Zinc in PDB 2vqw: 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;

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

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

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 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 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

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