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

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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: Wed Oct 30 20:42:00 2024

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