Zinc in PDB 3znr: HDAC7 Bound with Inhibitor TMP269

All present enzymatic activity of HDAC7 Bound with Inhibitor TMP269:
3.5.1.98;

The structure of HDAC7 Bound with Inhibitor TMP269, PDB code: 3znr was solved by M.Lobera, K.Madauss, D.Pohlhaus, R.Trump, M.Nolan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.49 / 2.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.393, 81.393, 149.265, 90.00, 90.00, 120.00
R / Rfree (%)	21.235 / 24.102

The structure of HDAC7 Bound with Inhibitor TMP269 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Potassium	(K)	6 atoms

The binding sites of Zinc atom in the HDAC7 Bound with Inhibitor TMP269 (pdb code 3znr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the HDAC7 Bound with Inhibitor TMP269, PDB code: 3znr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:28.7 occ:1.00 OD2 A:ASP801 1.9 22.4 1.0 OD1 A:ASP707 2.1 21.7 1.0 ND1 A:HIS709 2.1 20.8 1.0 O09 A:NU91000 2.7 69.2 1.0 OD2 A:ASP707 2.7 21.1 1.0 CG A:ASP707 2.7 21.5 1.0 F04 A:NU91000 3.0 69.8 1.0 CE1 A:HIS709 3.0 21.3 1.0 CG A:ASP801 3.0 22.7 1.0 C05 A:NU91000 3.1 69.3 1.0 CG A:HIS709 3.2 20.9 1.0 N08 A:NU91000 3.3 69.2 1.0 OD1 A:ASP801 3.5 23.1 1.0 CB A:HIS709 3.6 21.0 1.0 C02 A:NU91000 3.6 69.5 1.0 N06 A:NU91000 3.8 69.3 1.0 N A:HIS709 3.9 21.1 1.0 C07 A:NU91000 3.9 69.1 1.0 NE2 A:HIS709 4.1 21.6 1.0 CD2 A:HIS709 4.2 20.9 1.0 CB A:ASP707 4.2 21.5 1.0 CA A:GLY841 4.2 22.8 1.0 CG1 A:VAL708 4.3 21.1 1.0 CB A:ASP801 4.3 22.6 1.0 NE2 A:HIS669 4.3 19.1 1.0 CA A:HIS709 4.4 21.0 1.0 N A:VAL708 4.4 21.3 1.0 F01 A:NU91000 4.4 69.5 1.0 NE2 A:HIS670 4.6 20.5 1.0 F03 A:NU91000 4.6 69.3 1.0 CE1 A:HIS669 4.7 19.1 1.0 N A:GLY841 4.7 22.7 1.0 C A:ASP707 4.9 21.5 1.0 C A:VAL708 4.9 21.1 1.0 CA A:ASP707 5.0 21.5 1.0 C10 A:NU91000 5.0 68.9 1.0

Zinc binding site 2 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:24.3 occ:1.00 NE2 A:HIS541 2.0 24.2 1.0 SG A:CYS535 2.1 25.0 1.0 SG A:CYS618 2.3 24.9 1.0 SG A:CYS533 2.4 24.2 1.0 CD2 A:HIS541 3.0 24.1 1.0 CE1 A:HIS541 3.0 24.2 1.0 CB A:CYS535 3.2 25.6 1.0 CB A:CYS533 3.3 24.4 1.0 CB A:CYS618 3.4 24.9 1.0 ND1 A:HIS541 4.1 24.2 1.0 CG A:HIS541 4.1 24.4 1.0 N A:CYS535 4.2 25.4 1.0 CA A:CYS535 4.3 25.6 1.0 NE A:ARG540 4.4 26.5 1.0 CA A:CYS533 4.7 24.4 1.0 N A:GLY620 4.7 24.5 1.0 CA A:CYS618 4.8 24.9 1.0 NH2 A:ARG540 4.9 26.7 1.0 C A:CYS533 5.0 24.6 1.0 CA A:GLY620 5.0 24.4 1.0 C A:CYS618 5.0 24.8 1.0

Zinc binding site 3 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:32.0 occ:1.00 OD2 B:ASP801 1.9 20.5 1.0 OD1 B:ASP707 2.0 19.9 1.0 ND1 B:HIS709 2.1 19.2 1.0 CG B:ASP707 2.7 19.7 1.0 OD2 B:ASP707 2.7 19.2 1.0 CE1 B:HIS709 2.9 19.9 1.0 CG B:ASP801 3.0 21.0 1.0 CG B:HIS709 3.2 19.7 1.0 OD1 B:ASP801 3.5 21.0 1.0 CB B:HIS709 3.6 19.7 1.0 N B:HIS709 3.9 19.7 1.0 NE2 B:HIS709 4.1 20.1 1.0 CA B:GLY841 4.2 22.5 1.0 NE2 B:HIS669 4.2 20.7 1.0 CB B:ASP707 4.2 19.6 1.0 CG1 B:VAL708 4.2 19.2 1.0 CD2 B:HIS709 4.2 19.9 1.0 CB B:ASP801 4.3 21.1 1.0 N B:VAL708 4.4 19.6 1.0 CA B:HIS709 4.4 19.8 1.0 NE2 B:HIS670 4.5 22.2 1.0 CE1 B:HIS669 4.6 20.5 1.0 N B:GLY841 4.6 22.5 1.0 C B:ASP707 4.9 19.6 1.0 C B:VAL708 4.9 19.6 1.0 CA B:ASP707 5.0 19.7 1.0

Zinc binding site 4 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:19.5 occ:1.00 NE2 B:HIS541 2.1 21.9 1.0 SG B:CYS618 2.1 26.0 1.0 SG B:CYS535 2.2 24.1 1.0 SG B:CYS533 2.4 23.6 1.0 CD2 B:HIS541 3.0 22.1 1.0 CB B:CYS535 3.0 24.4 1.0 CE1 B:HIS541 3.1 22.1 1.0 CB B:CYS618 3.3 26.4 1.0 CB B:CYS533 3.3 24.0 1.0 NE B:ARG540 4.1 25.4 1.0 N B:CYS535 4.1 24.3 1.0 CA B:CYS535 4.2 24.4 1.0 CG B:HIS541 4.2 22.6 1.0 ND1 B:HIS541 4.2 22.4 1.0 CD B:ARG540 4.4 25.1 1.0 CA B:CYS618 4.6 26.3 1.0 CA B:CYS533 4.7 24.1 1.0 N B:GLY620 4.8 25.7 1.0 C B:CYS618 4.9 26.2 1.0 CA B:GLY620 4.9 25.6 1.0 C B:CYS533 5.0 24.2 1.0 C B:CYS535 5.0 24.5 1.0

Zinc binding site 5 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:27.2 occ:1.00 OD2 C:ASP801 1.9 23.2 1.0 ND1 C:HIS709 2.0 20.8 1.0 OD1 C:ASP707 2.2 21.8 1.0 OD2 C:ASP707 2.6 21.7 1.0 CG C:ASP707 2.8 21.6 1.0 CE1 C:HIS709 2.9 20.8 1.0 CG C:HIS709 3.1 20.6 1.0 CG C:ASP801 3.1 23.5 1.0 CB C:HIS709 3.5 20.5 1.0 OD1 C:ASP801 3.6 23.5 1.0 N C:HIS709 3.8 20.6 1.0 NE2 C:HIS709 4.0 20.9 1.0 CD2 C:HIS709 4.1 20.8 1.0 CA C:GLY841 4.2 24.5 1.0 CG1 C:VAL708 4.2 20.9 1.0 NE2 C:HIS669 4.2 21.6 1.0 CB C:ASP707 4.3 21.5 1.0 CA C:HIS709 4.3 20.5 1.0 CB C:ASP801 4.3 23.6 1.0 N C:VAL708 4.4 21.1 1.0 CE1 C:HIS669 4.5 21.6 1.0 NE2 C:HIS670 4.6 21.2 1.0 N C:GLY841 4.6 24.5 1.0 C C:VAL708 4.8 20.8 1.0 C C:ASP707 4.9 21.3 1.0

Zinc binding site 6 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:21.1 occ:1.00 SG C:CYS535 2.0 22.4 1.0 NE2 C:HIS541 2.1 23.4 1.0 SG C:CYS533 2.4 22.5 1.0 SG C:CYS618 2.5 23.6 1.0 CE1 C:HIS541 3.0 23.5 1.0 CD2 C:HIS541 3.0 23.5 1.0 CB C:CYS535 3.2 22.7 1.0 CB C:CYS533 3.3 22.6 1.0 CB C:CYS618 3.4 23.9 1.0 ND1 C:HIS541 4.1 23.6 1.0 CG C:HIS541 4.2 23.7 1.0 N C:CYS535 4.2 22.7 1.0 CA C:CYS535 4.3 22.7 1.0 CD C:ARG540 4.4 25.0 1.0 NE C:ARG540 4.5 25.4 1.0 CG C:ARG540 4.7 24.6 1.0 CA C:CYS533 4.7 22.6 1.0 CA C:CYS618 4.8 23.9 1.0 N C:GLY620 5.0 24.3 1.0 CG1 C:ILE628 5.0 23.9 1.0 C C:CYS533 5.0 22.6 1.0 C C:CYS535 5.0 22.8 1.0

M.Lobera, K.P.Madauss, D.T.Pohlhaus, Q.G.Wright, M.Trocha, D.R.Schmidt, E.Baloglu, R.P.Trump, M.S.Head, G.A.Hofmann, M.Murray-Thompson, B.Schwartz, S.Chakravorty, Z.Wu, P.K.Mander, L.Kruidenier, R.A.Reid, W.Burkhart, B.J.Turunen, J.X.Rong, C.Wagner, M.B.Moyer, C.Wells, X.Hong, J.T.Moore, J.D.Williams, D.Soler, S.Ghosh, M.A.Nolan. Selective Class Iia Histone Deacetylase Inhibition Via A Non-Chelating Zinc Binding Group Nat.Chem.Biol. V. 9 319 2013.
ISSN: ISSN 1552-4450
PubMed: 23524983
DOI: 10.1038/NCHEMBIO.1223