Zinc in PDB 5m8n: Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Mimosine

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Mimosine, PDB code: 5m8n 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)	48.07 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.786, 141.077, 192.262, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.5

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 in Complex with Mimosine (pdb code 5m8n). 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 Mimosine, PDB code: 5m8n:
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 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:33.5 occ:1.00 NE2 A:HIS377 2.0 31.1 1.0 NE2 A:HIS404 2.0 25.7 1.0 O A:HOH616 2.0 25.7 1.0 NE2 A:HIS381 2.1 32.8 1.0 CE1 A:HIS404 2.6 31.1 1.0 CD2 A:HIS381 2.9 28.4 1.0 CE1 A:HIS377 2.9 26.6 1.0 CD2 A:HIS377 3.1 30.9 1.0 CE1 A:HIS381 3.2 28.7 1.0 CD2 A:HIS404 3.2 28.1 1.0 O4 A:MMS514 3.3 36.3 1.0 ZN A:ZN512 3.6 29.6 1.0 CE2 A:PHE400 3.7 26.0 1.0 ND1 A:HIS404 3.8 30.6 1.0 ND1 A:HIS377 4.0 29.3 1.0 C7 A:MMS514 4.0 36.4 1.0 CG A:HIS381 4.0 35.3 1.0 O3 A:MMS514 4.1 34.7 1.0 CG A:HIS377 4.1 31.6 1.0 CG A:HIS404 4.2 29.4 1.0 ND1 A:HIS381 4.2 30.9 1.0 NE2 A:HIS224 4.2 35.5 1.0 CZ A:PHE400 4.2 27.7 1.0 CD2 A:HIS224 4.4 30.0 1.0 C6 A:MMS514 4.4 38.6 1.0 CD2 A:PHE400 4.5 29.8 1.0 NE2 A:HIS215 4.6 35.0 1.0 CE1 A:PHE220 4.6 35.8 1.0 CD2 A:LEU403 4.8 26.5 1.0 C8 A:MMS514 4.9 33.0 1.0 CD2 A:HIS215 4.9 32.0 1.0 CZ A:PHE220 4.9 31.8 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:29.6 occ:1.00 NE2 A:HIS192 2.0 25.1 1.0 NE2 A:HIS215 2.0 35.0 1.0 NE2 A:HIS224 2.1 35.5 1.0 O A:HOH616 2.1 25.7 1.0 CE1 A:HIS215 2.8 34.3 1.0 CD2 A:HIS192 2.9 24.9 1.0 CE1 A:HIS224 3.0 34.2 1.0 CE1 A:HIS192 3.0 24.4 1.0 CD2 A:HIS224 3.1 30.0 1.0 CD2 A:HIS215 3.2 32.0 1.0 ZN A:ZN511 3.6 33.5 1.0 O4 A:MMS514 3.7 36.3 1.0 CZ A:PHE400 3.8 27.7 1.0 ND1 A:HIS215 4.0 31.0 1.0 CG A:HIS192 4.1 23.5 1.0 CE2 A:PHE400 4.1 26.0 1.0 ND1 A:HIS192 4.1 26.9 1.0 NE2 A:HIS404 4.1 25.7 1.0 ND1 A:HIS224 4.1 40.2 1.0 CG A:HIS215 4.2 33.3 1.0 CG A:HIS224 4.2 37.8 1.0 CE1 A:HIS404 4.3 31.1 1.0 O3 A:MMS514 4.3 34.7 1.0 C7 A:MMS514 4.9 36.4 1.0 CE1 A:PHE220 4.9 35.8 1.0 NE2 A:HIS377 5.0 31.1 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:81.3 occ:1.00 OE2 C:GLU66 2.0 65.7 1.0 OE1 A:GLU66 2.4 55.7 1.0 ND1 A:HIS100 2.5 58.9 1.0 CD2 C:HIS100 2.7 65.4 1.0 CD C:GLU66 2.8 62.4 1.0 OE1 C:GLU66 2.9 62.9 1.0 CD A:GLU66 3.0 57.6 1.0 OE2 A:GLU66 3.1 61.6 1.0 CG A:HIS100 3.1 55.7 1.0 CE1 A:HIS100 3.3 60.5 1.0 CB A:HIS100 3.4 52.0 1.0 CG C:HIS100 3.5 63.6 1.0 NH2 A:ARG64 3.6 65.0 1.0 CB C:HIS100 3.7 62.4 1.0 NE A:ARG64 3.8 62.0 1.0 NE2 C:HIS100 3.9 66.1 1.0 CZ A:ARG64 3.9 69.2 1.0 CD2 A:HIS100 4.0 58.8 1.0 NE2 A:HIS100 4.1 54.4 1.0 CG C:GLU66 4.2 54.9 1.0 NE C:ARG64 4.2 63.6 1.0 CG A:GLU66 4.3 54.6 1.0 CZ C:ARG64 4.5 63.0 1.0 NH2 C:ARG64 4.6 54.4 1.0 ND1 C:HIS100 4.7 68.5 1.0 CD C:ARG64 4.7 62.0 1.0 CD A:ARG64 4.8 57.0 1.0 CE1 C:HIS100 4.9 72.6 1.0 NH1 A:ARG64 4.9 71.0 1.0 CA A:HIS100 4.9 45.0 1.0 CG A:ARG64 5.0 49.2 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn513 b:32.8 occ:1.00 NE2 B:HIS224 1.9 25.5 1.0 NE2 B:HIS215 2.0 38.0 1.0 NE2 B:HIS192 2.1 26.8 1.0 O B:HOH602 2.1 26.4 1.0 CE1 B:HIS224 2.7 28.6 1.0 CE1 B:HIS215 2.9 35.0 1.0 CE1 B:HIS192 3.0 29.7 1.0 CD2 B:HIS215 3.1 33.7 1.0 CD2 B:HIS192 3.1 28.3 1.0 CD2 B:HIS224 3.1 28.0 1.0 ZN B:ZN514 3.5 31.9 1.0 O3 B:MMS515 3.7 42.8 1.0 O4 B:MMS515 3.8 32.0 1.0 ND1 B:HIS224 3.9 30.8 1.0 NE2 B:HIS404 4.0 30.4 1.0 CZ B:PHE400 4.0 28.4 1.0 ND1 B:HIS215 4.0 40.5 1.0 CE2 B:PHE400 4.1 29.4 1.0 CG B:HIS224 4.1 24.5 1.0 ND1 B:HIS192 4.1 34.1 1.0 CG B:HIS215 4.2 41.7 1.0 CG B:HIS192 4.2 33.6 1.0 CE1 B:HIS404 4.4 29.2 1.0 C6 B:MMS515 4.6 42.9 1.0 C7 B:MMS515 4.7 33.9 1.0 NE2 B:HIS377 4.8 36.2 1.0 NE2 B:HIS381 4.8 31.7 1.0 CE1 B:PHE220 4.9 30.4 1.0 CG2 B:THR391 4.9 40.7 1.0 CD2 B:HIS404 5.0 29.3 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn514 b:31.9 occ:1.00 NE2 B:HIS381 1.7 31.7 1.0 NE2 B:HIS404 2.0 30.4 1.0 O B:HOH602 2.1 26.4 1.0 NE2 B:HIS377 2.2 36.2 1.0 CE1 B:HIS381 2.6 33.4 1.0 CD2 B:HIS381 2.8 34.4 1.0 CE1 B:HIS404 2.9 29.2 1.0 CD2 B:HIS377 3.0 31.9 1.0 CD2 B:HIS404 3.1 29.3 1.0 CE1 B:HIS377 3.2 29.2 1.0 O4 B:MMS515 3.5 32.0 1.0 O3 B:MMS515 3.5 42.8 1.0 ZN B:ZN513 3.5 32.8 1.0 ND1 B:HIS381 3.7 32.0 1.0 CE2 B:PHE400 3.8 29.4 1.0 CG B:HIS381 3.8 36.3 1.0 C7 B:MMS515 4.0 33.9 1.0 C6 B:MMS515 4.0 42.9 1.0 ND1 B:HIS404 4.0 22.7 1.0 NE2 B:HIS224 4.1 25.5 1.0 CG B:HIS404 4.2 28.2 1.0 CG B:HIS377 4.2 32.8 1.0 ND1 B:HIS377 4.3 32.0 1.0 CZ B:PHE400 4.3 28.4 1.0 CD2 B:LEU403 4.4 32.6 1.0 CD2 B:HIS224 4.5 28.0 1.0 CD2 B:PHE400 4.5 29.9 1.0 CE1 B:PHE220 4.7 30.4 1.0 NE2 B:HIS215 4.8 38.0 1.0 CE1 B:HIS224 4.9 28.6 1.0 C8 B:MMS515 4.9 39.0 1.0 NE2 B:HIS192 4.9 26.8 1.0 OG B:SER394 5.0 31.6 1.0 CZ B:PHE220 5.0 32.1 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn514 b:29.3 occ:1.00 NE2 C:HIS381 1.8 33.3 1.0 NE2 C:HIS377 2.0 27.7 1.0 NE2 C:HIS404 2.1 35.2 1.0 O C:HOH608 2.1 36.5 1.0 CD2 C:HIS381 2.8 33.1 1.0 CE1 C:HIS381 2.8 24.3 1.0 CE1 C:HIS404 2.8 40.3 1.0 CE1 C:HIS377 2.8 25.6 1.0 CD2 C:HIS377 3.2 32.9 1.0 CD2 C:HIS404 3.2 35.9 1.0 O4 C:MMS516 3.3 37.3 1.0 ZN C:ZN515 3.5 34.4 1.0 CE2 C:PHE400 3.6 32.9 1.0 O3 C:MMS516 3.8 28.8 1.0 C7 C:MMS516 3.8 33.3 1.0 ND1 C:HIS381 3.9 33.7 1.0 CG C:HIS381 3.9 33.9 1.0 ND1 C:HIS404 4.0 36.5 1.0 ND1 C:HIS377 4.0 28.7 1.0 C6 C:MMS516 4.0 32.6 1.0 CZ C:PHE400 4.1 33.6 1.0 NE2 C:HIS224 4.1 33.7 1.0 CG C:HIS377 4.2 34.7 1.0 CG C:HIS404 4.2 35.5 1.0 CD2 C:HIS224 4.4 34.0 1.0 CD2 C:PHE400 4.5 30.3 1.0 NE2 C:HIS215 4.5 32.5 1.0 CD2 C:LEU403 4.6 33.0 1.0 CE1 C:PHE220 4.6 33.2 1.0 C8 C:MMS516 4.7 35.7 1.0 CD2 C:HIS215 4.9 29.2 1.0 NE2 C:HIS192 4.9 26.9 1.0 CZ C:PHE220 5.0 30.1 1.0 OG C:SER394 5.0 37.3 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn515 b:34.4 occ:1.00 NE2 C:HIS192 1.9 26.9 1.0 O C:HOH608 1.9 36.5 1.0 NE2 C:HIS215 2.0 32.5 1.0 NE2 C:HIS224 2.2 33.7 1.0 CE1 C:HIS215 2.7 31.5 1.0 CE1 C:HIS192 2.8 31.4 1.0 CD2 C:HIS192 3.0 31.8 1.0 CE1 C:HIS224 3.2 35.3 1.0 CD2 C:HIS224 3.2 34.0 1.0 CD2 C:HIS215 3.2 29.2 1.0 ZN C:ZN514 3.5 29.3 1.0 O4 C:MMS516 3.5 37.3 1.0 O3 C:MMS516 3.8 28.8 1.0 CZ C:PHE400 3.8 33.6 1.0 ND1 C:HIS192 3.9 30.0 1.0 ND1 C:HIS215 3.9 25.7 1.0 CE2 C:PHE400 4.0 32.9 1.0 CG C:HIS192 4.1 29.2 1.0 NE2 C:HIS404 4.1 35.2 1.0 CG C:HIS215 4.2 32.6 1.0 ND1 C:HIS224 4.3 39.1 1.0 CG C:HIS224 4.3 39.2 1.0 C7 C:MMS516 4.5 33.3 1.0 CE1 C:HIS404 4.5 40.3 1.0 C6 C:MMS516 4.5 32.6 1.0 OG C:SER394 4.7 37.3 1.0 NE2 C:HIS381 4.9 33.3 1.0 CE1 C:PHE220 4.9 33.2 1.0 CG2 C:THR391 4.9 38.8 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn513 b:42.9 occ:1.00 NE2 D:HIS381 1.7 51.2 1.0 O D:HOH605 2.0 41.5 1.0 NE2 D:HIS404 2.1 42.1 1.0 NE2 D:HIS377 2.1 40.7 1.0 CE1 D:HIS381 2.5 54.4 1.0 CE1 D:HIS404 2.8 42.1 1.0 CD2 D:HIS381 2.9 49.0 1.0 CE1 D:HIS377 2.9 46.0 1.0 CD2 D:HIS404 3.2 42.2 1.0 CD2 D:HIS377 3.2 44.9 1.0 O4 D:MMS515 3.3 53.6 1.0 ZN D:ZN514 3.3 50.8 1.0 ND1 D:HIS381 3.6 53.6 1.0 CE2 D:PHE400 3.8 42.2 1.0 CG D:HIS381 3.9 51.5 1.0 ND1 D:HIS404 3.9 39.1 1.0 ND1 D:HIS377 4.1 46.9 1.0 NE2 D:HIS224 4.1 43.8 1.0 CG D:HIS404 4.1 44.2 1.0 C7 D:MMS515 4.1 53.9 1.0 O3 D:MMS515 4.2 58.1 1.0 CZ D:PHE400 4.2 43.2 1.0 CG D:HIS377 4.2 41.4 1.0 CD2 D:HIS224 4.4 44.8 1.0 C6 D:MMS515 4.5 58.2 1.0 CD2 D:PHE400 4.5 45.4 1.0 CE1 D:PHE220 4.7 42.6 1.0 NE2 D:HIS215 4.8 51.3 1.0 CD2 D:LEU403 4.9 43.4 1.0 CE1 D:HIS224 4.9 46.9 1.0 CD2 D:HIS215 4.9 46.2 1.0 OG D:SER394 5.0 48.2 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Human Tyrosinase Related Protein 1 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 in Complex with Mimosine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn514 b:50.8 occ:1.00 NE2 D:HIS224 2.0 43.8 1.0 O D:HOH605 2.0 41.5 1.0 NE2 D:HIS215 2.1 51.3 1.0 NE2 D:HIS192 2.1 38.4 1.0 CE1 D:HIS224 2.8 46.9 1.0 CD2 D:HIS215 2.9 46.2 1.0 CD2 D:HIS224 3.1 44.8 1.0 CE1 D:HIS192 3.1 40.5 1.0 CD2 D:HIS192 3.1 42.3 1.0 CE1 D:HIS215 3.2 45.9 1.0 ZN D:ZN513 3.3 42.9 1.0 O4 D:MMS515 3.6 53.6 1.0 NE2 D:HIS404 3.8 42.1 1.0 CZ D:PHE400 3.9 43.2 1.0 CE2 D:PHE400 4.0 42.2 1.0 ND1 D:HIS224 4.0 45.3 1.0 CE1 D:HIS404 4.1 42.1 1.0 CG D:HIS224 4.1 47.6 1.0 CG D:HIS215 4.1 48.5 1.0 ND1 D:HIS215 4.2 44.4 1.0 ND1 D:HIS192 4.2 38.6 1.0 CG D:HIS192 4.3 36.5 1.0 O3 D:MMS515 4.5 58.1 1.0 NE2 D:HIS381 4.8 51.2 1.0 C7 D:MMS515 4.8 53.9 1.0 NE2 D:HIS377 4.8 40.7 1.0 CD2 D:HIS404 4.9 42.2 1.0 CE1 D:PHE220 4.9 42.6 1.0 CE1 D:HIS377 5.0 46.0 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