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

Protein crystallography data

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

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 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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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 5m8q

Go back to Zinc Binding Sites List in 5m8q
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

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: Wed Dec 16 06:32:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy