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Zinc in PDB 4bz6: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha, PDB code: 4bz6 was solved by M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.74 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.640, 70.640, 97.990, 77.88, 75.48, 85.69
R / Rfree (%) 16.33 / 19.1

Other elements in 4bz6:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha 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 Saha (pdb code 4bz6). 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 Saha, PDB code: 4bz6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4bz6

Go back to Zinc Binding Sites List in 4bz6
Zinc binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:26.9
occ:1.00
OD2 A:ASP285 2.0 19.2 1.0
OD1 A:ASP186 2.1 18.8 1.0
ND1 A:HIS188 2.1 18.9 1.0
O1 A:SHH700 2.2 25.1 1.0
O2 A:SHH700 2.3 26.1 1.0
N1 A:SHH700 2.8 24.2 1.0
CG A:ASP186 2.8 17.9 1.0
C1 A:SHH700 2.9 27.0 1.0
CG A:ASP285 2.9 20.2 1.0
OD2 A:ASP186 2.9 17.4 1.0
CE1 A:HIS188 3.0 18.7 1.0
CG A:HIS188 3.2 17.2 1.0
OD1 A:ASP285 3.2 20.2 1.0
CB A:HIS188 3.6 13.1 1.0
N A:HIS188 3.8 13.3 1.0
CA A:GLY339 4.0 20.0 1.0
NE2 A:HIS188 4.2 19.1 1.0
CB A:ASP186 4.3 13.9 1.0
C2 A:SHH700 4.3 28.9 1.0
CB A:ASP285 4.3 15.1 1.0
CD2 A:HIS188 4.3 18.9 1.0
N A:LEU187 4.3 16.0 1.0
CA A:HIS188 4.3 13.2 1.0
O A:HOH2134 4.4 32.6 1.0
N A:GLY339 4.4 19.6 1.0
NE2 A:HIS141 4.5 19.0 1.0
CB A:LEU187 4.5 14.4 1.0
OH A:TYR341 4.6 28.8 1.0
C3 A:SHH700 4.7 33.2 1.0
C A:LEU187 4.7 17.4 1.0
CE2 A:TYR341 4.8 27.8 1.0
CA A:LEU187 4.8 14.2 1.0
CE1 A:HIS141 4.9 18.3 1.0
NE2 A:HIS142 4.9 19.2 1.0
C A:ASP186 5.0 19.4 1.0

Zinc binding site 2 out of 4 in 4bz6

Go back to Zinc Binding Sites List in 4bz6
Zinc binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:24.5
occ:1.00
OD2 B:ASP285 1.9 15.5 1.0
OD1 B:ASP186 2.0 15.7 1.0
ND1 B:HIS188 2.1 19.8 1.0
O1 B:SHH700 2.2 23.2 1.0
O2 B:SHH700 2.5 27.7 1.0
CG B:ASP186 2.8 14.9 1.0
N1 B:SHH700 2.8 24.3 1.0
CG B:ASP285 2.9 19.7 1.0
OD2 B:ASP186 2.9 16.1 1.0
C1 B:SHH700 3.0 27.0 1.0
CE1 B:HIS188 3.0 19.6 1.0
CG B:HIS188 3.2 18.8 1.0
OD1 B:ASP285 3.2 19.8 1.0
CB B:HIS188 3.6 15.3 1.0
N B:HIS188 3.8 15.2 1.0
CA B:GLY339 4.1 13.9 1.0
NE2 B:HIS188 4.2 20.3 1.0
CB B:ASP186 4.2 12.2 1.0
CB B:ASP285 4.2 12.4 1.0
CD2 B:HIS188 4.3 21.0 1.0
N B:LEU187 4.3 15.5 1.0
C2 B:SHH700 4.4 23.6 1.0
CB B:LEU187 4.4 13.6 1.0
CA B:HIS188 4.4 15.3 1.0
O B:HOH2106 4.4 34.7 1.0
NE2 B:HIS141 4.4 17.5 1.0
N B:GLY339 4.5 13.8 1.0
OH B:TYR341 4.6 29.1 1.0
CE1 B:TYR341 4.7 25.0 1.0
C B:LEU187 4.7 18.7 1.0
CA B:LEU187 4.7 14.6 1.0
CE1 B:HIS141 4.8 17.3 1.0
C3 B:SHH700 4.8 25.8 1.0
C B:ASP186 4.9 16.4 1.0
NE2 B:HIS142 5.0 20.8 1.0
CA B:ASP186 5.0 10.6 1.0

Zinc binding site 3 out of 4 in 4bz6

Go back to Zinc Binding Sites List in 4bz6
Zinc binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:26.1
occ:1.00
OD2 C:ASP285 2.0 15.6 1.0
OD1 C:ASP186 2.0 16.3 1.0
O1 C:SHH700 2.1 20.2 1.0
ND1 C:HIS188 2.2 20.6 1.0
O2 C:SHH700 2.4 23.2 1.0
N1 C:SHH700 2.7 19.1 1.0
CG C:ASP186 2.8 15.4 1.0
C1 C:SHH700 2.9 23.6 1.0
CG C:ASP285 2.9 17.9 1.0
OD2 C:ASP186 3.0 16.7 1.0
CE1 C:HIS188 3.0 20.3 1.0
OD1 C:ASP285 3.2 17.1 1.0
CG C:HIS188 3.3 19.0 1.0
CB C:HIS188 3.7 15.5 1.0
N C:HIS188 3.9 15.3 1.0
CA C:GLY339 4.0 17.1 1.0
NE2 C:HIS188 4.2 20.8 1.0
CB C:ASP186 4.3 11.7 1.0
CB C:ASP285 4.3 14.1 1.0
C2 C:SHH700 4.3 24.4 1.0
CD2 C:HIS188 4.4 20.9 1.0
N C:LEU187 4.4 14.0 1.0
NE2 C:HIS141 4.4 17.1 1.0
CA C:HIS188 4.4 15.5 1.0
N C:GLY339 4.4 17.8 1.0
OH C:TYR341 4.5 28.9 1.0
CB C:LEU187 4.5 12.5 1.0
CE2 C:TYR341 4.7 24.2 1.0
C3 C:SHH700 4.7 26.7 1.0
C C:LEU187 4.8 17.6 1.0
CE1 C:HIS141 4.8 16.5 1.0
CA C:LEU187 4.8 12.9 1.0
NE2 C:HIS142 4.9 20.8 1.0
C C:GLY339 5.0 19.4 1.0

Zinc binding site 4 out of 4 in 4bz6

Go back to Zinc Binding Sites List in 4bz6
Zinc binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:27.2
occ:1.00
OD2 D:ASP285 1.9 18.7 1.0
OD1 D:ASP186 2.0 18.1 1.0
ND1 D:HIS188 2.1 21.3 1.0
O1 D:SHH700 2.1 31.1 1.0
O2 D:SHH700 2.3 26.8 1.0
N1 D:SHH700 2.7 30.2 1.0
C1 D:SHH700 2.8 29.6 1.0
CG D:ASP186 2.9 17.9 1.0
CG D:ASP285 2.9 22.3 1.0
CE1 D:HIS188 3.0 21.3 1.0
OD2 D:ASP186 3.1 18.9 1.0
CG D:HIS188 3.2 19.5 1.0
OD1 D:ASP285 3.2 21.2 1.0
CB D:HIS188 3.6 15.7 1.0
N D:HIS188 3.8 16.6 1.0
CA D:GLY339 4.1 19.0 1.0
NE2 D:HIS188 4.1 21.6 1.0
C2 D:SHH700 4.2 31.3 1.0
CD2 D:HIS188 4.3 21.7 1.0
CB D:ASP285 4.3 16.3 1.0
CB D:ASP186 4.3 15.2 1.0
O D:HOH2107 4.3 28.7 1.0
N D:LEU187 4.3 15.7 1.0
CA D:HIS188 4.4 15.6 1.0
NE2 D:HIS141 4.4 19.1 1.0
OH D:TYR341 4.5 27.6 1.0
N D:GLY339 4.5 19.6 1.0
CB D:LEU187 4.5 15.9 1.0
C3 D:SHH700 4.6 34.0 1.0
C D:LEU187 4.7 19.5 1.0
CE2 D:TYR341 4.8 26.4 1.0
CA D:LEU187 4.8 15.8 1.0
CE1 D:HIS141 4.9 18.4 1.0
NE2 D:HIS142 4.9 18.6 1.0
C D:ASP186 5.0 19.6 1.0

Reference:

M.Marek, S.Kannan, A.Hauser, M.Moraes Mourao, S.Caby, V.Cura, D.A.Stolfa, K.Schmidtkunz, J.Lancelot, L.Andrade, J.Renaud, G.Oliveira, W.Sippl, M.Jung, J.Cavarelli, R.J.Pierce, C.Romier. Structural Basis For the Inhibition of Histone Deacetylase 8 (HDAC8), A Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni. Plos Pathog. V. 9 03645 2013.
ISSN: ISSN 1553-7366
PubMed: 24086136
DOI: 10.1371/JOURNAL.PPAT.1003645
Page generated: Wed Dec 16 05:06:50 2020

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