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Zinc in PDB 4rn2: Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.

Enzymatic activity of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.

All present enzymatic activity of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn2 was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.764, 84.712, 94.139, 90.00, 100.47, 90.00
R / Rfree (%) 18.7 / 22.4

Other elements in 4rn2:

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. (pdb code 4rn2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4rn2

Go back to Zinc Binding Sites List in 4rn2
Zinc binding site 1 out of 2 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.2
occ:1.00
OD2 A:ASP178 2.1 30.4 1.0
OD2 A:ASP267 2.1 26.8 1.0
ND1 A:HIS180 2.3 29.9 1.0
S1 A:L7G404 2.5 28.6 1.0
CG A:ASP178 2.8 30.3 1.0
OD1 A:ASP178 2.8 27.2 1.0
CE1 A:HIS180 3.1 34.9 1.0
C1 A:L7G404 3.2 27.3 1.0
CG A:ASP267 3.2 27.0 1.0
CG A:HIS180 3.3 29.6 1.0
OD1 A:ASP267 3.6 37.5 1.0
CB A:HIS180 3.7 28.1 1.0
N A:HIS180 3.8 24.7 1.0
C2 A:L7G404 4.1 33.2 1.0
CA A:GLY304 4.2 28.7 1.0
CB A:ASP178 4.2 29.1 1.0
N A:LEU179 4.2 31.3 1.0
NE2 A:HIS180 4.3 27.7 1.0
CD2 A:HIS180 4.4 25.1 1.0
CA A:HIS180 4.4 27.7 1.0
NE2 A:HIS143 4.4 35.5 1.0
CB A:ASP267 4.5 27.1 1.0
CB A:LEU179 4.5 27.3 1.0
NE2 A:HIS142 4.7 29.8 1.0
CE1 A:TYR306 4.7 32.4 1.0
N A:GLY304 4.7 26.8 1.0
OH A:TYR306 4.7 28.7 1.0
C A:LEU179 4.7 30.4 1.0
CA A:LEU179 4.7 23.8 1.0
C A:ASP178 5.0 31.9 1.0

Zinc binding site 2 out of 2 in 4rn2

Go back to Zinc Binding Sites List in 4rn2
Zinc binding site 2 out of 2 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:28.3
occ:1.00
OD2 B:ASP267 2.1 26.5 1.0
OD2 B:ASP178 2.1 21.5 1.0
ND1 B:HIS180 2.2 27.5 1.0
S1 B:L7G404 2.4 28.2 1.0
CG B:ASP178 2.9 24.4 1.0
OD1 B:ASP178 3.0 20.2 1.0
CE1 B:HIS180 3.0 32.2 1.0
C1 B:L7G404 3.1 37.9 1.0
CG B:ASP267 3.2 28.9 1.0
CG B:HIS180 3.3 28.7 1.0
OD1 B:ASP267 3.6 30.2 1.0
CB B:HIS180 3.8 24.0 1.0
N B:HIS180 3.8 22.9 1.0
C2 B:L7G404 3.9 35.0 1.0
CA B:GLY304 4.2 26.3 1.0
N B:LEU179 4.2 29.9 1.0
NE2 B:HIS180 4.2 35.4 1.0
CB B:ASP178 4.3 27.2 1.0
NE2 B:HIS143 4.3 39.9 1.0
CD2 B:HIS180 4.3 31.1 1.0
CB B:LEU179 4.4 22.4 1.0
CA B:HIS180 4.4 22.9 1.0
CB B:ASP267 4.4 26.9 1.0
NE2 B:HIS142 4.6 28.3 1.0
CE1 B:TYR306 4.6 27.3 1.0
OH B:TYR306 4.6 33.5 1.0
CA B:LEU179 4.7 23.1 1.0
C B:LEU179 4.7 29.5 1.0
N B:GLY304 4.7 26.8 1.0

Reference:

C.Decroos, D.J.Clausen, B.E.Haines, O.Wiest, R.M.Williams, D.W.Christianson. Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25793284
DOI: 10.1021/ACS.BIOCHEM.5B00010
Page generated: Wed Dec 16 05:46:05 2020

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