5 1.0 ND1 D:HIS192 4.2 22.3 1.0 CG D:HIS192 4.3 22.5 1.0 CE1 D:HIS404 4.4 33.5 1.0 O D:HOH625 4.6 30.9 1.0 CE1 D:PHE220 4.8 26.7 1.0 CD2 D:HIS404 4.9 31.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn519 b:42.7 occ:1.00 NE2 D:HIS404 1.9 33.9 1.0 NE2 D:HIS377 1.9 34.2 1.0 NE2 D:HIS381 2.1 29.3 1.0 O D:HOH629 2.1 55.0 1.0 CE1 D:HIS404 2.8 33.5 1.0 CE1 D:HIS377 2.8 33.1 1.0 CE1 D:HIS381 3.0 31.8 1.0 CD2 D:HIS404 3.0 31.1 1.0 CD2 D:HIS381 3.0 28.4 1.0 CD2 D:HIS377 3.1 33.6 1.0 ZN D:ZN518 3.6 31.8 1.0 ND1 D:HIS404 3.9 27.2 1.0 CE2 D:PHE400 3.9 25.2 1.0 ND1 D:HIS377 3.9 28.1 1.0 ND1 D:HIS381 4.0 28.4 1.0 CG D:HIS404 4.1 28.3 1.0 NE2 D:HIS224 4.1 25.1 1.0 CG D:HIS381 4.1 31.0 1.0 CG D:HIS377 4.1 31.1 1.0 O D:HOH625 4.3 30.9 1.0 CD2 D:HIS224 4.3 29.0 1.0 CD2 D:LEU403 4.5 27.3 1.0 CZ D:PHE400 4.5 25.8 1.0 CD2 D:PHE400 4.6 29.8 1.0 CE1 D:PHE220 4.6 26.7 1.0 NE2 D:HIS215 4.8 31.5 1.0 CZ D:PHE220 4.9 28.8 1.0 CE1 D:HIS224 4.9 27.3 1.0 CD2 D:HIS215 5.0 29.0 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