Zinc in PDB 7p3s: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12, PDB code: 7p3s was solved by T.B.Shaik, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.52 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.39, 70.39, 97.94, 78.05, 75.57, 85.69
R / Rfree (%) 16.9 / 19.3

Other elements in 7p3s:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 also contains other interesting chemical elements:

Potassium (K) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 (pdb code 7p3s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12, PDB code: 7p3s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7p3s

Go back to Zinc Binding Sites List in 7p3s
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:17.1
occ:1.00
OD2 A:ASP285 2.0 16.7 1.0
OD1 A:ASP186 2.0 14.5 1.0
ND1 A:HIS188 2.0 14.0 1.0
O1 A:5IB507 2.3 42.2 1.0
O2 A:5IB507 2.5 36.7 1.0
C5 A:5IB507 2.7 56.7 1.0
N A:5IB507 2.9 45.9 1.0
CG A:ASP186 2.9 15.4 1.0
CE1 A:HIS188 2.9 18.2 1.0
CG A:ASP285 3.0 17.1 1.0
OD2 A:ASP186 3.1 15.8 1.0
CG A:HIS188 3.1 15.2 1.0
OD1 A:ASP285 3.3 16.7 1.0
CB A:HIS188 3.6 14.1 1.0
N A:HIS188 3.7 14.6 1.0
C4 A:5IB507 3.9 67.0 1.0
NE2 A:HIS188 4.1 18.7 1.0
CA A:GLY339 4.1 16.0 1.0
N A:LEU187 4.2 14.5 1.0
CD2 A:HIS188 4.2 20.0 1.0
CB A:ASP186 4.3 12.6 1.0
CA A:HIS188 4.3 14.5 1.0
CB A:ASP285 4.3 13.1 1.0
CB A:LEU187 4.4 13.4 1.0
C6 A:5IB507 4.5 72.6 1.0
OH A:TYR341 4.5 20.0 1.0
N A:GLY339 4.5 13.8 1.0
NE2 A:HIS141 4.5 16.1 1.0
C A:LEU187 4.6 15.9 1.0
CE2 A:TYR341 4.6 18.7 1.0
CA A:LEU187 4.6 14.0 1.0
C3 A:5IB507 4.8 65.9 1.0
C A:ASP186 4.9 16.9 1.0
NE2 A:HIS142 4.9 17.9 1.0
CE1 A:HIS141 4.9 14.7 1.0
CA A:ASP186 5.0 12.5 1.0

Zinc binding site 2 out of 4 in 7p3s

Go back to Zinc Binding Sites List in 7p3s
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:15.4
occ:1.00
OD1 B:ASP186 1.9 13.7 1.0
OD2 B:ASP285 1.9 12.8 1.0
ND1 B:HIS188 2.1 17.7 1.0
O1 B:5IB501 2.1 26.2 1.0
O2 B:5IB501 2.4 23.4 1.0
C5 B:5IB501 2.6 46.2 1.0
N B:5IB501 2.8 37.2 1.0
CG B:ASP186 2.8 14.5 1.0
CG B:ASP285 2.9 15.1 1.0
CE1 B:HIS188 3.0 19.6 1.0
OD2 B:ASP186 3.1 12.6 1.0
CG B:HIS188 3.2 13.7 1.0
OD1 B:ASP285 3.3 13.5 1.0
CB B:HIS188 3.6 11.7 1.0
C4 B:5IB501 3.8 52.4 1.0
N B:HIS188 3.8 11.6 1.0
CA B:GLY339 4.1 12.6 1.0
NE2 B:HIS188 4.1 16.8 1.0
N B:LEU187 4.2 11.6 1.0
CB B:ASP186 4.2 11.8 1.0
CD2 B:HIS188 4.2 14.1 1.0
C6 B:5IB501 4.3 58.1 1.0
CB B:ASP285 4.3 13.1 1.0
CA B:HIS188 4.3 13.0 1.0
CB B:LEU187 4.4 11.4 1.0
NE2 B:HIS141 4.5 12.8 1.0
OH B:TYR341 4.5 19.8 1.0
N B:GLY339 4.5 14.1 1.0
CE2 B:TYR341 4.6 13.0 1.0
C B:LEU187 4.6 13.6 1.0
CA B:LEU187 4.7 9.7 1.0
CE1 B:HIS141 4.8 11.9 1.0
C3 B:5IB501 4.8 47.1 1.0
C B:ASP186 4.9 11.6 1.0
NE2 B:HIS142 4.9 17.6 1.0
CA B:ASP186 5.0 11.6 1.0

Zinc binding site 3 out of 4 in 7p3s

Go back to Zinc Binding Sites List in 7p3s
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:15.2
occ:1.00
OD1 C:ASP186 1.9 12.5 1.0
OD2 C:ASP285 2.0 13.8 1.0
ND1 C:HIS188 2.1 16.2 1.0
O1 C:5IB501 2.2 44.2 1.0
O2 C:5IB501 2.3 35.9 1.0
C5 C:5IB501 2.5 52.6 1.0
N C:5IB501 2.6 34.9 1.0
CG C:ASP186 2.8 13.4 1.0
CG C:ASP285 3.0 15.3 1.0
CE1 C:HIS188 3.0 17.1 1.0
OD2 C:ASP186 3.0 12.1 1.0
CG C:HIS188 3.2 12.3 1.0
OD1 C:ASP285 3.3 12.6 1.0
CB C:HIS188 3.6 11.0 1.0
C4 C:5IB501 3.8 60.7 1.0
N C:HIS188 3.8 10.4 1.0
CA C:GLY339 4.1 12.4 1.0
NE2 C:HIS188 4.1 17.4 1.0
N C:LEU187 4.2 12.6 1.0
CB C:ASP186 4.2 10.5 1.0
CD2 C:HIS188 4.2 17.1 1.0
C6 C:5IB501 4.3 66.7 1.0
CB C:ASP285 4.3 11.0 1.0
CA C:HIS188 4.3 12.1 1.0
CB C:LEU187 4.4 10.9 1.0
NE2 C:HIS141 4.5 14.6 1.0
OH C:TYR341 4.5 18.6 1.0
N C:GLY339 4.5 12.5 1.0
CE2 C:TYR341 4.6 16.4 1.0
C C:LEU187 4.6 13.0 1.0
CA C:LEU187 4.6 10.8 1.0
CE1 C:HIS141 4.8 12.8 1.0
C3 C:5IB501 4.8 58.7 1.0
C C:ASP186 4.9 13.5 1.0
CA C:ASP186 4.9 10.6 1.0
NE2 C:HIS142 4.9 16.4 1.0

Zinc binding site 4 out of 4 in 7p3s

Go back to Zinc Binding Sites List in 7p3s
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:17.5
occ:1.00
OD2 D:ASP285 1.9 16.3 1.0
OD1 D:ASP186 1.9 15.2 1.0
ND1 D:HIS188 2.1 16.6 1.0
O1 D:5IB501 2.3 39.7 1.0
O2 D:5IB501 2.4 36.6 1.0
C5 D:5IB501 2.7 57.9 1.0
N D:5IB501 2.7 51.9 1.0
CG D:ASP186 2.8 14.7 1.0
CG D:ASP285 3.0 16.9 1.0
CE1 D:HIS188 3.0 19.2 1.0
OD2 D:ASP186 3.1 14.9 1.0
CG D:HIS188 3.2 14.2 1.0
OD1 D:ASP285 3.4 16.3 1.0
CB D:HIS188 3.6 14.9 1.0
N D:HIS188 3.8 14.4 1.0
C4 D:5IB501 3.9 57.9 1.0
CA D:GLY339 4.1 13.7 1.0
NE2 D:HIS188 4.2 18.0 1.0
N D:LEU187 4.2 13.8 1.0
CB D:ASP186 4.2 13.0 1.0
CD2 D:HIS188 4.3 16.9 1.0
CB D:ASP285 4.3 14.5 1.0
CA D:HIS188 4.3 15.0 1.0
OH D:TYR341 4.4 20.8 1.0
CB D:LEU187 4.4 15.3 1.0
N D:GLY339 4.5 16.7 1.0
C6 D:5IB501 4.5 60.6 1.0
NE2 D:HIS141 4.5 16.9 1.0
CE2 D:TYR341 4.6 23.3 1.0
C D:LEU187 4.6 15.6 1.0
CA D:LEU187 4.7 16.0 1.0
C3 D:5IB501 4.8 54.3 1.0
CE1 D:HIS141 4.9 14.8 1.0
C D:ASP186 4.9 16.3 1.0
NE2 D:HIS142 4.9 18.0 1.0
CA D:ASP186 5.0 14.5 1.0

Reference:

T.B.Shaik, C.Romier. Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 12 To Be Published.
Page generated: Fri Sep 24 17:11:40 2021

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