Zinc in PDB 8g44: Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Benzylamino)-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-(Benzylamino)-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-(Benzylamino)-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-(Benzylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid, PDB code: 8g44 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) 33.08 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.95, 44.43, 56.13, 90, 90, 90
R / Rfree (%) 16.4 / 19.3

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-(Benzylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid (pdb code 8g44). 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-(Benzylamino)-2-Oxoethyl)-4-Oxo-3,4-Dihydroquinazolin-2- Yl)Propanoic Acid, PDB code: 8g44:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8g44

Go back to Zinc Binding Sites List in 8g44
Zinc binding site 1 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Benzylamino)-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-(Benzylamino)-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:6.9
occ:1.00
 NE2 A:HIS1164 2.1 8.1 1.0
ND1 A:HIS1170 2.1 6.2 1.0
SG A:CYS1148 2.3 8.7 1.0
SG A:CYS1145 2.3 7.8 1.0
CE1 A:HIS1170 3.0 6.7 1.0
CE1 A:HIS1164 3.0 7.5 1.0
CG A:HIS1170 3.1 6.4 1.0
CD2 A:HIS1164 3.1 7.2 1.0
CB A:CYS1145 3.2 6.8 1.0
CB A:CYS1148 3.3 8.5 1.0
CB A:HIS1170 3.5 6.2 1.0
N A:CYS1148 3.8 8.0 1.0
CA A:CYS1148 4.1 7.8 1.0
NE2 A:HIS1170 4.1 7.0 1.0
ND1 A:HIS1164 4.2 8.3 1.0
CD2 A:HIS1170 4.2 6.5 1.0
CG A:HIS1164 4.3 6.9 1.0
OG A:SER1168 4.3 7.7 1.0
CB A:SER1147 4.6 7.6 1.0
CA A:CYS1145 4.6 6.2 1.0
O A:HOH1466 4.8 21.3 1.0
C A:CYS1148 4.8 7.9 1.0
C A:SER1147 4.8 9.0 1.0
CB A:SER1168 4.8 7.7 1.0
N A:TYR1149 4.9 7.8 1.0
N A:SER1147 4.9 6.7 1.0
CA A:SER1147 5.0 7.7 1.0
CA A:HIS1170 5.0 6.2 1.0

Zinc binding site 2 out of 3 in 8g44

Go back to Zinc Binding Sites List in 8g44
Zinc binding site 2 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Benzylamino)-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-(Benzylamino)-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:7.8
occ:1.00
 ND1 A:HIS1160 2.0 9.2 1.0
SG A:CYS1136 2.3 9.1 1.0
SG A:CYS1153 2.3 7.9 1.0
SG A:CYS1133 2.4 8.1 1.0
CE1 A:HIS1160 3.0 9.4 1.0
CG A:HIS1160 3.1 8.5 1.0
CB A:CYS1133 3.3 7.4 1.0
CB A:CYS1153 3.4 7.7 1.0
CB A:CYS1136 3.4 10.0 1.0
CB A:HIS1160 3.5 7.8 1.0
N A:CYS1136 3.7 10.8 1.0
N A:CYS1153 4.0 6.6 1.0
CA A:CYS1136 4.1 10.4 1.0
CB A:ASN1158 4.1 10.1 1.0
NE2 A:HIS1160 4.1 11.0 1.0
CG2 A:THR1138 4.2 9.8 1.0
CD2 A:HIS1160 4.2 10.0 1.0
CA A:CYS1153 4.3 7.0 1.0
ND2 A:ASN1158 4.4 12.9 1.0
N A:HIS1160 4.6 7.2 1.0
CB A:ASP1135 4.6 13.2 1.0
CA A:HIS1160 4.6 7.6 1.0
CA A:CYS1133 4.7 7.9 1.0
C A:ASP1135 4.8 13.5 1.0
C A:CYS1136 4.8 9.8 1.0
CG A:ASN1158 4.9 10.8 1.0
CA A:ASN1158 5.0 9.0 1.0
N A:GLY1137 5.0 10.0 1.0

Zinc binding site 3 out of 3 in 8g44

Go back to Zinc Binding Sites List in 8g44
Zinc binding site 3 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with 3-(3-(2-(Benzylamino)-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-(Benzylamino)-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:6.2
occ:1.00
 ND1 A:HIS1115 2.1 7.7 1.0
SG A:CYS1183 2.3 6.2 1.0
SG A:CYS1186 2.3 7.4 1.0
SG A:CYS1113 2.3 6.5 1.0
CE1 A:HIS1115 3.1 7.1 1.0
CG A:HIS1115 3.1 7.0 1.0
CB A:CYS1113 3.2 6.5 1.0
CB A:CYS1183 3.3 6.4 1.0
CB A:CYS1186 3.3 7.2 1.0
CB A:HIS1115 3.5 6.7 1.0
N A:CYS1186 3.9 6.8 1.0
N A:HIS1115 4.0 6.9 1.0
CD A:PRO1114 4.1 7.7 1.0
CA A:CYS1186 4.2 7.6 1.0
NE2 A:HIS1115 4.2 7.0 1.0
CD2 A:HIS1115 4.2 7.2 1.0
CA A:HIS1115 4.4 6.9 1.0
N A:PRO1114 4.4 7.3 1.0
CA A:CYS1113 4.4 6.8 1.0
CG A:PRO1114 4.5 8.5 1.0
C A:CYS1113 4.6 6.5 1.0
CB A:TYR1185 4.6 7.9 1.0
CA A:CYS1183 4.7 5.8 1.0
O A:HOH1495 4.9 14.4 1.0
C A:TYR1185 4.9 7.5 1.0
C A:PRO1114 5.0 7.1 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 20:42:42 2024

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