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Zinc in PDB 3f0r: Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form

Enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r was solved by D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.97 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.895, 90.705, 92.141, 90.00, 94.63, 90.00
R / Rfree (%) 21 / 25.8

Other elements in 3f0r:

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form also contains other interesting chemical elements:

Potassium (K) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form (pdb code 3f0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3f0r

Go back to Zinc Binding Sites List in 3f0r
Zinc binding site 1 out of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:42.4
occ:1.00
 OD2 A:ASP178 1.8 34.5 1.0
OD2 A:ASP267 2.0 26.4 1.0
O2 A:TSN801 2.2 77.7 1.0
O1 A:TSN801 2.2 77.6 1.0
ND1 A:HIS180 2.3 42.6 1.0
N1 A:TSN801 2.6 77.8 1.0
C13 A:TSN801 2.6 77.9 1.0
CG A:ASP178 2.8 35.1 1.0
CE1 A:HIS180 3.1 39.3 1.0
CG A:HIS180 3.1 39.2 1.0
CG A:ASP267 3.2 31.9 1.0
OD1 A:ASP178 3.2 35.6 1.0
CB A:HIS180 3.5 37.4 1.0
OD1 A:ASP267 3.7 30.6 1.0
N A:HIS180 3.8 33.6 1.0
C12 A:TSN801 3.9 78.0 1.0
NE2 A:HIS180 4.1 43.1 1.0
CD2 A:HIS180 4.1 40.0 1.0
CA A:GLY304 4.1 36.0 1.0
CB A:ASP178 4.2 31.6 1.0
CA A:HIS180 4.3 35.3 1.0
N A:LEU179 4.3 37.4 1.0
NE2 A:HIS142 4.4 44.1 1.0
CB A:ASP267 4.4 30.9 1.0
N A:GLY304 4.5 39.0 1.0
NE2 A:HIS143 4.6 37.7 1.0
OH A:TYR306 4.6 52.1 1.0
C11 A:TSN801 4.6 78.2 1.0
CB A:LEU179 4.7 36.9 1.0
C A:LEU179 4.8 36.3 1.0
CE1 A:HIS142 4.8 43.3 1.0
CE1 A:TYR306 4.9 47.6 1.0
CA A:LEU179 4.9 36.4 1.0
C A:ASP178 4.9 33.0 1.0

Zinc binding site 2 out of 3 in 3f0r

Go back to Zinc Binding Sites List in 3f0r
Zinc binding site 2 out of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:35.4
occ:1.00
 OD2 B:ASP267 1.9 27.8 1.0
OD2 B:ASP178 2.0 35.2 1.0
O2 B:TSN804 2.2 60.4 1.0
ND1 B:HIS180 2.3 34.4 1.0
O1 B:TSN804 2.4 55.0 1.0
CG B:ASP178 2.9 36.3 1.0
C13 B:TSN804 2.9 59.5 1.0
N1 B:TSN804 3.0 59.6 1.0
CG B:ASP267 3.0 35.5 1.0
OD1 B:ASP178 3.1 35.8 1.0
CE1 B:HIS180 3.2 34.6 1.0
CG B:HIS180 3.3 33.1 1.0
OD1 B:ASP267 3.4 39.3 1.0
CB B:HIS180 3.7 33.0 1.0
N B:HIS180 3.8 32.0 1.0
CA B:GLY304 4.1 39.4 1.0
N B:LEU179 4.3 34.9 1.0
CB B:ASP178 4.3 33.2 1.0
C12 B:TSN804 4.3 59.0 1.0
CB B:ASP267 4.3 35.1 1.0
NE2 B:HIS180 4.3 36.7 1.0
CA B:HIS180 4.4 31.7 1.0
CD2 B:HIS180 4.4 34.6 1.0
N B:GLY304 4.4 39.8 1.0
NE2 B:HIS142 4.4 32.0 1.0
OH B:TYR306 4.4 45.5 1.0
CB B:LEU179 4.6 33.7 1.0
CE1 B:TYR306 4.7 42.6 1.0
C B:LEU179 4.7 33.7 1.0
CE1 B:HIS142 4.8 32.4 1.0
CA B:LEU179 4.8 32.1 1.0
C11 B:TSN804 4.9 59.4 1.0
NE2 B:HIS143 5.0 31.1 1.0
C B:ASP178 5.0 34.5 1.0

Zinc binding site 3 out of 3 in 3f0r

Go back to Zinc Binding Sites List in 3f0r
Zinc binding site 3 out of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:48.0
occ:1.00
 OD2 C:ASP267 2.1 58.6 1.0
OD1 C:ASP178 2.1 32.1 1.0
ND1 C:HIS180 2.2 55.3 1.0
O2 C:TSN802 2.3 88.1 1.0
O1 C:TSN802 2.5 86.8 1.0
OD2 C:ASP178 2.6 30.0 1.0
CG C:ASP178 2.7 35.8 1.0
CE1 C:HIS180 2.8 57.4 1.0
C13 C:TSN802 3.0 89.7 1.0
CG C:HIS180 3.0 55.8 1.0
N1 C:TSN802 3.1 88.5 1.0
CG C:ASP267 3.1 58.0 1.0
OD1 C:ASP267 3.5 59.0 1.0
CB C:HIS180 3.6 54.5 1.0
NE2 C:HIS180 3.8 57.6 1.0
N C:HIS180 3.8 53.0 1.0
CD2 C:HIS180 3.9 55.9 1.0
CA C:GLY304 3.9 53.2 1.0
CB C:ASP178 4.2 37.5 1.0
N C:LEU179 4.2 47.5 1.0
N C:GLY304 4.3 52.6 1.0
C12 C:TSN802 4.3 90.5 1.0
CA C:HIS180 4.3 53.5 1.0
CB C:ASP267 4.4 56.0 1.0
OH C:TYR306 4.4 59.0 1.0
NE2 C:HIS142 4.4 61.9 1.0
CB C:LEU179 4.7 48.1 1.0
CE1 C:TYR306 4.7 58.2 1.0
C C:LEU179 4.7 52.2 1.0
CA C:LEU179 4.8 49.8 1.0
CE1 C:HIS142 4.9 62.6 1.0
C C:ASP178 4.9 45.4 1.0
C C:GLY304 4.9 54.3 1.0
C11 C:TSN802 5.0 92.3 1.0
CA C:ASP178 5.0 43.6 1.0
CZ C:TYR306 5.0 58.3 1.0

Reference:

D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors. Biochemistry V. 47 13554 2008.
ISSN: ISSN 0006-2960
PubMed: 19053282
DOI: 10.1021/BI801610C
Page generated: Thu Oct 24 13:00:57 2024

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