Atomistry » Zinc » PDB 2vh5-2vqw » 2vqw
Atomistry »
  Zinc »
    PDB 2vh5-2vqw »
      2vqw »

Zinc in PDB 2vqw: Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR)

Enzymatic activity of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR)

All present enzymatic activity of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR):
3.5.1.98;

Protein crystallography data

The structure of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR), PDB code: 2vqw was solved by M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.0
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 137.911, 137.911, 69.519, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 26.1

Other elements in 2vqw:

The structure of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR) also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR) (pdb code 2vqw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR), PDB code: 2vqw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2vqw

Go back to Zinc Binding Sites List in 2vqw
Zinc binding site 1 out of 2 in the Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1409

b:68.8
occ:1.00
OD2 G:ASP196 2.0 70.7 1.0
OD2 G:ASP290 2.0 83.8 1.0
ND1 G:HIS198 2.0 64.4 1.0
OD1 G:ASP196 2.5 70.8 1.0
CG G:ASP196 2.6 70.1 1.0
CE1 G:HIS198 2.9 64.4 1.0
CG G:ASP290 2.9 84.3 1.0
CG G:HIS198 3.1 64.6 1.0
OD1 G:ASP290 3.4 85.0 1.0
CB G:HIS198 3.5 65.2 1.0
N G:HIS198 3.8 66.0 1.0
NE2 G:HIS198 4.0 64.7 1.0
CB G:ASP196 4.1 69.3 1.0
OH G:TYR332 4.1 84.7 1.0
CB G:ASP290 4.1 84.1 1.0
CD2 G:HIS198 4.1 64.6 1.0
NE2 G:HIS159 4.2 64.4 1.0
CA G:HIS198 4.3 65.4 1.0
N G:VAL197 4.3 67.7 1.0
NE2 G:HIS158 4.3 66.1 1.0
CA G:GLY330 4.3 82.2 1.0
CG1 G:VAL197 4.5 67.0 1.0
CE1 G:HIS158 4.5 66.5 1.0
CE2 G:TYR332 4.7 84.4 1.0
C G:ASP196 4.7 68.5 1.0
N G:GLY330 4.8 81.7 1.0
C G:VAL197 4.8 66.5 1.0
CA G:ASP196 4.8 69.2 1.0
CZ G:TYR332 4.8 84.5 1.0
CA G:VAL197 4.9 67.0 1.0
CE1 G:HIS159 5.0 64.3 1.0

Zinc binding site 2 out of 2 in 2vqw

Go back to Zinc Binding Sites List in 2vqw
Zinc binding site 2 out of 2 in the Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Inhibitor-Free HDAC4 Catalytic Domain (with Gain-of-Function Mutation HIS332TYR) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1410

b:85.5
occ:1.00
NE2 G:HIS31 2.1 86.2 1.0
SG G:CYS107 2.3 86.0 1.0
SG G:CYS23 2.3 81.0 1.0
SG G:CYS25 2.5 82.7 1.0
CE1 G:HIS31 2.9 86.3 1.0
CB G:CYS23 3.1 82.0 1.0
CD2 G:HIS31 3.2 86.2 1.0
CB G:CYS107 3.6 85.3 1.0
CB G:CYS25 4.0 82.5 1.0
ND1 G:HIS31 4.1 86.2 1.0
CG G:HIS31 4.2 86.2 1.0
CA G:CYS23 4.5 82.0 1.0
CD2 G:LEU105 4.6 86.9 1.0
N G:CYS25 4.7 82.5 1.0
N G:GLY109 4.7 82.0 1.0
CA G:GLY109 4.8 81.1 1.0
CA G:CYS25 4.9 82.5 1.0
OG G:SER30 4.9 87.0 1.0
CA G:CYS107 4.9 85.2 1.0
C G:CYS23 4.9 82.3 1.0
O G:CYS107 5.0 84.8 1.0
C G:CYS107 5.0 84.7 1.0

Reference:

M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi. Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals A Regulatory Structural Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200
Page generated: Wed Dec 16 03:55:54 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