Zinc in PDB 5m8m: Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Kojic Acid

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Kojic Acid, PDB code: 5m8m 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)	49.00 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.255, 141.535, 192.128, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.9

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Kojic Acid (pdb code 5m8m). 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 Kojic Acid, PDB code: 5m8m:
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 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:40.5 occ:1.00 O A:HOH601 1.8 34.8 1.0 NE2 A:HIS192 1.9 27.1 1.0 NE2 A:HIS215 2.1 29.0 1.0 NE2 A:HIS224 2.4 28.0 1.0 CE1 A:HIS192 2.8 24.7 1.0 CE1 A:HIS215 2.9 28.3 1.0 CD2 A:HIS192 3.0 24.0 1.0 CE1 A:HIS224 3.1 29.6 1.0 CD2 A:HIS215 3.2 26.7 1.0 O2 A:KOJ514 3.3 32.6 1.0 ZN A:ZN513 3.3 28.1 1.0 O3 A:KOJ514 3.5 46.6 1.0 CD2 A:HIS224 3.6 27.4 1.0 ND1 A:HIS192 4.0 24.4 1.0 NE2 A:HIS404 4.0 23.5 1.0 CZ A:PHE400 4.0 23.8 1.0 CG A:HIS192 4.1 23.8 1.0 ND1 A:HIS215 4.1 28.8 1.0 CE2 A:PHE400 4.1 21.4 1.0 CG A:HIS215 4.3 29.6 1.0 ND1 A:HIS224 4.3 29.1 1.0 C2 A:KOJ514 4.4 38.5 1.0 C3 A:KOJ514 4.4 44.1 1.0 CE1 A:HIS404 4.6 23.5 1.0 CG A:HIS224 4.6 27.7 1.0 NE2 A:HIS377 4.8 27.3 1.0 NE2 A:HIS381 4.9 27.0 1.0 CD2 A:HIS404 5.0 24.3 1.0 OG A:SER394 5.0 28.7 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:28.1 occ:1.00 O A:HOH601 1.9 34.8 1.0 NE2 A:HIS404 2.0 23.5 1.0 NE2 A:HIS377 2.0 27.3 1.0 NE2 A:HIS381 2.2 27.0 1.0 CE1 A:HIS404 2.8 23.5 1.0 CE1 A:HIS377 3.0 26.8 1.0 CD2 A:HIS377 3.0 27.0 1.0 CD2 A:HIS381 3.0 31.2 1.0 CD2 A:HIS404 3.1 24.3 1.0 CE1 A:HIS381 3.2 28.9 1.0 ZN A:ZN512 3.3 40.5 1.0 O3 A:KOJ514 3.4 46.6 1.0 CE2 A:PHE400 3.9 21.4 1.0 ND1 A:HIS404 3.9 22.5 1.0 O2 A:KOJ514 4.0 32.6 1.0 C3 A:KOJ514 4.0 44.1 1.0 ND1 A:HIS377 4.1 25.4 1.0 CG A:HIS404 4.1 22.8 1.0 CG A:HIS377 4.1 27.0 1.0 NE2 A:HIS224 4.2 28.0 1.0 CG A:HIS381 4.2 30.9 1.0 ND1 A:HIS381 4.2 29.5 1.0 CZ A:PHE400 4.3 23.8 1.0 C2 A:KOJ514 4.4 38.5 1.0 CD2 A:LEU403 4.5 25.6 1.0 CD2 A:HIS224 4.6 27.4 1.0 CD2 A:PHE400 4.7 22.2 1.0 CE1 A:PHE220 4.7 22.9 1.0 NE2 A:HIS215 4.7 29.0 1.0 CE1 A:HIS224 4.7 29.6 1.0 NE2 A:HIS192 4.9 27.1 1.0 CZ A:PHE220 4.9 26.8 1.0 C4 A:KOJ514 5.0 39.4 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn515 b:95.2 occ:1.00 OE2 B:GLU66 1.8 62.1 1.0 CD2 A:HIS100 2.4 63.0 1.0 OE1 A:GLU66 2.6 62.1 1.0 CD B:GLU66 2.7 66.5 1.0 ND1 B:HIS100 2.8 80.1 1.0 OE1 B:GLU66 2.9 68.2 1.0 NH2 B:ARG64 2.9 62.2 1.0 OE2 A:GLU66 2.9 63.8 1.0 CD A:GLU66 3.1 59.8 1.0 CG A:HIS100 3.1 62.0 1.0 CG B:HIS100 3.2 69.1 1.0 NE2 A:HIS100 3.2 59.0 1.0 CB B:HIS100 3.5 55.0 1.0 CE1 B:HIS100 3.6 73.8 1.0 CB A:HIS100 3.6 53.2 1.0 CZ B:ARG64 3.9 62.9 1.0 CD2 B:HIS100 4.1 69.8 1.0 CG B:GLU66 4.1 58.3 1.0 ND1 A:HIS100 4.1 59.8 1.0 NE B:ARG64 4.2 63.8 1.0 CE1 A:HIS100 4.2 59.1 1.0 NE2 B:HIS100 4.2 70.3 1.0 NE A:ARG64 4.3 67.5 1.0 NH2 A:ARG64 4.4 74.5 1.0 CG A:GLU66 4.5 51.9 1.0 CB B:GLU66 4.6 48.3 1.0 CZ A:ARG64 4.7 74.2 1.0 CA B:HIS100 5.0 53.6 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn514 b:40.4 occ:1.00 NE2 B:HIS192 1.9 24.1 1.0 O B:HOH601 2.0 30.4 1.0 NE2 B:HIS215 2.1 30.3 1.0 NE2 B:HIS224 2.4 22.9 1.0 CE1 B:HIS192 2.8 22.2 1.0 CE1 B:HIS215 2.9 27.7 1.0 CE1 B:HIS224 2.9 26.5 1.0 O2 B:KOJ516 3.0 29.6 1.0 CD2 B:HIS192 3.0 21.8 1.0 CD2 B:HIS215 3.3 28.0 1.0 ZN B:ZN515 3.5 27.1 1.0 CD2 B:HIS224 3.6 24.1 1.0 O3 B:KOJ516 3.7 42.3 1.0 CZ B:PHE400 3.9 22.9 1.0 CE2 B:PHE400 3.9 23.1 1.0 ND1 B:HIS192 4.0 26.2 1.0 C2 B:KOJ516 4.1 34.8 1.0 ND1 B:HIS215 4.1 25.3 1.0 NE2 B:HIS404 4.1 24.4 1.0 CG B:HIS192 4.1 23.7 1.0 ND1 B:HIS224 4.2 27.6 1.0 CG B:HIS215 4.3 25.0 1.0 C3 B:KOJ516 4.3 40.0 1.0 CE1 B:HIS404 4.5 22.8 1.0 CG B:HIS224 4.5 25.8 1.0 OG B:SER394 4.8 27.5 1.0 NE2 B:HIS377 4.9 29.0 1.0 NE2 B:HIS381 4.9 26.1 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn515 b:27.1 occ:1.00 NE2 B:HIS377 1.9 29.0 1.0 O B:HOH601 1.9 30.4 1.0 NE2 B:HIS381 2.0 26.1 1.0 NE2 B:HIS404 2.1 24.4 1.0 CE1 B:HIS404 2.7 22.8 1.0 CE1 B:HIS377 2.7 28.5 1.0 CD2 B:HIS381 3.0 29.1 1.0 CD2 B:HIS377 3.0 28.1 1.0 CE1 B:HIS381 3.0 26.9 1.0 CD2 B:HIS404 3.3 24.4 1.0 ZN B:ZN514 3.5 40.4 1.0 O3 B:KOJ516 3.6 42.3 1.0 O2 B:KOJ516 3.9 29.6 1.0 C3 B:KOJ516 3.9 40.0 1.0 ND1 B:HIS377 3.9 27.2 1.0 ND1 B:HIS404 3.9 22.0 1.0 CE2 B:PHE400 3.9 23.1 1.0 C2 B:KOJ516 4.0 34.8 1.0 CG B:HIS377 4.1 27.0 1.0 ND1 B:HIS381 4.1 26.2 1.0 CG B:HIS381 4.1 27.0 1.0 CG B:HIS404 4.2 23.9 1.0 CD2 B:LEU403 4.4 24.9 1.0 NE2 B:HIS224 4.4 22.9 1.0 CZ B:PHE400 4.4 22.9 1.0 CD2 B:PHE400 4.6 23.9 1.0 C4 B:KOJ516 4.7 37.0 1.0 CE1 B:HIS224 4.7 26.5 1.0 NE2 B:HIS215 4.8 30.3 1.0 CE1 B:PHE220 4.8 24.7 1.0 CD2 B:HIS224 4.9 24.1 1.0 C1 B:KOJ516 5.0 36.3 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn518 b:37.5 occ:1.00 NE2 C:HIS215 2.0 30.9 1.0 NE2 C:HIS224 2.2 20.6 1.0 O C:HOH603 2.2 26.6 1.0 NE2 C:HIS192 2.3 22.9 1.0 CE1 C:HIS215 2.9 31.2 1.0 CE1 C:HIS224 2.9 23.5 1.0 CD2 C:HIS192 3.1 22.2 1.0 CD2 C:HIS215 3.1 27.0 1.0 O2 C:KOJ520 3.2 43.1 1.0 CE1 C:HIS192 3.3 25.6 1.0 CD2 C:HIS224 3.4 24.3 1.0 ZN C:ZN519 3.7 39.6 1.0 O3 C:KOJ520 3.7 42.5 1.0 ND1 C:HIS215 4.0 29.8 1.0 CE2 C:PHE400 4.0 24.3 1.0 CZ C:PHE400 4.1 22.9 1.0 ND1 C:HIS224 4.1 24.5 1.0 CG C:HIS215 4.1 30.3 1.0 NE2 C:HIS404 4.2 24.8 1.0 C2 C:KOJ520 4.3 40.7 1.0 CG C:HIS192 4.3 20.5 1.0 ND1 C:HIS192 4.4 22.1 1.0 CG C:HIS224 4.4 21.1 1.0 C3 C:KOJ520 4.4 40.6 1.0 CE1 C:HIS404 4.5 23.6 1.0 OG C:SER394 4.8 29.0 1.0 NE2 C:HIS377 4.9 26.5 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn519 b:39.6 occ:1.00 NE2 C:HIS404 1.8 24.8 1.0 NE2 C:HIS377 1.9 26.5 1.0 O C:HOH603 2.0 26.6 1.0 NE2 C:HIS381 2.1 27.3 1.0 CE1 C:HIS404 2.6 23.6 1.0 CE1 C:HIS377 2.9 26.7 1.0 CD2 C:HIS377 3.0 27.1 1.0 CD2 C:HIS381 3.0 24.9 1.0 CD2 C:HIS404 3.0 23.6 1.0 CE1 C:HIS381 3.2 28.8 1.0 O3 C:KOJ520 3.6 42.5 1.0 ZN C:ZN518 3.7 37.5 1.0 ND1 C:HIS404 3.8 19.8 1.0 ND1 C:HIS377 4.0 30.3 1.0 CG C:HIS404 4.0 26.1 1.0 O2 C:KOJ520 4.0 43.1 1.0 CG C:HIS377 4.1 26.4 1.0 C3 C:KOJ520 4.1 40.6 1.0 CE2 C:PHE400 4.2 24.3 1.0 CG C:HIS381 4.2 27.0 1.0 NE2 C:HIS224 4.2 20.6 1.0 CD2 C:LEU403 4.2 23.1 1.0 ND1 C:HIS381 4.2 27.5 1.0 C2 C:KOJ520 4.4 40.7 1.0 CD2 C:HIS224 4.5 24.3 1.0 CZ C:PHE400 4.5 22.9 1.0 CD2 C:PHE400 4.7 26.0 1.0 CE1 C:PHE220 4.7 24.9 1.0 CZ C:PHE220 4.9 24.4 1.0 NE2 C:HIS215 4.9 30.9 1.0 CE1 C:HIS224 4.9 23.5 1.0 C4 C:KOJ520 5.0 42.8 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn513 b:50.9 occ:1.00 NE2 D:HIS192 2.0 37.4 1.0 NE2 D:HIS215 2.0 39.5 1.0 O D:HOH601 2.2 36.0 1.0 NE2 D:HIS224 2.4 39.9 1.0 CD2 D:HIS192 2.9 34.7 1.0 CE1 D:HIS215 2.9 41.4 1.0 CE1 D:HIS192 3.0 37.2 1.0 CE1 D:HIS224 3.1 40.1 1.0 CD2 D:HIS215 3.1 37.0 1.0 O2 D:KOJ515 3.3 55.7 1.0 CD2 D:HIS224 3.5 38.1 1.0 ZN D:ZN514 3.6 39.2 1.0 O3 D:KOJ515 3.6 59.1 1.0 CE2 D:PHE400 4.0 30.7 1.0 CZ D:PHE400 4.0 29.8 1.0 ND1 D:HIS215 4.1 42.7 1.0 CG D:HIS192 4.1 33.3 1.0 ND1 D:HIS192 4.1 40.8 1.0 NE2 D:HIS404 4.2 37.2 1.0 CG D:HIS215 4.2 42.2 1.0 ND1 D:HIS224 4.3 38.5 1.0 C2 D:KOJ515 4.3 58.0 1.0 C3 D:KOJ515 4.4 60.8 1.0 CE1 D:HIS404 4.5 39.0 1.0 CG D:HIS224 4.5 38.0 1.0 OG D:SER394 4.7 38.3 1.0 NE2 D:HIS377 4.9 39.7 1.0 CE1 D:PHE220 5.0 33.9 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Kojic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn514 b:39.2 occ:1.00 NE2 D:HIS404 1.9 37.2 1.0 NE2 D:HIS381 2.0 41.6 1.0 NE2 D:HIS377 2.0 39.7 1.0 O D:HOH601 2.0 36.0 1.0 CE1 D:HIS404 2.7 39.0 1.0 CE1 D:HIS381 2.8 39.7 1.0 CE1 D:HIS377 2.9 38.1 1.0 CD2 D:HIS377 3.0 39.9 1.0 CD2 D:HIS381 3.0 41.5 1.0 CD2 D:HIS404 3.1 35.8 1.0 O3 D:KOJ515 3.4 59.1 1.0 ZN D:ZN513 3.6 50.9 1.0 ND1 D:HIS404 3.9 36.9 1.0 ND1 D:HIS381 3.9 43.9 1.0 C3 D:KOJ515 4.0 60.8 1.0 CE2 D:PHE400 4.0 30.7 1.0 ND1 D:HIS377 4.1 38.0 1.0 CG D:HIS381 4.1 42.1 1.0 CG D:HIS404 4.1 37.8 1.0 O2 D:KOJ515 4.1 55.7 1.0 CG D:HIS377 4.1 38.6 1.0 NE2 D:HIS224 4.3 39.9 1.0 C2 D:KOJ515 4.3 58.0 1.0 CD2 D:LEU403 4.4 35.2 1.0 CZ D:PHE400 4.4 29.8 1.0 CD2 D:PHE400 4.6 34.0 1.0 CD2 D:HIS224 4.7 38.1 1.0 CE1 D:PHE220 4.7 33.9 1.0 C4 D:KOJ515 4.8 55.9 1.0 CZ D:PHE220 4.8 36.2 1.0 NE2 D:HIS215 4.9 39.5 1.0 CE1 D:HIS224 4.9 40.1 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