Zinc in PDB 5m8s: Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Phenylthiourea (Ptu)

Protein crystallography data

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Phenylthiourea (Ptu), PDB code: 5m8s 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) 45.88 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.081, 141.767, 191.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V- R374S-Y362F) in Complex with Phenylthiourea (Ptu) (pdb code 5m8s). 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 Phenylthiourea (Ptu), PDB code: 5m8s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:29.6
occ:1.00
 NE2 A:HIS404 2.0 27.5 1.0
NE2 A:HIS381 2.0 29.0 1.0
O A:HOH763 2.0 30.8 1.0
NE2 A:HIS377 2.1 27.5 1.0
CE1 A:HIS404 2.8 25.3 1.0
CD2 A:HIS381 2.9 30.2 1.0
CD2 A:HIS377 3.0 26.5 1.0
CE1 A:HIS381 3.1 29.0 1.0
CE1 A:HIS377 3.1 26.9 1.0
CD2 A:HIS404 3.1 22.7 1.0
ZN A:ZN511 3.6 29.8 1.0
O A:HOH735 3.9 32.0 1.0
CE2 A:PHE400 3.9 28.1 1.0
ND1 A:HIS404 4.0 28.8 1.0
O A:HOH657 4.0 39.2 1.0
CG A:HIS381 4.1 33.4 1.0
ND1 A:HIS381 4.1 35.5 1.0
CG A:HIS404 4.1 25.5 1.0
CG A:HIS377 4.2 26.4 1.0
ND1 A:HIS377 4.2 29.9 1.0
CD2 A:LEU403 4.3 27.0 1.0
NE2 A:HIS224 4.3 26.7 1.0
CD2 A:PHE400 4.5 27.7 1.0
CZ A:PHE400 4.5 28.6 1.0
CD2 A:HIS224 4.5 27.2 1.0
CE1 A:PHE220 4.6 30.6 1.0
NE2 A:HIS215 4.7 31.1 1.0
CZ A:PHE220 4.9 27.4 1.0

Zinc binding site 2 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:29.8
occ:1.00
 NE2 A:HIS192 2.0 21.6 1.0
O A:HOH763 2.0 30.8 1.0
NE2 A:HIS215 2.1 31.1 1.0
NE2 A:HIS224 2.1 26.7 1.0
CE1 A:HIS192 2.8 25.8 1.0
CE1 A:HIS215 2.9 30.5 1.0
CE1 A:HIS224 3.0 28.4 1.0
CD2 A:HIS192 3.1 24.9 1.0
CD2 A:HIS224 3.1 27.2 1.0
CD2 A:HIS215 3.2 27.2 1.0
ZN A:ZN510 3.6 29.6 1.0
O A:HOH735 3.8 32.0 1.0
CE2 A:PHE400 3.9 28.1 1.0
NE2 A:HIS404 4.0 27.5 1.0
CZ A:PHE400 4.0 28.6 1.0
ND1 A:HIS192 4.0 24.4 1.0
ND1 A:HIS215 4.1 27.6 1.0
ND1 A:HIS224 4.1 24.3 1.0
CG A:HIS192 4.2 29.1 1.0
CG A:HIS215 4.2 28.6 1.0
CG A:HIS224 4.2 27.3 1.0
O A:HOH736 4.3 34.8 1.0
CE1 A:HIS404 4.3 25.3 1.0
O A:HOH657 4.7 39.2 1.0
CE1 A:PHE220 4.8 30.6 1.0
NE2 A:HIS377 4.8 27.5 1.0
CD2 A:HIS404 4.9 22.7 1.0
OG A:SER214 5.0 30.4 1.0

Zinc binding site 3 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:51.5
occ:1.00
 OE2 B:GLU66 2.0 44.8 1.0
ND1 B:HIS100 2.0 50.1 1.0
ND1 A:HIS100 2.0 46.1 1.0
OE2 A:GLU66 2.1 44.2 1.0
CD B:GLU66 2.6 50.4 1.0
OE1 B:GLU66 2.6 49.4 1.0
CE1 B:HIS100 2.7 48.8 1.0
CD A:GLU66 2.8 47.1 1.0
CE1 A:HIS100 2.8 43.0 1.0
OE1 A:GLU66 2.8 48.6 1.0
CG B:HIS100 3.2 46.4 1.0
CG A:HIS100 3.2 46.1 1.0
CB A:HIS100 3.7 41.9 1.0
CB B:HIS100 3.7 40.5 1.0
NH2 A:ARG64 3.8 50.2 1.0
NE2 B:HIS100 3.9 48.6 1.0
NE A:ARG64 3.9 51.9 1.0
NE2 A:HIS100 4.0 50.2 1.0
NH2 B:ARG64 4.0 45.1 1.0
CG B:GLU66 4.1 40.0 1.0
NE B:ARG64 4.1 47.3 1.0
CD2 B:HIS100 4.2 47.3 1.0
CD2 A:HIS100 4.2 45.6 1.0
CG A:GLU66 4.2 45.3 1.0
CZ A:ARG64 4.3 52.5 1.0
CZ B:ARG64 4.5 49.8 1.0
CB B:GLU66 4.8 38.8 1.0
CB A:GLU66 4.9 43.2 1.0

Zinc binding site 4 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn517

b:29.8
occ:1.00
 NE2 B:HIS192 2.0 22.1 1.0
NE2 B:HIS215 2.1 33.0 1.0
NE2 B:HIS224 2.1 27.4 1.0
O B:HOH733 2.1 31.4 1.0
CE1 B:HIS215 2.9 27.9 1.0
CE1 B:HIS192 2.9 29.9 1.0
CE1 B:HIS224 3.0 29.4 1.0
CD2 B:HIS192 3.0 27.5 1.0
CD2 B:HIS224 3.2 27.6 1.0
CD2 B:HIS215 3.2 28.8 1.0
ZN B:ZN518 3.6 30.9 1.0
CZ B:PHE400 3.8 31.1 1.0
CE2 B:PHE400 3.9 32.1 1.0
O B:HOH748 3.9 35.4 1.0
NE2 B:HIS404 4.1 27.2 1.0
ND1 B:HIS192 4.1 25.8 1.0
ND1 B:HIS215 4.1 28.2 1.0
ND1 B:HIS224 4.1 23.8 1.0
CG B:HIS192 4.2 27.6 1.0
CE1 B:HIS404 4.2 31.9 1.0
CG B:HIS215 4.2 29.1 1.0
CG B:HIS224 4.3 29.6 1.0
O B:HOH727 4.4 32.2 1.0
O B:HOH700 4.6 39.6 1.0
CE1 B:PHE220 4.8 30.8 1.0
NE2 B:HIS377 4.9 27.8 1.0
OG B:SER394 4.9 34.5 1.0

Zinc binding site 5 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn518

b:30.9
occ:1.00
 NE2 B:HIS377 2.0 27.8 1.0
O B:HOH733 2.0 31.4 1.0
NE2 B:HIS381 2.0 29.1 1.0
NE2 B:HIS404 2.1 27.2 1.0
CE1 B:HIS404 2.6 31.9 1.0
CE1 B:HIS377 2.9 27.9 1.0
CD2 B:HIS381 3.0 28.4 1.0
CD2 B:HIS377 3.0 32.9 1.0
CE1 B:HIS381 3.1 29.3 1.0
CD2 B:HIS404 3.3 28.5 1.0
ZN B:ZN517 3.6 29.8 1.0
ND1 B:HIS404 3.8 28.3 1.0
O B:HOH748 3.9 35.4 1.0
CE2 B:PHE400 3.9 32.1 1.0
ND1 B:HIS377 4.0 28.9 1.0
O B:HOH700 4.1 39.6 1.0
ND1 B:HIS381 4.1 28.4 1.0
CG B:HIS381 4.1 33.2 1.0
CG B:HIS377 4.1 29.2 1.0
CG B:HIS404 4.2 32.8 1.0
NE2 B:HIS224 4.3 27.4 1.0
CZ B:PHE400 4.4 31.1 1.0
CD2 B:LEU403 4.5 22.1 1.0
CE1 B:PHE220 4.5 30.8 1.0
CD2 B:HIS224 4.6 27.6 1.0
CD2 B:PHE400 4.6 26.7 1.0
NE2 B:HIS215 4.8 33.0 1.0
CZ B:PHE220 4.8 28.0 1.0

Zinc binding site 6 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn511

b:35.6
occ:1.00
 NE2 C:HIS377 2.0 32.8 1.0
NE2 C:HIS381 2.1 43.1 1.0
NE2 C:HIS404 2.1 39.0 1.0
O C:HOH739 2.1 27.6 1.0
CE1 C:HIS404 2.7 37.6 1.0
CE1 C:HIS377 2.8 36.7 1.0
CD2 C:HIS381 2.9 38.0 1.0
CD2 C:HIS377 3.0 35.5 1.0
CE1 C:HIS381 3.1 42.7 1.0
CD2 C:HIS404 3.3 35.5 1.0
ZN C:ZN512 3.6 36.6 1.0
CE2 C:PHE400 3.8 37.2 1.0
ND1 C:HIS404 3.9 35.5 1.0
O C:HOH743 4.0 37.5 1.0
ND1 C:HIS377 4.0 36.4 1.0
CG C:HIS381 4.1 45.6 1.0
ND1 C:HIS381 4.1 40.5 1.0
CG C:HIS377 4.1 35.4 1.0
CG C:HIS404 4.2 37.0 1.0
NE2 C:HIS224 4.2 34.5 1.0
CD2 C:LEU403 4.4 36.5 1.0
CZ C:PHE400 4.4 32.8 1.0
CD2 C:PHE400 4.5 31.3 1.0
CD2 C:HIS224 4.6 37.0 1.0
CE1 C:PHE220 4.6 38.0 1.0
NE2 C:HIS215 4.8 38.7 1.0
CZ C:PHE220 4.9 34.4 1.0

Zinc binding site 7 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn512

b:36.6
occ:1.00
 NE2 C:HIS192 2.0 29.7 1.0
NE2 C:HIS224 2.1 34.5 1.0
O C:HOH739 2.1 27.6 1.0
NE2 C:HIS215 2.1 38.7 1.0
CE1 C:HIS215 2.9 36.2 1.0
CE1 C:HIS192 2.9 32.5 1.0
CE1 C:HIS224 2.9 34.4 1.0
CD2 C:HIS192 3.1 32.6 1.0
CD2 C:HIS224 3.2 37.0 1.0
CD2 C:HIS215 3.2 32.6 1.0
ZN C:ZN511 3.6 35.6 1.0
O C:HOH743 3.8 37.5 1.0
CE2 C:PHE400 3.9 37.2 1.0
CZ C:PHE400 3.9 32.8 1.0
NE2 C:HIS404 4.0 39.0 1.0
ND1 C:HIS192 4.1 34.8 1.0
ND1 C:HIS215 4.1 36.4 1.0
ND1 C:HIS224 4.1 32.8 1.0
CG C:HIS192 4.2 33.2 1.0
CG C:HIS224 4.2 37.7 1.0
CE1 C:HIS404 4.2 37.6 1.0
CG C:HIS215 4.3 34.8 1.0
CE1 C:PHE220 4.9 38.0 1.0
NE2 C:HIS377 4.9 32.8 1.0
OG C:SER394 5.0 43.9 1.0
CD2 C:HIS404 5.0 35.5 1.0

Zinc binding site 8 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn519

b:30.7
occ:1.00
 NE2 D:HIS224 2.0 21.8 1.0
O D:HOH758 2.0 29.5 1.0
NE2 D:HIS215 2.0 33.0 1.0
NE2 D:HIS192 2.1 25.0 1.0
CE1 D:HIS215 2.9 34.2 1.0
CE1 D:HIS224 2.9 28.9 1.0
CD2 D:HIS192 3.1 30.6 1.0
CD2 D:HIS215 3.1 34.2 1.0
CD2 D:HIS224 3.1 27.1 1.0
CE1 D:HIS192 3.1 29.9 1.0
ZN D:ZN520 3.6 30.6 1.0
CZ D:PHE400 3.9 28.2 1.0
CE2 D:PHE400 3.9 28.5 1.0
O D:HOH697 4.0 32.9 1.0
NE2 D:HIS404 4.0 27.4 1.0
ND1 D:HIS215 4.0 37.0 1.0
ND1 D:HIS224 4.1 29.5 1.0
CG D:HIS215 4.2 33.7 1.0
CG D:HIS224 4.2 27.8 1.0
ND1 D:HIS192 4.2 29.3 1.0
CG D:HIS192 4.2 26.4 1.0
CE1 D:HIS404 4.3 33.7 1.0
O D:HOH732 4.4 33.2 1.0
O D:HOH703 4.8 36.4 1.0
NE2 D:HIS377 4.8 30.1 1.0
CE1 D:PHE220 5.0 34.6 1.0
OG D:SER394 5.0 35.1 1.0
CD2 D:HIS404 5.0 28.9 1.0

Zinc binding site 9 out of 9 in 5m8s

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


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 Phenylthiourea (Ptu) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn520

b:30.6
occ:1.00
 NE2 D:HIS381 2.0 26.2 1.0
NE2 D:HIS377 2.0 30.1 1.0
O D:HOH758 2.1 29.5 1.0
NE2 D:HIS404 2.1 27.4 1.0
CE1 D:HIS377 2.9 33.1 1.0
CE1 D:HIS404 3.0 33.7 1.0
CD2 D:HIS381 3.0 29.0 1.0
CE1 D:HIS381 3.0 29.0 1.0
CD2 D:HIS377 3.1 32.1 1.0
CD2 D:HIS404 3.1 28.9 1.0
ZN D:ZN519 3.6 30.7 1.0
CE2 D:PHE400 3.9 28.5 1.0
O D:HOH697 4.0 32.9 1.0
ND1 D:HIS377 4.1 35.1 1.0
ND1 D:HIS381 4.1 28.3 1.0
CG D:HIS381 4.1 31.2 1.0
ND1 D:HIS404 4.1 27.6 1.0
CG D:HIS377 4.2 34.3 1.0
CG D:HIS404 4.2 29.5 1.0
NE2 D:HIS224 4.3 21.8 1.0
CD2 D:LEU403 4.3 29.9 1.0
O D:HOH703 4.4 36.4 1.0
CZ D:PHE400 4.4 28.2 1.0
CD2 D:PHE400 4.5 28.9 1.0
CD2 D:HIS224 4.6 27.1 1.0
NE2 D:HIS215 4.8 33.0 1.0
CE1 D:PHE220 4.9 34.6 1.0

Reference:

X.Lai, M.Soler-Lopez, H.J.Wichers, B.W.Dijkstra. Crystal Structure of Human Tyrosinase Related Protein 1 Mutant (T391V-R374S-Y362F) in Complex with Phenylthiourea (Ptu) To Be Published.
Page generated: Wed Dec 16 06:32:39 2020

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