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Potassium in PDB 3znr: HDAC7 Bound with Inhibitor TMP269

Enzymatic activity of HDAC7 Bound with Inhibitor TMP269

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

Protein crystallography data

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

Other elements in 3znr:

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

Fluorine (F) 3 atoms
Zinc (Zn) 6 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 1 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:36.6
occ:1.00
 O A:ASP707 2.6 21.5 1.0
O A:HIS709 2.8 21.0 1.0
OG A:SER728 2.8 21.5 1.0
O A:ASP705 2.9 21.9 1.0
O A:LEU729 3.0 22.1 1.0
OD1 A:ASP705 3.1 21.6 1.0
CG A:ASP705 3.5 22.1 1.0
C A:ASP705 3.6 21.9 1.0
C A:ASP707 3.7 21.5 1.0
C A:HIS709 3.8 20.9 1.0
C A:LEU729 3.8 22.1 1.0
N A:ASP707 3.9 21.7 1.0
CB A:HIS730 3.9 22.2 1.0
CB A:ASP705 4.0 22.1 1.0
CB A:SER728 4.0 21.7 1.0
N A:LEU729 4.0 21.9 1.0
OD2 A:ASP705 4.1 22.5 1.0
CA A:HIS710 4.2 20.7 1.0
CA A:ASP707 4.2 21.5 1.0
C A:TRP706 4.4 21.8 1.0
N A:TRP706 4.4 21.8 1.0
CB A:ASP707 4.4 21.5 1.0
N A:GLY711 4.4 20.4 1.0
N A:HIS710 4.4 20.8 1.0
CA A:SER728 4.4 21.6 1.0
CA A:ASP705 4.4 21.9 1.0
ND1 A:HIS730 4.5 22.2 1.0
N A:HIS730 4.5 22.2 1.0
CA A:TRP706 4.5 21.8 1.0
CA A:HIS730 4.5 22.2 1.0
N A:HIS709 4.6 21.1 1.0
C A:SER728 4.6 21.8 1.0
CA A:LEU729 4.6 22.0 1.0
CG A:HIS730 4.7 22.2 1.0
C A:VAL708 4.7 21.1 1.0
OH A:TYR726 4.7 22.1 1.0
C A:HIS710 4.7 20.6 1.0
N A:VAL708 4.8 21.3 1.0
O A:HOH2011 4.8 15.8 1.0
CA A:HIS709 4.8 21.0 1.0
CE1 A:HIS669 4.8 19.1 1.0
ND1 A:HIS669 5.0 19.3 1.0

Potassium binding site 2 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 2 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:80.4
occ:1.00
 O A:HOH2015 2.5 9.2 1.0
O A:PHE718 2.7 20.7 1.0
O A:HOH2014 2.9 9.0 1.0
O A:VAL724 2.9 21.0 1.0
O A:PHE755 3.1 17.9 1.0
O A:ASP721 3.6 22.0 1.0
C A:PHE718 3.7 20.8 1.0
C A:PHE755 3.7 18.0 1.0
CB A:PHE718 3.9 20.6 1.0
C A:VAL724 3.9 20.9 1.0
CB A:PHE755 4.1 18.1 1.0
N A:TYR726 4.2 20.9 1.0
N A:ASN756 4.2 17.9 1.0
CB A:TYR726 4.4 21.0 1.0
CB A:ASN756 4.4 17.9 1.0
CA A:ASN756 4.4 17.9 1.0
CA A:PHE718 4.5 20.7 1.0
CA A:LEU725 4.5 20.7 1.0
N A:TYR719 4.6 21.0 1.0
CA A:PHE755 4.6 18.2 1.0
ND2 A:ASN756 4.6 17.1 1.0
CA A:TYR719 4.6 21.1 1.0
N A:LEU725 4.7 20.8 1.0
CG1 A:VAL724 4.7 20.8 1.0
CB A:VAL724 4.7 20.9 1.0
C A:LEU725 4.7 20.8 1.0
C A:ASP721 4.7 21.8 1.0
O A:TYR719 4.8 21.2 1.0
C A:TYR719 4.8 21.3 1.0
CA A:VAL724 4.9 20.9 1.0
CA A:TYR726 4.9 21.0 1.0

Potassium binding site 3 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 3 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K201

b:38.2
occ:1.00
 O B:ASP707 2.7 19.5 1.0
OG B:SER728 2.8 21.3 1.0
O B:HIS709 2.8 20.1 1.0
O B:ASP705 2.8 20.2 1.0
O B:LEU729 3.0 21.3 1.0
OD1 B:ASP705 3.1 20.9 1.0
CG B:ASP705 3.3 20.7 1.0
C B:ASP705 3.6 20.3 1.0
C B:ASP707 3.7 19.6 1.0
OD2 B:ASP705 3.8 20.8 1.0
C B:LEU729 3.8 21.2 1.0
C B:HIS709 3.8 19.8 1.0
CB B:HIS730 3.9 21.3 1.0
CB B:ASP705 3.9 20.4 1.0
N B:ASP707 3.9 19.8 1.0
CB B:SER728 4.0 21.2 1.0
N B:LEU729 4.1 21.2 1.0
CA B:ASP707 4.2 19.7 1.0
CA B:HIS710 4.3 19.7 1.0
N B:TRP706 4.3 20.1 1.0
C B:TRP706 4.4 19.9 1.0
CA B:ASP705 4.4 20.4 1.0
CB B:ASP707 4.4 19.6 1.0
CA B:SER728 4.4 21.1 1.0
N B:GLY711 4.4 19.4 1.0
N B:HIS710 4.5 19.8 1.0
CA B:TRP706 4.5 20.0 1.0
N B:HIS730 4.5 21.3 1.0
CA B:HIS730 4.5 21.4 1.0
CG B:HIS730 4.6 21.0 1.0
CD2 B:HIS730 4.6 20.5 1.0
C B:SER728 4.6 21.1 1.0
OH B:TYR726 4.6 21.7 1.0
CA B:LEU729 4.6 21.2 1.0
N B:HIS709 4.7 19.7 1.0
O B:HOH2013 4.7 14.4 1.0
C B:HIS710 4.8 19.5 1.0
C B:VAL708 4.8 19.6 1.0
N B:VAL708 4.8 19.6 1.0
CE1 B:HIS669 4.8 20.5 1.0
CA B:HIS709 4.9 19.8 1.0
ND1 B:HIS669 5.0 20.5 1.0

Potassium binding site 4 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 4 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K202

b:42.2
occ:1.00
 O B:HOH2018 2.4 20.7 1.0
O B:HOH2017 2.4 15.3 1.0
O B:PHE718 2.5 19.4 1.0
O B:VAL724 2.7 18.8 1.0
O B:ASP721 2.7 19.4 1.0
O B:PHE755 3.4 19.2 1.0
C B:PHE718 3.7 19.4 1.0
C B:ASP721 3.8 19.3 1.0
C B:VAL724 3.8 18.9 1.0
CB B:PHE755 3.8 19.3 1.0
O B:HOH2016 4.0 13.9 1.0
CB B:PHE718 4.0 19.4 1.0
C B:PHE755 4.0 19.3 1.0
N B:ASP721 4.2 19.4 1.0
CA B:ASP721 4.4 19.4 1.0
CA B:PHE718 4.5 19.4 1.0
O B:TYR719 4.5 19.6 1.0
O B:GLY752 4.5 19.9 1.0
C B:TYR719 4.5 19.5 1.0
CA B:PHE755 4.6 19.3 1.0
N B:TYR719 4.6 19.5 1.0
CB B:ASP721 4.6 19.5 1.0
CB B:VAL724 4.6 18.7 1.0
CA B:VAL724 4.6 18.7 1.0
CA B:TYR719 4.7 19.5 1.0
N B:LEU725 4.7 19.0 1.0
N B:VAL724 4.8 18.7 1.0
N B:PRO722 4.8 19.1 1.0
CA B:LEU725 4.8 19.1 1.0
N B:ASN756 4.8 19.3 1.0
CA B:GLY752 4.8 19.8 1.0
N B:TYR726 4.8 19.5 1.0
CA B:PRO722 4.9 19.0 1.0

Potassium binding site 5 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 5 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K201

b:45.3
occ:1.00
 O C:ASP707 2.7 21.4 1.0
O C:ASP705 2.8 22.1 1.0
OG C:SER728 2.9 21.7 1.0
O C:HIS709 2.9 20.4 1.0
O C:LEU729 3.0 22.3 1.0
OD1 C:ASP705 3.3 23.1 1.0
CG C:ASP705 3.4 22.6 1.0
C C:ASP705 3.7 22.1 1.0
C C:ASP707 3.8 21.3 1.0
OD2 C:ASP705 3.8 22.6 1.0
C C:LEU729 3.8 22.2 1.0
C C:HIS709 3.9 20.4 1.0
CB C:HIS730 3.9 22.3 1.0
N C:ASP707 4.0 21.6 1.0
CB C:ASP705 4.0 22.3 1.0
N C:LEU729 4.0 22.0 1.0
CB C:SER728 4.1 21.8 1.0
CA C:ASP707 4.3 21.5 1.0
CA C:HIS710 4.3 20.1 1.0
CA C:SER728 4.4 21.8 1.0
C C:TRP706 4.4 21.8 1.0
CB C:ASP707 4.4 21.5 1.0
N C:TRP706 4.4 22.0 1.0
N C:HIS730 4.4 22.3 1.0
C C:SER728 4.5 21.9 1.0
N C:GLY711 4.5 20.0 1.0
CA C:ASP705 4.5 22.3 1.0
N C:HIS710 4.5 20.2 1.0
CA C:HIS730 4.5 22.4 1.0
CA C:TRP706 4.6 21.9 1.0
CA C:LEU729 4.6 22.2 1.0
CG C:HIS730 4.7 22.3 1.0
CD2 C:HIS730 4.7 22.1 1.0
N C:HIS709 4.7 20.6 1.0
OH C:TYR726 4.7 21.3 1.0
O C:HOH2002 4.8 17.8 1.0
C C:VAL708 4.8 20.8 1.0
C C:HIS710 4.8 20.1 1.0
N C:VAL708 4.9 21.1 1.0
CA C:HIS709 4.9 20.5 1.0

Potassium binding site 6 out of 6 in 3znr

Go back to Potassium Binding Sites List in 3znr
Potassium binding site 6 out of 6 in the HDAC7 Bound with Inhibitor TMP269


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of HDAC7 Bound with Inhibitor TMP269 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K202

b:73.1
occ:1.00
 O C:HOH2004 2.6 5.3 1.0
O C:PHE718 2.7 22.3 1.0
O C:HOH2003 3.0 7.9 1.0
O C:PHE755 3.1 20.3 1.0
O C:VAL724 3.1 21.8 1.0
O C:ASP721 3.7 23.0 1.0
C C:PHE718 3.8 22.3 1.0
C C:PHE755 3.8 20.3 1.0
C C:VAL724 4.1 21.7 1.0
CB C:PHE718 4.1 22.3 1.0
N C:TYR726 4.2 21.3 1.0
CB C:PHE755 4.2 20.3 1.0
ND2 C:ASN756 4.3 19.2 1.0
N C:ASN756 4.4 20.2 1.0
CB C:TYR726 4.4 21.3 1.0
CB C:ASN756 4.4 20.1 1.0
CA C:ASN756 4.5 20.1 1.0
CA C:TYR719 4.6 22.5 1.0
N C:TYR719 4.6 22.4 1.0
CA C:LEU725 4.6 21.4 1.0
CA C:PHE718 4.6 22.2 1.0
CA C:PHE755 4.7 20.3 1.0
N C:LEU725 4.7 21.5 1.0
C C:LEU725 4.8 21.4 1.0
CG1 C:VAL724 4.8 21.7 1.0
O C:TYR719 4.8 22.5 1.0
CB C:VAL724 4.8 21.8 1.0
C C:TYR719 4.9 22.6 1.0
C C:ASP721 4.9 22.9 1.0
CG C:ASN756 4.9 20.0 1.0
CA C:TYR726 4.9 21.3 1.0

Reference:

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
Page generated: Mon Aug 12 09:56:23 2024

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