Atomistry » Zinc » PDB 8fqx-8g45 » 8g43
Atomistry »
  Zinc »
    PDB 8fqx-8g45 »
      8g43 »

Zinc in PDB 8g43: Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid

Enzymatic activity of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid

All present enzymatic activity of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid:
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid, PDB code: 8g43 was solved by R.J.Harding, I.Franzoni, M.K.Mann, M.Szewczyk, B.Mirabi, D.D.G.Owens, S.Ackloo, A.Scheremetjew, K.A.Juarez-Ornelas, R.Sanichar, R.J.Baker, C.Dank, P.J.Brown, D.Barsyte-Lovejoy, V.Santhakumar, M.Schapira, M.Lautens, C.H.Arrowsmith, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.87, 44.04, 55.87, 90, 90, 90
R / Rfree (%) 16.1 / 17.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid (pdb code 8g43). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid, PDB code: 8g43:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8g43

Go back to Zinc Binding Sites List in 8g43
Zinc binding site 1 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:8.8
occ:1.00
 NE2 A:HIS1164 2.0 8.8 1.0
ND1 A:HIS1170 2.0 8.6 1.0
SG A:CYS1145 2.3 8.0 1.0
CE1 A:HIS1170 3.0 8.3 1.0
CE1 A:HIS1164 3.0 8.5 1.0
CD2 A:HIS1164 3.0 8.3 1.0
CG A:HIS1170 3.1 8.3 1.0
SG A:CYS1148 3.1 12.1 1.0
CB A:CYS1145 3.1 7.4 1.0
CB A:HIS1170 3.4 8.6 1.0
N A:CYS1148 3.9 10.3 1.0
CB A:CYS1148 4.0 9.9 1.0
NE2 A:HIS1170 4.2 8.8 1.0
ND1 A:HIS1164 4.2 9.1 1.0
CD2 A:HIS1170 4.2 8.6 1.0
CG A:HIS1164 4.2 8.0 1.0
OG A:SER1168 4.2 9.9 1.0
CB A:SER1147 4.4 10.2 1.0
CA A:CYS1148 4.4 9.7 1.0
O A:HOH1447 4.5 23.2 1.0
CA A:CYS1145 4.5 7.8 1.0
CB A:SER1168 4.8 10.1 1.0
C A:SER1147 4.8 10.0 1.0
N A:SER1147 4.9 9.3 1.0
CA A:HIS1170 4.9 8.4 1.0
CA A:SER1147 4.9 10.0 1.0
C A:CYS1145 5.0 8.1 1.0

Zinc binding site 2 out of 3 in 8g43

Go back to Zinc Binding Sites List in 8g43
Zinc binding site 2 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:9.4
occ:1.00
 ND1 A:HIS1160 2.0 10.5 1.0
SG A:CYS1136 2.3 10.6 1.0
SG A:CYS1153 2.3 9.3 1.0
SG A:CYS1133 2.4 9.5 1.0
CE1 A:HIS1160 3.0 10.8 1.0
CG A:HIS1160 3.1 9.6 1.0
CB A:CYS1133 3.2 8.8 1.0
CB A:CYS1136 3.4 11.4 1.0
CB A:CYS1153 3.4 8.7 1.0
CB A:HIS1160 3.5 9.3 1.0
N A:CYS1136 3.8 11.2 1.0
N A:CYS1153 3.9 7.6 1.0
CB A:ASN1158 4.1 11.8 1.0
CA A:CYS1136 4.2 11.2 1.0
CG2 A:THR1138 4.2 11.9 1.0
NE2 A:HIS1160 4.2 11.4 1.0
CD2 A:HIS1160 4.2 12.1 1.0
CA A:CYS1153 4.3 8.0 1.0
ND2 A:ASN1158 4.5 13.6 1.0
N A:HIS1160 4.5 9.3 1.0
CB A:ASP1135 4.6 14.3 0.7
CB A:ASP1135 4.6 12.2 0.3
CA A:HIS1160 4.6 9.1 1.0
CA A:CYS1133 4.7 9.0 1.0
C A:ASP1135 4.8 11.8 0.3
C A:CYS1136 4.9 11.3 1.0
CG A:ASN1158 4.9 13.3 1.0
C A:ASP1135 4.9 12.8 0.7
CA A:ASN1158 4.9 11.4 1.0
N A:GLY1137 5.0 12.2 1.0

Zinc binding site 3 out of 3 in 8g43

Go back to Zinc Binding Sites List in 8g43
Zinc binding site 3 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Methylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:10.2
occ:1.00
 ND1 A:HIS1115 2.1 10.5 1.0
SG A:CYS1113 2.3 9.6 1.0
SG A:CYS1183 2.3 8.5 1.0
SG A:CYS1186 2.4 13.4 1.0
CE1 A:HIS1115 3.1 11.1 1.0
CG A:HIS1115 3.1 9.3 1.0
CB A:CYS1113 3.3 10.8 1.0
CB A:CYS1183 3.3 9.2 1.0
CB A:CYS1186 3.4 11.4 1.0
CB A:HIS1115 3.5 9.2 1.0
N A:CYS1186 4.0 10.1 1.0
N A:HIS1115 4.0 11.2 1.0
CD A:PRO1114 4.1 12.0 1.0
NE2 A:HIS1115 4.2 11.0 1.0
CD2 A:HIS1115 4.2 10.3 1.0
CA A:CYS1186 4.3 10.6 1.0
CA A:HIS1115 4.4 10.5 1.0
N A:PRO1114 4.4 11.1 1.0
CA A:CYS1113 4.5 11.0 1.0
CB A:TYR1185 4.5 9.1 1.0
C A:CYS1113 4.6 10.7 1.0
CG A:PRO1114 4.7 14.0 1.0
CA A:CYS1183 4.7 8.8 1.0
O A:HOH1486 4.9 20.3 1.0
C A:TYR1185 4.9 9.4 1.0
C A:PRO1114 4.9 12.3 1.0

Reference:

R.J.Harding, I.Franzoni, M.K.Mann, M.Szewczyk, B.Mirabi, D.D.G.Owens, S.Ackloo, A.Scheremetjew, K.A.Juarez-Ornelas, R.Sanichar, R.J.Baker, C.Dank, P.J.Brown, D.Barsyte-Lovejoy, V.Santhakumar, M.Schapira, M.Lautens, C.H.Arrowsmith. Discovery and Characterization of A Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6 To Be Published.
Page generated: Fri Aug 22 10:11:53 2025

Last articles

Zn in 9MYP
Zn in 9MU8
Zn in 9N1F
Zn in 9MUX
Zn in 9MT6
Zn in 9MT2
Zn in 9MUG
Zn in 9MSJ
Zn in 9MSH
Zn in 9MSG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy