Zinc in PDB 5m8r: Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine, PDB code: 5m8r 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)	47.74 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.353, 139.727, 190.951, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.9

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine (pdb code 5m8r). 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 (T391V-R374S- Y362F) in Complex with Mimosine, PDB code: 5m8r:
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 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:28.1 occ:1.00 O A:HOH602 2.0 23.7 1.0 NE2 A:HIS377 2.1 27.0 1.0 NE2 A:HIS381 2.1 27.2 1.0 NE2 A:HIS404 2.1 29.0 1.0 CD2 A:HIS377 3.0 30.4 1.0 CE1 A:HIS381 3.0 29.9 1.0 CD2 A:HIS381 3.1 28.4 1.0 CE1 A:HIS404 3.1 27.9 1.0 CE1 A:HIS377 3.1 31.9 1.0 CD2 A:HIS404 3.1 23.7 1.0 O4 A:MMS511 3.2 31.9 1.0 ZN A:ZN509 3.6 27.8 1.0 O3 A:MMS511 3.8 28.7 1.0 CE2 A:PHE400 3.9 23.4 1.0 C7 A:MMS511 4.0 29.4 1.0 ND1 A:HIS381 4.1 33.2 1.0 ND1 A:HIS404 4.2 24.5 1.0 CG A:HIS381 4.2 31.8 1.0 ND1 A:HIS377 4.2 28.8 1.0 CG A:HIS377 4.2 26.7 1.0 C6 A:MMS511 4.2 30.9 1.0 CG A:HIS404 4.2 24.0 1.0 NE2 A:HIS224 4.2 26.4 1.0 CD2 A:LEU403 4.4 30.9 1.0 CZ A:PHE400 4.4 24.3 1.0 CD2 A:PHE400 4.5 23.2 1.0 CD2 A:HIS224 4.5 23.1 1.0 CE1 A:PHE220 4.6 30.6 1.0 NE2 A:HIS215 4.8 28.3 1.0 CZ A:PHE220 4.9 27.1 1.0 C8 A:MMS511 4.9 29.9 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:27.8 occ:1.00 NE2 A:HIS192 2.0 22.2 1.0 NE2 A:HIS224 2.0 26.4 1.0 NE2 A:HIS215 2.1 28.3 1.0 O A:HOH602 2.1 23.7 1.0 CE1 A:HIS224 2.8 26.4 1.0 CE1 A:HIS192 2.9 20.0 1.0 CE1 A:HIS215 2.9 28.4 1.0 CD2 A:HIS192 3.1 22.8 1.0 CD2 A:HIS215 3.1 24.1 1.0 CD2 A:HIS224 3.2 23.1 1.0 ZN A:ZN508 3.6 28.1 1.0 O4 A:MMS511 3.7 31.9 1.0 ND1 A:HIS224 4.0 26.7 1.0 NE2 A:HIS404 4.0 29.0 1.0 CE2 A:PHE400 4.0 23.4 1.0 CZ A:PHE400 4.0 24.3 1.0 ND1 A:HIS192 4.1 13.4 1.0 ND1 A:HIS215 4.1 28.7 1.0 O3 A:MMS511 4.1 28.7 1.0 CG A:HIS192 4.2 18.2 1.0 CG A:HIS224 4.2 25.1 1.0 CG A:HIS215 4.2 29.2 1.0 CE1 A:HIS404 4.5 27.9 1.0 CG2 A:VAL391 4.7 26.0 1.0 CE1 A:PHE220 4.8 30.6 1.0 C7 A:MMS511 4.8 29.4 1.0 NE2 A:HIS377 4.9 27.0 1.0 C6 A:MMS511 4.9 30.9 1.0 CD2 A:HIS404 4.9 23.7 1.0 OG A:SER214 5.0 27.5 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:46.4 occ:1.00 OE2 B:GLU66 1.9 46.3 1.0 ND1 B:HIS100 2.1 47.1 1.0 ND1 A:HIS100 2.1 41.5 1.0 OE2 A:GLU66 2.2 34.1 1.0 CD B:GLU66 2.6 46.3 1.0 OE1 B:GLU66 2.7 49.0 1.0 OE1 A:GLU66 2.8 43.4 1.0 CD A:GLU66 2.9 38.8 1.0 CE1 A:HIS100 2.9 39.8 1.0 CE1 B:HIS100 2.9 46.5 1.0 CG A:HIS100 3.2 42.2 1.0 CG B:HIS100 3.2 44.0 1.0 CB B:HIS100 3.6 37.6 1.0 CB A:HIS100 3.6 35.4 1.0 NE B:ARG64 3.8 45.5 1.0 NH2 B:ARG64 3.9 39.9 1.0 NH2 A:ARG64 3.9 43.0 1.0 NE2 A:HIS100 4.0 43.6 1.0 CG B:GLU66 4.0 38.0 1.0 NE A:ARG64 4.1 44.2 1.0 NE2 B:HIS100 4.1 42.2 1.0 CD2 A:HIS100 4.2 44.9 1.0 CD2 B:HIS100 4.2 43.6 1.0 CZ B:ARG64 4.3 43.5 1.0 CG A:GLU66 4.3 35.6 1.0 CZ A:ARG64 4.5 44.1 1.0 CB B:GLU66 4.7 39.0 1.0 CD B:ARG64 4.9 44.2 1.0 CG B:ARG64 4.9 40.5 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn512 b:24.6 occ:1.00 O B:HOH602 2.0 25.6 1.0 NE2 B:HIS192 2.0 21.3 1.0 NE2 B:HIS224 2.1 27.8 1.0 NE2 B:HIS215 2.1 23.7 1.0 CE1 B:HIS224 2.8 22.0 1.0 CE1 B:HIS192 2.9 25.6 1.0 CE1 B:HIS215 2.9 23.5 1.0 CD2 B:HIS192 3.1 21.7 1.0 CD2 B:HIS224 3.2 22.9 1.0 CD2 B:HIS215 3.2 24.6 1.0 ZN B:ZN513 3.6 23.8 1.0 O4 B:MMS514 3.6 28.1 1.0 CZ B:PHE400 3.8 24.7 1.0 CE2 B:PHE400 3.9 26.1 1.0 ND1 B:HIS224 4.0 21.6 1.0 ND1 B:HIS192 4.0 20.5 1.0 O3 B:MMS514 4.1 24.3 1.0 NE2 B:HIS404 4.1 22.9 1.0 ND1 B:HIS215 4.1 26.7 1.0 CG B:HIS192 4.2 26.7 1.0 CG B:HIS224 4.2 23.9 1.0 CG B:HIS215 4.3 26.5 1.0 CE1 B:HIS404 4.3 24.3 1.0 CG2 B:VAL391 4.6 27.7 1.0 C7 B:MMS514 4.7 24.5 1.0 C6 B:MMS514 4.8 27.0 1.0 CE1 B:PHE220 4.9 27.1 1.0 NE2 B:HIS377 4.9 23.5 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn513 b:23.8 occ:1.00 O B:HOH602 2.0 25.6 1.0 NE2 B:HIS377 2.0 23.5 1.0 NE2 B:HIS404 2.0 22.9 1.0 NE2 B:HIS381 2.1 23.6 1.0 CE1 B:HIS404 2.8 24.3 1.0 CD2 B:HIS377 3.0 28.0 1.0 CD2 B:HIS381 3.0 21.8 1.0 CE1 B:HIS381 3.0 21.9 1.0 CE1 B:HIS377 3.0 23.9 1.0 O4 B:MMS514 3.2 28.1 1.0 CD2 B:HIS404 3.2 23.8 1.0 ZN B:ZN512 3.6 24.6 1.0 O3 B:MMS514 3.7 24.3 1.0 CE2 B:PHE400 3.9 26.1 1.0 C7 B:MMS514 3.9 24.5 1.0 ND1 B:HIS404 4.0 19.6 1.0 ND1 B:HIS381 4.1 24.9 1.0 C6 B:MMS514 4.1 27.0 1.0 CG B:HIS381 4.1 28.0 1.0 ND1 B:HIS377 4.1 26.0 1.0 CG B:HIS377 4.1 27.0 1.0 CG B:HIS404 4.2 24.1 1.0 NE2 B:HIS224 4.3 27.8 1.0 CD2 B:LEU403 4.4 22.2 1.0 CZ B:PHE400 4.4 24.7 1.0 CD2 B:PHE400 4.5 22.1 1.0 CE1 B:PHE220 4.6 27.1 1.0 CD2 B:HIS224 4.7 22.9 1.0 NE2 B:HIS215 4.8 23.7 1.0 C8 B:MMS514 4.8 25.1 1.0 CZ B:PHE220 4.9 26.3 1.0 CE1 B:HIS224 5.0 22.0 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn514 b:25.0 occ:1.00 O C:HOH603 1.9 20.0 1.0 NE2 C:HIS404 2.0 20.4 1.0 NE2 C:HIS377 2.1 25.8 1.0 NE2 C:HIS381 2.1 25.8 1.0 CE1 C:HIS404 2.7 22.5 1.0 CD2 C:HIS381 3.0 20.9 1.0 CD2 C:HIS377 3.0 30.0 1.0 CE1 C:HIS381 3.1 25.1 1.0 CE1 C:HIS377 3.1 27.6 1.0 CD2 C:HIS404 3.2 21.9 1.0 O4 C:MMS516 3.4 28.4 1.0 ZN C:ZN515 3.6 23.5 1.0 O3 C:MMS516 3.8 30.4 1.0 ND1 C:HIS404 3.9 18.3 1.0 CE2 C:PHE400 4.0 21.7 1.0 C7 C:MMS516 4.1 33.0 1.0 CG C:HIS381 4.1 23.6 1.0 ND1 C:HIS381 4.1 24.9 1.0 CG C:HIS377 4.2 25.8 1.0 CG C:HIS404 4.2 25.7 1.0 ND1 C:HIS377 4.2 28.9 1.0 NE2 C:HIS224 4.2 18.5 1.0 C6 C:MMS516 4.2 30.1 1.0 CZ C:PHE400 4.4 18.7 1.0 CD2 C:HIS224 4.4 21.2 1.0 CD2 C:LEU403 4.4 22.3 1.0 CD2 C:PHE400 4.6 22.5 1.0 CE1 C:PHE220 4.7 27.6 1.0 CZ C:PHE220 4.9 27.3 1.0 NE2 C:HIS215 5.0 26.9 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn515 b:23.5 occ:1.00 O C:HOH603 2.0 20.0 1.0 NE2 C:HIS224 2.0 18.5 1.0 NE2 C:HIS192 2.1 21.5 1.0 NE2 C:HIS215 2.1 26.9 1.0 CE1 C:HIS224 2.8 22.0 1.0 CD2 C:HIS192 3.0 19.2 1.0 CD2 C:HIS215 3.0 25.0 1.0 CE1 C:HIS192 3.0 21.0 1.0 CE1 C:HIS215 3.1 28.0 1.0 CD2 C:HIS224 3.2 21.2 1.0 ZN C:ZN514 3.6 25.0 1.0 O4 C:MMS516 3.9 28.4 1.0 CZ C:PHE400 4.0 18.7 1.0 ND1 C:HIS224 4.0 21.2 1.0 CE2 C:PHE400 4.0 21.7 1.0 O3 C:MMS516 4.1 30.4 1.0 ND1 C:HIS215 4.1 30.1 1.0 ND1 C:HIS192 4.2 21.2 1.0 NE2 C:HIS404 4.2 20.4 1.0 CG C:HIS215 4.2 28.6 1.0 CG C:HIS192 4.2 19.5 1.0 CG C:HIS224 4.2 20.6 1.0 CE1 C:HIS404 4.4 22.5 1.0 CG2 C:VAL391 4.7 27.9 1.0 C7 C:MMS516 4.9 33.0 1.0 CE1 C:PHE220 4.9 27.6 1.0 C6 C:MMS516 4.9 30.1 1.0 NE2 C:HIS377 5.0 25.8 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn507 b:32.5 occ:1.00 NE2 D:HIS192 1.9 28.8 1.0 O D:HOH606 2.0 24.4 1.0 NE2 D:HIS224 2.1 37.4 1.0 NE2 D:HIS215 2.1 37.5 1.0 CE1 D:HIS192 2.8 31.3 1.0 CE1 D:HIS224 2.9 31.8 1.0 CE1 D:HIS215 3.0 34.5 1.0 CD2 D:HIS192 3.1 30.8 1.0 CD2 D:HIS215 3.1 30.4 1.0 CD2 D:HIS224 3.2 32.5 1.0 ZN D:ZN508 3.5 31.8 1.0 O4 D:MMS509 3.7 46.8 1.0 CE2 D:PHE400 3.9 30.6 1.0 ND1 D:HIS192 3.9 23.4 1.0 CZ D:PHE400 4.0 26.6 1.0 NE2 D:HIS404 4.0 36.2 1.0 O3 D:MMS509 4.1 34.8 1.0 ND1 D:HIS224 4.1 29.1 1.0 CG D:HIS192 4.1 27.7 1.0 ND1 D:HIS215 4.1 36.4 1.0 CG D:HIS215 4.2 31.7 1.0 CE1 D:HIS404 4.2 33.1 1.0 CG D:HIS224 4.3 31.5 1.0 C7 D:MMS509 4.7 39.9 1.0 CE1 D:PHE220 4.8 28.8 1.0 C6 D:MMS509 4.8 39.9 1.0 CG2 D:VAL391 4.9 39.9 1.0 NE2 D:HIS377 4.9 32.9 1.0 OG D:SER394 5.0 37.4 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Mimosine


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 (T391V-R374S- Y362F) in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn508 b:31.8 occ:1.00 O D:HOH606 1.8 24.4 1.0 NE2 D:HIS377 2.0 32.9 1.0 NE2 D:HIS404 2.0 36.2 1.0 NE2 D:HIS381 2.1 36.1 1.0 CE1 D:HIS404 2.6 33.1 1.0 CE1 D:HIS381 2.9 36.4 1.0 CE1 D:HIS377 2.9 31.2 1.0 CD2 D:HIS377 3.0 33.5 1.0 CD2 D:HIS381 3.1 38.3 1.0 CD2 D:HIS404 3.2 31.7 1.0 O4 D:MMS509 3.3 46.8 1.0 ZN D:ZN507 3.5 32.5 1.0 ND1 D:HIS404 3.8 30.5 1.0 O3 D:MMS509 3.9 34.8 1.0 CE2 D:PHE400 3.9 30.6 1.0 C7 D:MMS509 4.0 39.9 1.0 ND1 D:HIS381 4.0 38.7 1.0 ND1 D:HIS377 4.1 33.8 1.0 CG D:HIS381 4.1 40.7 1.0 CG D:HIS377 4.1 26.9 1.0 CG D:HIS404 4.1 33.4 1.0 NE2 D:HIS224 4.2 37.4 1.0 C6 D:MMS509 4.2 39.9 1.0 CE1 D:PHE220 4.4 28.8 1.0 CD2 D:HIS224 4.5 32.5 1.0 CD2 D:PHE400 4.5 28.1 1.0 CZ D:PHE400 4.5 26.6 1.0 CD2 D:LEU403 4.7 32.2 1.0 CZ D:PHE220 4.7 30.6 1.0 NE2 D:HIS215 4.8 37.5 1.0 C8 D:MMS509 4.9 39.6 1.0 CD2 D:HIS215 5.0 30.4 1.0 CE1 D:HIS224 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