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Zinc in PDB 5m8t: Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone

Protein crystallography data

The structure of Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone, PDB code: 5m8t 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) 48.75 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.732, 140.605, 191.253, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone (pdb code 5m8t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone, PDB code: 5m8t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5m8t

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


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

b:33.4
occ:1.00
 NE2 A:HIS404 2.0 31.4 1.0
O A:HOH601 2.0 40.9 1.0
NE2 A:HIS377 2.1 35.0 1.0
NE2 A:HIS381 2.2 40.2 1.0
CE1 A:HIS404 2.8 31.7 1.0
CD2 A:HIS377 3.0 31.6 1.0
CE1 A:HIS377 3.1 33.5 1.0
CD2 A:HIS381 3.1 38.4 1.0
CD2 A:HIS404 3.1 31.0 1.0
CE1 A:HIS381 3.1 39.9 1.0
OA1 A:0TR513 3.3 52.6 1.0
ZN A:ZN512 3.3 47.4 1.0
OA2 A:0TR513 3.5 52.5 1.0
CE2 A:PHE400 3.8 34.9 1.0
ND1 A:HIS404 4.0 29.1 1.0
CA1 A:0TR513 4.0 52.7 1.0
CA2 A:0TR513 4.1 53.7 1.0
NE2 A:HIS224 4.1 37.4 1.0
CG A:HIS404 4.1 36.6 1.0
ND1 A:HIS377 4.2 33.6 1.0
CG A:HIS377 4.2 33.3 1.0
CG A:HIS381 4.2 42.3 1.0
ND1 A:HIS381 4.2 41.0 1.0
CZ A:PHE400 4.2 29.6 1.0
CD2 A:HIS224 4.4 32.5 1.0
CD2 A:PHE400 4.6 32.2 1.0
CE1 A:PHE220 4.6 35.5 1.0
CD2 A:LEU403 4.7 34.0 1.0
NE2 A:HIS215 4.8 42.7 1.0
CE1 A:HIS224 4.9 34.0 1.0
CZ A:PHE220 4.9 33.5 1.0
CA6 A:0TR513 5.0 52.8 1.0
NE2 A:HIS192 5.0 36.1 1.0

Zinc binding site 2 out of 8 in 5m8t

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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

b:47.4
occ:1.00
 NE2 A:HIS192 2.1 36.1 1.0
O A:HOH601 2.1 40.9 1.0
NE2 A:HIS215 2.1 42.7 1.0
NE2 A:HIS224 2.3 37.4 1.0
OA2 A:0TR513 2.9 52.5 1.0
CE1 A:HIS224 3.0 34.0 1.0
CD2 A:HIS192 3.0 33.1 1.0
CE1 A:HIS215 3.0 33.8 1.0
CE1 A:HIS192 3.2 32.9 1.0
CD2 A:HIS215 3.2 38.5 1.0
ZN A:ZN511 3.3 33.4 1.0
CD2 A:HIS224 3.5 32.5 1.0
OA1 A:0TR513 3.6 52.6 1.0
CZ A:PHE400 3.9 29.6 1.0
CE2 A:PHE400 4.0 34.9 1.0
NE2 A:HIS404 4.0 31.4 1.0
CA2 A:0TR513 4.2 53.7 1.0
ND1 A:HIS215 4.2 40.8 1.0
CG A:HIS192 4.2 31.8 1.0
ND1 A:HIS224 4.2 33.5 1.0
ND1 A:HIS192 4.2 33.2 1.0
CG A:HIS215 4.3 42.6 1.0
CE1 A:HIS404 4.3 31.7 1.0
CG A:HIS224 4.5 32.2 1.0
CA1 A:0TR513 4.5 52.7 1.0
NE2 A:HIS377 4.7 35.0 1.0
NE2 A:HIS381 4.9 40.2 1.0
CE1 A:PHE220 4.9 35.5 1.0
OG A:SER394 5.0 42.0 1.0

Zinc binding site 3 out of 8 in 5m8t

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Zinc binding site 3 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn515

b:40.2
occ:1.00
 NE2 B:HIS192 2.1 29.9 1.0
NE2 B:HIS224 2.1 31.0 1.0
O B:HOH601 2.1 36.5 1.0
NE2 B:HIS215 2.2 36.0 1.0
CD2 B:HIS192 2.9 25.1 1.0
CE1 B:HIS224 2.9 31.2 1.0
CE1 B:HIS215 3.0 28.9 1.0
CE1 B:HIS192 3.2 28.6 1.0
CD2 B:HIS224 3.2 27.7 1.0
OA2 B:0TR517 3.2 52.5 1.0
CD2 B:HIS215 3.3 30.9 1.0
ZN B:ZN516 3.4 32.3 1.0
CZ B:PHE400 3.8 28.0 1.0
CE2 B:PHE400 3.9 32.9 1.0
OA1 B:0TR517 4.0 52.6 1.0
NE2 B:HIS404 4.0 29.9 1.0
ND1 B:HIS224 4.1 29.3 1.0
CG B:HIS192 4.1 29.0 1.0
ND1 B:HIS215 4.1 32.3 1.0
ND1 B:HIS192 4.2 29.8 1.0
CE1 B:HIS404 4.2 29.4 1.0
CG B:HIS224 4.3 32.3 1.0
CG B:HIS215 4.3 31.6 1.0
CA2 B:0TR517 4.5 52.6 1.0
CE1 B:PHE220 4.8 29.8 1.0
NE2 B:HIS377 4.8 29.7 1.0
CA1 B:0TR517 4.8 52.7 1.0
OG B:SER394 5.0 36.5 1.0

Zinc binding site 4 out of 8 in 5m8t

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Zinc binding site 4 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn516

b:32.3
occ:1.00
 NE2 B:HIS404 2.0 29.9 1.0
O B:HOH601 2.0 36.5 1.0
NE2 B:HIS381 2.1 34.0 1.0
NE2 B:HIS377 2.1 29.7 1.0
CE1 B:HIS404 2.7 29.4 1.0
CE1 B:HIS381 3.0 35.4 1.0
CE1 B:HIS377 3.0 29.9 1.0
CD2 B:HIS381 3.1 35.1 1.0
CD2 B:HIS377 3.1 30.8 1.0
CD2 B:HIS404 3.2 26.4 1.0
ZN B:ZN515 3.4 40.2 1.0
OA1 B:0TR517 3.6 52.6 1.0
OA2 B:0TR517 3.6 52.5 1.0
CE2 B:PHE400 3.8 32.9 1.0
ND1 B:HIS404 3.9 28.4 1.0
CA1 B:0TR517 4.1 52.7 1.0
CA2 B:0TR517 4.1 52.6 1.0
ND1 B:HIS381 4.1 33.5 1.0
NE2 B:HIS224 4.1 31.0 1.0
ND1 B:HIS377 4.2 23.9 1.0
CG B:HIS404 4.2 27.2 1.0
CG B:HIS381 4.2 36.7 1.0
CZ B:PHE400 4.2 28.0 1.0
CG B:HIS377 4.2 27.6 1.0
CD2 B:HIS224 4.4 27.7 1.0
CD2 B:LEU403 4.4 31.9 1.0
CD2 B:PHE400 4.5 31.0 1.0
CE1 B:PHE220 4.6 29.8 1.0
NE2 B:HIS215 4.8 36.0 1.0
NE2 B:HIS192 4.9 29.9 1.0
CZ B:PHE220 4.9 31.0 1.0
CE1 B:HIS224 5.0 31.2 1.0

Zinc binding site 5 out of 8 in 5m8t

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn514

b:47.2
occ:1.00
 NE2 C:HIS215 2.1 43.0 1.0
NE2 C:HIS192 2.1 42.4 1.0
O C:HOH601 2.1 39.0 1.0
NE2 C:HIS224 2.4 36.7 1.0
CE1 C:HIS215 2.8 39.0 1.0
CE1 C:HIS192 3.0 38.1 1.0
CD2 C:HIS192 3.1 36.1 1.0
CD2 C:HIS215 3.2 37.8 1.0
CE1 C:HIS224 3.2 38.2 1.0
OA2 C:0TR516 3.3 52.5 1.0
ZN C:ZN515 3.4 34.1 1.0
CD2 C:HIS224 3.6 35.2 1.0
OA1 C:0TR516 3.6 53.5 1.0
CE2 C:PHE400 4.0 36.0 1.0
ND1 C:HIS215 4.0 39.3 1.0
CZ C:PHE400 4.1 34.4 1.0
NE2 C:HIS404 4.1 37.7 1.0
ND1 C:HIS192 4.1 39.3 1.0
CG C:HIS215 4.2 39.9 1.0
CG C:HIS192 4.2 39.1 1.0
CA2 C:0TR516 4.4 52.6 1.0
ND1 C:HIS224 4.4 31.5 1.0
CA1 C:0TR516 4.5 54.1 1.0
CG C:HIS224 4.6 31.4 1.0
CE1 C:HIS404 4.6 35.5 1.0
NE2 C:HIS377 4.7 40.2 1.0
OG C:SER394 4.9 40.5 1.0
NE2 C:HIS381 5.0 41.1 1.0
CE1 C:PHE220 5.0 36.0 1.0

Zinc binding site 6 out of 8 in 5m8t

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Zinc binding site 6 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn515

b:34.1
occ:1.00
 NE2 C:HIS377 2.0 40.2 1.0
NE2 C:HIS404 2.0 37.7 1.0
NE2 C:HIS381 2.0 41.1 1.0
O C:HOH601 2.1 39.0 1.0
CE1 C:HIS404 2.8 35.5 1.0
CE1 C:HIS381 2.9 43.9 1.0
CD2 C:HIS377 3.0 32.3 1.0
CD2 C:HIS381 3.0 41.9 1.0
CE1 C:HIS377 3.1 35.3 1.0
CD2 C:HIS404 3.2 35.2 1.0
OA1 C:0TR516 3.4 53.5 1.0
ZN C:ZN514 3.4 47.2 1.0
CE2 C:PHE400 3.9 36.0 1.0
ND1 C:HIS404 4.0 30.6 1.0
ND1 C:HIS381 4.0 44.6 1.0
OA2 C:0TR516 4.0 52.5 1.0
CG C:HIS381 4.1 45.3 1.0
CA1 C:0TR516 4.1 54.1 1.0
CG C:HIS377 4.1 33.8 1.0
ND1 C:HIS377 4.2 37.0 1.0
NE2 C:HIS224 4.2 36.7 1.0
CG C:HIS404 4.2 38.6 1.0
CZ C:PHE400 4.4 34.4 1.0
CA2 C:0TR516 4.4 52.6 1.0
CD2 C:HIS224 4.4 35.2 1.0
CD2 C:LEU403 4.5 35.5 1.0
CD2 C:PHE400 4.6 34.0 1.0
CE1 C:PHE220 4.7 36.0 1.0
NE2 C:HIS215 4.8 43.0 1.0
CA6 C:0TR516 4.9 52.8 1.0
CZ C:PHE220 5.0 31.6 1.0

Zinc binding site 7 out of 8 in 5m8t

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Zinc binding site 7 out of 8 in the Crystal Structure of Human Tyrosinase Related Protein 1 (T391V-R374S- Y362F) in Complex with Tropolone


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn516

b:41.2
occ:1.00
 NE2 D:HIS224 2.2 27.4 1.0
O D:HOH601 2.2 34.9 1.0
NE2 D:HIS215 2.2 34.7 1.0
NE2 D:HIS192 2.3 24.5 1.0
CE1 D:HIS224 3.0 28.2 1.0
CE1 D:HIS215 3.0 34.5 1.0
CD2 D:HIS192 3.1 24.8 1.0
CD2 D:HIS224 3.3 27.4 1.0
CD2 D:HIS215 3.3 36.1 1.0
ZN D:ZN517 3.4 31.1 1.0
CE1 D:HIS192 3.4 31.4 1.0
OA2 D:0TR518 3.5 52.6 0.8
OA1 D:0TR518 3.7 52.5 0.8
CE2 D:PHE400 4.0 28.4 1.0
CZ D:PHE400 4.0 27.5 1.0
NE2 D:HIS404 4.1 27.9 1.0
ND1 D:HIS215 4.1 34.9 1.0
ND1 D:HIS224 4.2 27.8 1.0
CG D:HIS215 4.3 34.4 1.0
CG D:HIS224 4.3 26.2 1.0
CG D:HIS192 4.3 27.5 1.0
CE1 D:HIS404 4.4 28.7 1.0
ND1 D:HIS192 4.5 28.8 1.0
CA2 D:0TR518 4.6 52.7 0.8
CA1 D:0TR518 4.7 52.6 0.8
NE2 D:HIS377 4.7 32.1 1.0
CE1 D:PHE220 4.8 32.5 1.0

Zinc binding site 8 out of 8 in 5m8t

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


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 Tropolone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn517

b:31.1
occ:1.00
 NE2 D:HIS404 2.0 27.9 1.0
NE2 D:HIS377 2.1 32.1 1.0
O D:HOH601 2.2 34.9 1.0
NE2 D:HIS381 2.2 34.9 1.0
CE1 D:HIS404 2.8 28.7 1.0
CE1 D:HIS377 3.0 35.0 1.0
CD2 D:HIS404 3.1 27.6 1.0
CD2 D:HIS377 3.1 29.9 1.0
CD2 D:HIS381 3.1 35.1 1.0
CE1 D:HIS381 3.2 35.0 1.0
ZN D:ZN516 3.4 41.2 1.0
OA1 D:0TR518 3.5 52.5 0.8
CE2 D:PHE400 3.8 28.4 1.0
OA2 D:0TR518 3.9 52.6 0.8
ND1 D:HIS404 4.0 26.9 1.0
ND1 D:HIS377 4.1 30.1 1.0
CA1 D:0TR518 4.1 52.6 0.8
CG D:HIS404 4.1 28.8 1.0
NE2 D:HIS224 4.2 27.4 1.0
CG D:HIS377 4.2 29.0 1.0
CG D:HIS381 4.2 36.8 1.0
ND1 D:HIS381 4.3 36.6 1.0
CA2 D:0TR518 4.3 52.7 0.8
CZ D:PHE400 4.3 27.5 1.0
CD2 D:HIS224 4.4 27.4 1.0
CD2 D:PHE400 4.5 31.9 1.0
CD2 D:LEU403 4.5 32.8 1.0
CE1 D:PHE220 4.7 32.5 1.0
NE2 D:HIS215 4.8 34.7 1.0
CE1 D:HIS224 5.0 28.2 1.0
CZ D:PHE220 5.0 31.8 1.0

Reference:

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
Page generated: Sun Oct 27 22:02:20 2024

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