Zinc in PDB 7zyu: HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10

All present enzymatic activity of HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10:
3.5.1.98;

The structure of HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10, PDB code: 7zyu was solved by L.Wang, G.Kempf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.29 / 2.43
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.391, 81.391, 103.644, 90, 90, 120
R / Rfree (%)	21.7 / 25

The binding sites of Zinc atom in the HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10 (pdb code 7zyu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10, PDB code: 7zyu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:48.8 occ:1.00 SG A:CYS1113 2.0 43.8 1.0 ND1 A:HIS1115 2.0 51.7 1.0 SG A:CYS1186 2.3 47.7 1.0 SG A:CYS1183 2.3 47.9 1.0 CE1 A:HIS1115 2.8 47.1 1.0 HE1 A:HIS1115 3.0 57.2 1.0 HB2 A:CYS1186 3.0 51.1 1.0 H A:CYS1186 3.0 61.1 1.0 HB2 A:HIS1115 3.1 58.6 1.0 HD2 A:PRO1114 3.1 54.8 1.0 CG A:HIS1115 3.1 48.9 1.0 CB A:CYS1186 3.2 42.0 1.0 CB A:CYS1183 3.4 49.5 1.0 HB3 A:CYS1183 3.4 60.1 1.0 HB2 A:CYS1183 3.5 60.1 1.0 CB A:HIS1115 3.6 48.3 1.0 H A:HIS1115 3.6 68.3 1.0 HG2 A:PRO1114 3.7 49.2 1.0 N A:CYS1186 3.7 50.4 1.0 HB2 A:TYR1185 3.7 63.4 1.0 CB A:CYS1113 3.7 51.6 1.0 CD A:PRO1114 3.9 45.1 1.0 NE2 A:HIS1115 4.0 49.3 1.0 HB3 A:CYS1186 4.0 51.1 1.0 CA A:CYS1186 4.1 40.2 1.0 N A:HIS1115 4.1 56.4 1.0 HB2 A:CYS1113 4.1 62.6 1.0 CD2 A:HIS1115 4.1 52.1 1.0 HA A:CYS1113 4.2 49.2 1.0 N A:PRO1114 4.3 46.7 1.0 HB3 A:CYS1113 4.3 62.6 1.0 CG A:PRO1114 4.3 43.5 1.0 HB3 A:HIS1115 4.3 58.6 1.0 HG21 A:VAL1190 4.4 66.5 1.0 CA A:CYS1113 4.4 40.4 1.0 HD21 A:LEU1172 4.5 67.0 1.0 HA A:CYS1186 4.5 48.9 1.0 CA A:HIS1115 4.5 44.6 1.0 C A:CYS1113 4.6 50.5 1.0 HB2 A:PRO1171 4.6 64.3 1.0 CB A:TYR1185 4.6 52.3 1.0 HD3 A:PRO1114 4.7 54.8 1.0 H A:TYR1185 4.7 53.3 1.0 HE2 A:HIS1115 4.7 59.8 1.0 C A:TYR1185 4.8 53.8 1.0 CA A:CYS1183 4.8 45.8 1.0 HB3 A:TYR1185 4.8 63.4 1.0 C A:PRO1114 4.9 51.3 1.0 HD2 A:TYR1185 4.9 56.9 1.0 HG3 A:PRO1114 4.9 49.2 1.0

Zinc binding site 2 out of 3 in the HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:85.9 occ:1.00 SG A:CYS1136 1.9 93.9 1.0 ND1 A:HIS1160 2.0 69.1 1.0 SG A:CYS1133 2.4 72.4 1.0 SG A:CYS1153 2.5 80.5 1.0 HB2 A:HIS1160 2.9 105.0 1.0 CE1 A:HIS1160 2.9 87.4 1.0 CG A:HIS1160 3.0 86.5 1.0 HB3 A:CYS1153 3.0 102.2 1.0 HE1 A:HIS1160 3.1 105.6 1.0 HB3 A:CYS1136 3.1 103.7 1.0 H A:CYS1153 3.1 91.6 1.0 CB A:CYS1136 3.1 85.9 1.0 CB A:CYS1153 3.3 84.6 1.0 CB A:HIS1160 3.4 86.9 1.0 HB2 A:ASN1158 3.4 102.3 1.0 HD22 A:ASN1158 3.4 88.0 1.0 HB3 A:CYS1133 3.4 96.7 1.0 CB A:CYS1133 3.4 80.0 1.0 H A:CYS1136 3.5 105.3 1.0 HB2 A:CYS1133 3.5 96.7 1.0 HB3 A:HIS1160 3.7 105.0 1.0 N A:CYS1136 3.8 87.2 1.0 HB2 A:CYS1136 3.8 103.7 1.0 N A:CYS1153 3.9 75.8 1.0 HG1 A:THR1138 4.0 103.1 1.0 NE2 A:HIS1160 4.0 84.4 1.0 CD2 A:HIS1160 4.0 91.5 1.0 CA A:CYS1136 4.1 78.8 1.0 HB2 A:CYS1153 4.1 102.2 1.0 HB2 A:ASP1135 4.1 85.0 1.0 HB A:THR1138 4.2 119.7 1.0 H A:ASP1135 4.2 95.1 1.0 ND2 A:ASN1158 4.2 72.8 1.0 HG22 A:ILE1157 4.2 92.4 1.0 CA A:CYS1153 4.2 82.5 1.0 CB A:ASN1158 4.3 84.7 1.0 H A:HIS1160 4.4 87.2 1.0 H A:THR1138 4.4 100.9 1.0 OG1 A:THR1138 4.4 85.4 1.0 C A:ASP1135 4.5 86.2 1.0 HB3 A:ASN1158 4.6 102.3 1.0 HG21 A:ILE1157 4.7 92.4 1.0 HA A:TYR1152 4.7 88.5 1.0 HD1 A:TYR1152 4.7 85.6 1.0 HE2 A:HIS1160 4.7 102.0 1.0 CA A:HIS1160 4.7 79.9 1.0 C A:CYS1136 4.8 77.9 1.0 H A:GLY1137 4.8 93.3 1.0 CB A:THR1138 4.8 99.2 1.0 HD21 A:ASN1158 4.9 88.0 1.0 CG A:ASN1158 4.9 90.5 1.0 HD2 A:HIS1160 4.9 110.4 1.0 HA A:CYS1136 4.9 95.2 1.0 CA A:CYS1133 4.9 71.4 1.0 CB A:ASP1135 4.9 70.2 1.0 HB3 A:TYR1152 4.9 91.5 1.0 CG2 A:ILE1157 4.9 76.4 1.0 N A:HIS1160 4.9 72.2 1.0 H A:ASN1158 4.9 101.0 1.0 N A:ASP1135 5.0 78.7 1.0 HA A:CYS1153 5.0 99.6 1.0

Zinc binding site 3 out of 3 in the HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HDAC6 Znf Domain Inhibitor - Darpin (Designed Ankyrin Repeat Protein) F10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:63.9 occ:0.92 NE2 A:HIS1164 2.0 58.9 1.0 ND1 A:HIS1170 2.0 68.3 1.0 SG A:CYS1145 2.2 57.0 1.0 SG A:CYS1148 2.3 67.7 1.0 CE1 A:HIS1170 2.8 71.1 1.0 HE1 A:HIS1170 2.9 85.9 1.0 CD2 A:HIS1164 2.9 69.0 1.0 CE1 A:HIS1164 3.1 76.8 1.0 HD2 A:HIS1164 3.1 83.5 1.0 CG A:HIS1170 3.1 70.3 1.0 HB2 A:HIS1170 3.2 76.0 1.0 CB A:CYS1145 3.2 56.9 1.0 HB3 A:CYS1145 3.3 69.0 1.0 HE1 A:HIS1164 3.3 92.8 1.0 HB2 A:CYS1145 3.3 69.0 1.0 H A:CYS1148 3.3 82.2 1.0 HB3 A:CYS1148 3.5 81.7 1.0 CB A:CYS1148 3.5 67.6 1.0 CB A:HIS1170 3.6 62.8 1.0 HB2 A:SER1147 3.7 88.7 1.0 OG A:SER1168 3.8 66.0 1.0 HB3 A:HIS1170 3.8 76.0 1.0 NE2 A:HIS1170 3.9 52.5 1.0 N A:CYS1148 4.0 68.0 1.0 CD2 A:HIS1170 4.1 78.0 1.0 CG A:HIS1164 4.1 59.9 1.0 ND1 A:HIS1164 4.1 71.9 1.0 HB2 A:SER1168 4.2 87.6 1.0 HG A:SER1168 4.2 79.8 1.0 HB2 A:CYS1148 4.3 81.7 1.0 CA A:CYS1148 4.3 69.3 1.0 CB A:SER1168 4.4 72.5 1.0 HB2 A:GLN1150 4.4 93.9 1.0 HB3 A:SER1168 4.5 87.6 1.0 CB A:SER1147 4.6 73.4 1.0 H A:SER1147 4.6 82.6 1.0 CA A:CYS1145 4.7 50.5 1.0 H A:GLN1150 4.7 77.6 1.0 HE2 A:HIS1170 4.7 63.6 1.0 H A:TYR1149 4.7 81.2 1.0 H A:HIS1170 4.8 78.7 1.0 HB3 A:SER1147 4.8 88.7 1.0 HA A:CYS1145 4.9 61.3 1.0 HD1 A:HIS1164 4.9 87.0 1.0 C A:SER1147 4.9 60.5 1.0 HD2 A:HIS1170 5.0 94.3 1.0

L.Wang, E.A.Moreira, G.Kempf, Y.Miyake, B.I.Oliveira Esteves, A.Fahmi, J.V.Schaefer, B.Dreier, Y.Yamauchi, M.P.Alves, A.Pluckthun, P.Matthias. Disrupting the HDAC6-Ubiquitin Interaction Impairs Infection By Influenza and Zika Virus and Cellular Stress Pathways. Cell Rep V. 39 10736 2022.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2022.110736