Zinc in PDB 5m8q: Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid, PDB code: 5m8q 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)	47.88 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.640, 140.426, 191.559, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.5

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid (pdb code 5m8q). 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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid, PDB code: 5m8q:
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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn514 b:40.4 occ:1.00 NE2 A:HIS381 1.6 40.2 1.0 NE2 A:HIS404 2.0 28.2 1.0 O A:HOH601 2.0 43.0 1.0 NE2 A:HIS377 2.2 33.8 1.0 CE1 A:HIS381 2.5 41.3 1.0 CD2 A:HIS381 2.8 41.4 1.0 CD2 A:HIS404 2.9 30.6 1.0 CD2 A:HIS377 3.1 34.3 1.0 CE1 A:HIS404 3.1 35.6 1.0 CE1 A:HIS377 3.2 39.6 1.0 O3 A:KOJ516 3.5 54.3 1.0 ZN A:ZN515 3.5 51.4 1.0 ND1 A:HIS381 3.6 42.2 1.0 O2 A:KOJ516 3.8 55.1 1.0 CG A:HIS381 3.8 44.5 1.0 CE2 A:PHE400 4.0 41.3 1.0 C3 A:KOJ516 4.0 54.3 1.0 CG A:HIS404 4.1 31.7 1.0 NE2 A:HIS224 4.1 29.2 1.0 ND1 A:HIS404 4.2 32.1 1.0 CG A:HIS377 4.2 41.7 1.0 ND1 A:HIS377 4.2 38.3 1.0 C2 A:KOJ516 4.2 54.1 1.0 CZ A:PHE400 4.4 33.7 1.0 CD2 A:HIS224 4.5 34.7 1.0 CD2 A:LEU403 4.6 32.0 1.0 CD2 A:PHE400 4.7 36.1 1.0 CE1 A:PHE220 4.7 37.6 1.0 CE1 A:HIS224 4.9 35.8 1.0 NE2 A:HIS215 5.0 49.6 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn515 b:51.4 occ:1.00 NE2 A:HIS215 2.1 49.6 1.0 O A:HOH601 2.1 43.0 1.0 NE2 A:HIS192 2.2 39.2 1.0 NE2 A:HIS224 2.4 29.2 1.0 CE1 A:HIS224 3.0 35.8 1.0 CE1 A:HIS215 3.0 50.5 1.0 O2 A:KOJ516 3.0 55.1 1.0 CD2 A:HIS215 3.1 48.7 1.0 CE1 A:HIS192 3.2 39.3 1.0 CD2 A:HIS192 3.2 37.7 1.0 O3 A:KOJ516 3.4 54.3 1.0 ZN A:ZN514 3.5 40.4 1.0 CD2 A:HIS224 3.6 34.7 1.0 CE2 A:PHE400 4.1 41.3 1.0 ND1 A:HIS215 4.1 49.6 1.0 C2 A:KOJ516 4.1 54.1 1.0 C3 A:KOJ516 4.2 54.3 1.0 CG A:HIS215 4.2 43.6 1.0 CZ A:PHE400 4.2 33.7 1.0 ND1 A:HIS224 4.2 36.9 1.0 NE2 A:HIS404 4.3 28.2 1.0 ND1 A:HIS192 4.3 41.0 1.0 CG A:HIS192 4.3 41.0 1.0 CG A:HIS224 4.6 36.6 1.0 NE2 A:HIS381 4.6 40.2 1.0 NE2 A:HIS377 4.7 33.8 1.0 OG A:SER214 4.8 39.8 1.0 CE1 A:HIS404 4.8 35.6 1.0 OG A:SER394 4.8 43.6 1.0 CE1 A:HIS381 4.9 41.3 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:78.4 occ:1.00 O B:HOH601 1.9 66.9 1.0 NE2 B:HIS192 2.3 59.1 1.0 NE2 B:HIS215 2.3 68.7 1.0 NE2 B:HIS224 2.6 62.1 1.0 ZN B:ZN507 2.8 68.7 1.0 CE1 B:HIS192 2.9 61.3 1.0 CE1 B:HIS215 3.1 69.7 1.0 CE1 B:HIS224 3.3 70.8 1.0 O3 B:KOJ508 3.4 75.4 1.0 O2 B:KOJ508 3.4 74.8 1.0 CD2 B:HIS192 3.4 54.4 1.0 CD2 B:HIS215 3.5 63.9 1.0 CD2 B:HIS224 3.7 66.0 1.0 CE2 B:PHE400 3.7 59.1 1.0 NE2 B:HIS404 4.0 64.8 1.0 CZ B:PHE400 4.0 53.5 1.0 ND1 B:HIS192 4.1 57.8 1.0 C3 B:KOJ508 4.2 75.5 1.0 C2 B:KOJ508 4.3 74.1 1.0 ND1 B:HIS215 4.3 66.4 1.0 CG B:HIS192 4.4 53.5 1.0 ND1 B:HIS224 4.5 71.5 1.0 CG B:HIS215 4.5 70.0 1.0 CE1 B:HIS381 4.5 68.0 1.0 NE2 B:HIS377 4.5 72.1 1.0 CE1 B:HIS404 4.6 65.8 1.0 OG B:SER394 4.7 67.9 1.0 CG B:HIS224 4.7 64.1 1.0 NE2 B:HIS381 4.7 66.7 1.0 CE1 B:HIS377 4.8 71.2 1.0 CD2 B:HIS404 4.9 64.6 1.0 CD2 B:PHE400 5.0 55.5 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:68.7 occ:1.00 O B:HOH601 1.9 66.9 1.0 NE2 B:HIS404 2.1 64.8 1.0 NE2 B:HIS377 2.2 72.1 1.0 NE2 B:HIS381 2.3 66.7 1.0 CE1 B:HIS381 2.8 68.0 1.0 ZN B:ZN506 2.8 78.4 1.0 CE1 B:HIS404 3.0 65.8 1.0 CD2 B:HIS404 3.1 64.6 1.0 CE1 B:HIS377 3.1 71.2 1.0 CD2 B:HIS377 3.2 70.9 1.0 CD2 B:HIS381 3.3 68.8 1.0 O3 B:KOJ508 3.5 75.4 1.0 CE2 B:PHE400 3.6 59.1 1.0 ND1 B:HIS381 3.9 68.5 1.0 NE2 B:HIS224 3.9 62.1 1.0 CZ B:PHE400 4.1 53.5 1.0 C3 B:KOJ508 4.1 75.5 1.0 ND1 B:HIS404 4.2 62.1 1.0 CG B:HIS381 4.2 70.6 1.0 CG B:HIS404 4.2 64.5 1.0 ND1 B:HIS377 4.2 74.4 1.0 CD2 B:HIS224 4.2 66.0 1.0 NE2 B:HIS215 4.3 68.7 1.0 CG B:HIS377 4.3 72.0 1.0 O2 B:KOJ508 4.4 74.8 1.0 CD2 B:PHE400 4.4 55.5 1.0 CE1 B:HIS224 4.5 70.8 1.0 C2 B:KOJ508 4.5 74.1 1.0 CD2 B:LEU403 4.5 59.3 1.0 CE1 B:PHE220 4.7 67.1 1.0 CD2 B:HIS215 4.8 63.9 1.0 NE2 B:HIS192 4.9 59.1 1.0 CG B:HIS224 5.0 64.1 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn512 b:42.6 occ:1.00 NE2 C:HIS404 2.0 40.2 1.0 O C:HOH601 2.1 45.2 1.0 NE2 C:HIS377 2.1 42.3 1.0 NE2 C:HIS381 2.1 45.9 1.0 CE1 C:HIS404 2.8 44.6 1.0 CD2 C:HIS377 3.0 42.6 1.0 CD2 C:HIS381 3.0 45.0 1.0 CE1 C:HIS381 3.1 44.4 1.0 CD2 C:HIS404 3.1 40.9 1.0 CE1 C:HIS377 3.1 43.1 1.0 O3 C:KOJ514 3.4 53.4 1.0 ZN C:ZN513 3.5 60.4 1.0 O2 C:KOJ514 3.8 57.2 1.0 CE2 C:PHE400 3.9 50.4 1.0 C3 C:KOJ514 3.9 54.7 1.0 ND1 C:HIS404 4.0 42.0 1.0 C2 C:KOJ514 4.1 55.4 1.0 NE2 C:HIS224 4.1 44.5 1.0 ND1 C:HIS381 4.1 48.8 1.0 CG C:HIS377 4.1 41.8 1.0 CG C:HIS381 4.1 47.4 1.0 CG C:HIS404 4.2 43.3 1.0 ND1 C:HIS377 4.2 43.2 1.0 CZ C:PHE400 4.2 45.1 1.0 CE1 C:PHE220 4.5 45.0 1.0 CD2 C:PHE400 4.6 45.7 1.0 CD2 C:HIS224 4.6 47.0 1.0 NE2 C:HIS215 4.7 45.3 1.0 CD2 C:LEU403 4.7 42.4 1.0 CE1 C:HIS224 4.7 45.3 1.0 CZ C:PHE220 4.9 46.9 1.0 C4 C:KOJ514 4.9 54.8 1.0 NE2 C:HIS192 5.0 52.5 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn513 b:60.4 occ:1.00 O C:HOH601 2.0 45.2 1.0 NE2 C:HIS192 2.0 52.5 1.0 NE2 C:HIS215 2.1 45.3 1.0 NE2 C:HIS224 2.3 44.5 1.0 CE1 C:HIS215 2.8 42.5 1.0 CE1 C:HIS224 2.9 45.3 1.0 CD2 C:HIS192 3.0 45.6 1.0 CE1 C:HIS192 3.0 49.5 1.0 CD2 C:HIS215 3.3 43.3 1.0 O3 C:KOJ514 3.5 53.4 1.0 ZN C:ZN512 3.5 42.6 1.0 O2 C:KOJ514 3.5 57.2 1.0 CD2 C:HIS224 3.6 47.0 1.0 CZ C:PHE400 3.9 45.1 1.0 ND1 C:HIS215 4.0 40.6 1.0 CE2 C:PHE400 4.0 50.4 1.0 ND1 C:HIS224 4.1 46.4 1.0 ND1 C:HIS192 4.1 50.7 1.0 CG C:HIS192 4.1 43.8 1.0 CG C:HIS215 4.2 39.6 1.0 NE2 C:HIS404 4.3 40.2 1.0 C3 C:KOJ514 4.4 54.7 1.0 C2 C:KOJ514 4.4 55.4 1.0 CG C:HIS224 4.5 47.3 1.0 CE1 C:HIS404 4.6 44.6 1.0 CG2 C:VAL391 4.7 50.5 1.0 OG C:SER394 4.8 55.2 1.0 NE2 C:HIS377 4.8 42.3 1.0 CE1 C:PHE220 4.9 45.0 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn515 b:58.8 occ:1.00 OE1 C:GLU66 1.9 59.5 1.0 OE2 D:GLU66 2.1 42.5 1.0 ND1 D:HIS100 2.1 58.5 1.0 ND1 C:HIS100 2.3 58.4 1.0 OE2 C:GLU66 2.3 60.7 1.0 CD C:GLU66 2.3 60.0 1.0 NH2 D:ARG64 2.5 60.0 1.0 CD D:GLU66 2.7 49.6 1.0 OE1 D:GLU66 2.8 52.4 1.0 CE1 C:HIS100 3.0 57.2 1.0 CE1 D:HIS100 3.1 59.5 1.0 CG D:HIS100 3.2 53.4 1.0 CG C:HIS100 3.3 56.1 1.0 CZ D:ARG64 3.4 58.7 1.0 CB D:HIS100 3.5 51.5 1.0 NE D:ARG64 3.6 61.2 1.0 CB C:HIS100 3.8 53.7 1.0 CG C:GLU66 3.8 58.9 1.0 NE2 C:HIS100 4.2 49.5 1.0 CG D:GLU66 4.2 49.8 1.0 NE2 D:HIS100 4.2 54.0 1.0 CD2 D:HIS100 4.3 55.3 1.0 CD2 C:HIS100 4.3 55.1 1.0 CZ C:ARG64 4.4 58.1 1.0 NE C:ARG64 4.5 60.0 1.0 NH2 C:ARG64 4.6 55.4 1.0 NH1 D:ARG64 4.6 58.3 1.0 NH1 C:ARG64 4.7 60.4 1.0 CB C:GLU66 4.7 54.4 1.0 CB D:GLU66 4.8 47.7 1.0 CD C:ARG64 4.9 48.3 1.0 CA D:HIS100 5.0 48.0 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn508 b:39.6 occ:1.00 O D:HOH601 1.9 47.8 1.0 NE2 D:HIS404 1.9 35.1 1.0 NE2 D:HIS377 2.0 44.8 1.0 NE2 D:HIS381 2.1 44.5 1.0 CE1 D:HIS404 2.8 39.7 1.0 CD2 D:HIS377 2.8 42.8 1.0 CD2 D:HIS381 2.9 42.6 1.0 CD2 D:HIS404 3.0 39.4 1.0 CE1 D:HIS377 3.1 41.8 1.0 CE1 D:HIS381 3.1 47.2 1.0 O3 D:KOJ510 3.3 56.1 1.0 ZN D:ZN509 3.4 53.4 1.0 CE2 D:PHE400 3.8 40.0 1.0 C3 D:KOJ510 3.9 52.9 1.0 ND1 D:HIS404 3.9 42.0 1.0 CG D:HIS377 4.0 44.1 1.0 ND1 D:HIS377 4.1 42.5 1.0 CG D:HIS381 4.1 47.3 1.0 O2 D:KOJ510 4.1 45.8 1.0 CG D:HIS404 4.1 43.4 1.0 ND1 D:HIS381 4.1 47.7 1.0 C2 D:KOJ510 4.3 51.4 1.0 NE2 D:HIS224 4.3 35.8 1.0 CZ D:PHE400 4.4 39.7 1.0 CE1 D:PHE220 4.5 42.1 1.0 CD2 D:PHE400 4.5 42.1 1.0 CD2 D:HIS224 4.6 39.4 1.0 C4 D:KOJ510 4.7 46.2 1.0 CD2 D:LEU403 4.8 41.2 1.0 CZ D:PHE220 4.9 44.1 1.0 NE2 D:HIS215 4.9 45.1 1.0

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


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 Mutant (T391V- R374S-Y362F) in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn509 b:53.4 occ:1.00 O D:HOH601 2.0 47.8 1.0 NE2 D:HIS215 2.1 45.1 1.0 NE2 D:HIS192 2.2 42.4 1.0 NE2 D:HIS224 2.7 35.8 1.0 O2 D:KOJ510 3.0 45.8 1.0 CE1 D:HIS215 3.0 42.6 1.0 CD2 D:HIS215 3.1 40.8 1.0 CE1 D:HIS192 3.1 42.8 1.0 CD2 D:HIS192 3.2 40.1 1.0 O3 D:KOJ510 3.2 56.1 1.0 CE1 D:HIS224 3.4 47.0 1.0 ZN D:ZN508 3.4 39.6 1.0 CD2 D:HIS224 3.8 39.4 1.0 C2 D:KOJ510 4.0 51.4 1.0 C3 D:KOJ510 4.0 52.9 1.0 CE2 D:PHE400 4.1 40.0 1.0 ND1 D:HIS215 4.1 40.7 1.0 CG D:HIS215 4.2 42.3 1.0 NE2 D:HIS404 4.2 35.1 1.0 ND1 D:HIS192 4.3 48.1 1.0 CG D:HIS192 4.3 36.2 1.0 CZ D:PHE400 4.3 39.7 1.0 CE1 D:HIS404 4.6 39.7 1.0 ND1 D:HIS224 4.6 44.9 1.0 NE2 D:HIS377 4.6 44.8 1.0 NE2 D:HIS381 4.8 44.5 1.0 CG D:HIS224 4.8 43.9 1.0 OG D:SER394 4.8 41.9 1.0 CE1 D:PHE220 4.9 42.1 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