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Zinc in PDB 8g45: Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe

Enzymatic activity of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe

All present enzymatic activity of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe:
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe, PDB code: 8g45 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) 34.96 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.61, 44.91, 55.7, 90, 90, 90
R / Rfree (%) 16 / 19

Other elements in 8g45:

The structure of Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe (pdb code 8g45). 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 Sgc-UBD253 Chemical Probe, PDB code: 8g45:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8g45

Go back to Zinc Binding Sites List in 8g45
Zinc binding site 1 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe


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 Sgc-UBD253 Chemical Probe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:27.0
occ:1.00
 NE2 A:HIS1164 2.0 23.6 1.0
ND1 A:HIS1170 2.0 22.0 1.0
SG A:CYS1145 2.4 27.4 1.0
SG A:CYS1148 2.9 34.0 1.0
CE1 A:HIS1170 3.0 28.0 1.0
CE1 A:HIS1164 3.0 27.9 1.0
CD2 A:HIS1164 3.0 24.0 1.0
CG A:HIS1170 3.1 25.0 1.0
CB A:CYS1145 3.3 24.7 1.0
CB A:HIS1170 3.4 22.7 1.0
CB A:CYS1148 4.0 29.5 1.0
N A:CYS1148 4.1 24.5 1.0
OG A:SER1168 4.1 27.1 1.0
ND1 A:HIS1164 4.1 27.1 1.0
NE2 A:HIS1170 4.1 25.5 1.0
CG A:HIS1164 4.2 25.3 1.0
CD2 A:HIS1170 4.2 26.7 1.0
CB A:SER1147 4.5 24.7 1.0
CA A:CYS1148 4.6 24.8 1.0
CB A:SER1168 4.6 27.6 1.0
CA A:CYS1145 4.7 22.1 1.0
CA A:HIS1170 4.9 24.7 1.0

Zinc binding site 2 out of 3 in 8g45

Go back to Zinc Binding Sites List in 8g45
Zinc binding site 2 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe


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 Sgc-UBD253 Chemical Probe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:27.3
occ:1.00
 ND1 A:HIS1160 2.0 29.6 1.0
SG A:CYS1153 2.3 25.4 1.0
SG A:CYS1136 2.3 30.0 1.0
SG A:CYS1133 2.4 26.9 1.0
CE1 A:HIS1160 3.0 31.0 1.0
CG A:HIS1160 3.1 31.1 1.0
CB A:CYS1133 3.2 25.6 1.0
CB A:CYS1153 3.3 26.2 1.0
CB A:CYS1136 3.4 34.5 1.0
CB A:HIS1160 3.5 25.4 1.0
N A:CYS1136 3.7 31.5 1.0
N A:CYS1153 4.0 23.8 1.0
CB A:ASN1158 4.0 35.9 1.0
CA A:CYS1136 4.1 31.5 1.0
CG2 A:THR1138 4.1 31.2 1.0
NE2 A:HIS1160 4.2 32.8 1.0
CD2 A:HIS1160 4.2 32.9 1.0
CA A:CYS1153 4.3 23.4 1.0
ND2 A:ASN1158 4.5 35.6 1.0
CB A:ASP1135 4.5 39.1 1.0
N A:HIS1160 4.6 25.6 1.0
CA A:HIS1160 4.6 24.1 1.0
CA A:CYS1133 4.7 24.0 1.0
C A:ASP1135 4.8 38.7 1.0
C A:CYS1136 4.8 30.9 1.0
CG A:ASN1158 4.8 37.7 1.0
N A:GLY1137 4.9 29.5 1.0
CA A:ASN1158 4.9 30.4 1.0

Zinc binding site 3 out of 3 in 8g45

Go back to Zinc Binding Sites List in 8g45
Zinc binding site 3 out of 3 in the Structure of HDAC6 Zinc-Finger Ubiquitin Binding Domain in Complex with Sgc-UBD253 Chemical Probe


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 Sgc-UBD253 Chemical Probe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:26.2
occ:1.00
 ND1 A:HIS1115 2.1 25.6 1.0
SG A:CYS1186 2.3 28.9 1.0
SG A:CYS1183 2.4 23.6 1.0
SG A:CYS1113 2.4 25.1 1.0
CE1 A:HIS1115 3.0 30.1 1.0
CG A:HIS1115 3.1 26.1 1.0
CB A:CYS1113 3.3 22.4 1.0
CB A:CYS1183 3.3 23.3 1.0
CB A:CYS1186 3.4 26.2 1.0
CB A:HIS1115 3.5 24.4 1.0
N A:CYS1186 3.9 27.9 1.0
N A:HIS1115 4.0 26.3 1.0
CD A:PRO1114 4.1 27.7 1.0
NE2 A:HIS1115 4.2 29.8 1.0
CD2 A:HIS1115 4.2 30.6 1.0
CA A:CYS1186 4.3 28.4 1.0
CA A:HIS1115 4.3 27.0 1.0
N A:PRO1114 4.4 26.1 1.0
CA A:CYS1113 4.4 24.2 1.0
CB A:TYR1185 4.5 25.3 1.0
C A:CYS1113 4.6 24.1 1.0
CG A:PRO1114 4.6 33.7 1.0
CA A:CYS1183 4.7 23.7 1.0
O A:HOH1455 4.9 36.2 1.0
C A:TYR1185 4.9 29.8 1.0
C A:PRO1114 5.0 29.7 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 10:12:33 2025

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