Zinc in PDB 6gyt: Transcription Factor Dimerization Activates the P300 Acetyltransferase

All present enzymatic activity of Transcription Factor Dimerization Activates the P300 Acetyltransferase:
2.3.1.48;

The structure of Transcription Factor Dimerization Activates the P300 Acetyltransferase, PDB code: 6gyt was solved by D.Panne, E.Ortega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.640, 83.710, 165.620, 90.00, 90.00, 90.00
R / Rfree (%)	26.1 / 28.8

The binding sites of Zinc atom in the Transcription Factor Dimerization Activates the P300 Acetyltransferase (pdb code 6gyt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Transcription Factor Dimerization Activates the P300 Acetyltransferase, PDB code: 6gyt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1301 b:70.8 occ:1.00 ND1 A:HIS1255 2.1 64.8 1.0 SG A:CYS1163 2.3 61.6 1.0 SG A:CYS1258 2.3 45.8 1.0 SG A:CYS1164 2.4 60.8 1.0 HB2 A:HIS1255 2.9 57.6 1.0 HB2 A:CYS1163 2.9 60.1 1.0 CE1 A:HIS1255 3.1 65.0 1.0 CG A:HIS1255 3.2 61.1 1.0 HB2 A:CYS1258 3.2 47.6 1.0 H A:CYS1164 3.2 61.2 1.0 HE1 A:HIS1255 3.2 65.0 1.0 CB A:CYS1163 3.2 60.1 1.0 CB A:CYS1258 3.3 47.6 1.0 H A:HIS1255 3.4 53.9 1.0 CB A:CYS1164 3.5 63.2 1.0 HB3 A:CYS1164 3.5 63.2 1.0 N A:CYS1164 3.5 61.2 1.0 CB A:HIS1255 3.5 57.6 1.0 HB3 A:CYS1258 3.6 47.6 1.0 HB3 A:CYS1163 3.9 60.1 1.0 CA A:CYS1164 4.0 62.6 1.0 C A:CYS1163 4.0 58.9 1.0 N A:HIS1255 4.2 53.9 1.0 HB3 A:HIS1255 4.2 57.6 1.0 NE2 A:HIS1255 4.2 65.2 1.0 CA A:CYS1163 4.2 58.1 1.0 CD2 A:HIS1255 4.3 63.6 1.0 HB2 A:CYS1164 4.3 63.2 1.0 HH2 A:TRP1115 4.4 58.0 1.0 CA A:HIS1255 4.5 54.6 1.0 C A:CYS1164 4.5 64.6 1.0 HZ2 B:LYS1284 4.5 67.6 1.0 HZ2 A:TRP1115 4.6 56.9 1.0 O A:CYS1164 4.6 64.5 1.0 H A:CYS1163 4.7 56.3 1.0 HD23 A:LEU1168 4.7 93.3 1.0 H A:CYS1258 4.7 46.6 1.0 CA A:CYS1258 4.8 46.6 1.0 O A:CYS1163 4.8 58.8 1.0 HA A:CYS1164 4.8 62.6 1.0 N A:CYS1163 4.9 56.3 1.0 HE2 A:HIS1255 5.0 65.2 1.0 HA A:CYS1163 5.0 58.1 1.0

Zinc binding site 2 out of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:82.5 occ:1.00 SG A:CYS1272 2.3 56.0 1.0 SG A:CYS1247 2.3 59.4 1.0 SG A:CYS1250 2.4 69.5 1.0 SG A:CYS1275 2.4 69.9 1.0 H A:CYS1250 2.8 67.3 1.0 HB2 A:CYS1275 3.1 67.5 1.0 HB3 A:CYS1247 3.2 62.1 1.0 HB3 A:CYS1250 3.3 69.7 1.0 CB A:CYS1247 3.3 62.1 1.0 CB A:CYS1275 3.4 67.5 1.0 CB A:CYS1250 3.4 69.7 1.0 H A:CYS1272 3.4 56.9 1.0 HB3 A:CYS1272 3.5 57.9 1.0 HB2 A:CYS1247 3.5 62.1 1.0 CB A:CYS1272 3.6 57.9 1.0 HB2 A:GLU1249 3.6 62.8 1.0 O A:CYS1250 3.6 75.3 1.0 N A:CYS1250 3.6 67.3 1.0 H A:CYS1275 3.6 64.2 1.0 O A:HOH1410 4.0 60.2 1.0 HB3 A:CYS1275 4.0 67.5 1.0 CA A:CYS1250 4.0 68.9 1.0 HD2 A:ARG1252 4.1 57.1 1.0 N A:CYS1272 4.2 56.9 1.0 C A:CYS1250 4.2 69.6 1.0 HB2 A:CYS1250 4.2 69.7 1.0 HB2 A:CYS1272 4.3 57.9 1.0 N A:CYS1275 4.3 64.2 1.0 H A:GLU1249 4.3 60.2 1.0 HH11 A:ARG1252 4.3 55.4 1.0 HB2 A:ARG1252 4.4 58.9 1.0 CA A:CYS1272 4.4 56.9 1.0 CA A:CYS1275 4.4 65.9 1.0 CB A:GLU1249 4.5 62.8 1.0 HG13 A:VAL1271 4.5 51.9 1.0 H A:ARG1252 4.6 61.1 1.0 CA A:CYS1247 4.7 59.6 1.0 C A:GLU1249 4.7 64.9 1.0 HA A:CYS1275 4.8 65.9 1.0 HB3 A:GLU1249 4.8 62.8 1.0 O A:CYS1272 4.8 58.1 1.0 HA A:VAL1271 4.8 53.7 1.0 HG12 A:VAL1271 4.8 51.9 1.0 HE2 A:MET1254 4.8 55.6 1.0 N A:GLU1249 4.9 60.2 1.0 CA A:GLU1249 4.9 62.8 1.0 C A:CYS1272 4.9 57.7 1.0 HA A:CYS1250 5.0 68.9 1.0

Zinc binding site 3 out of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:76.3 occ:1.00 ND1 B:HIS1255 2.1 70.7 1.0 SG B:CYS1163 2.3 67.4 1.0 SG B:CYS1258 2.3 61.0 1.0 SG B:CYS1164 2.3 68.1 1.0 HB2 B:HIS1255 2.8 64.5 1.0 HB2 B:CYS1163 2.9 64.2 1.0 CE1 B:HIS1255 3.0 70.7 1.0 CG B:HIS1255 3.1 67.1 1.0 H B:CYS1164 3.1 64.7 1.0 HE1 B:HIS1255 3.2 70.7 1.0 CB B:CYS1163 3.2 64.2 1.0 HB2 B:CYS1258 3.2 60.9 1.0 N B:CYS1164 3.4 64.7 1.0 H B:HIS1255 3.4 62.5 1.0 CB B:CYS1258 3.4 60.9 1.0 CB B:HIS1255 3.4 64.5 1.0 CB B:CYS1164 3.4 67.4 1.0 HB3 B:CYS1164 3.5 67.4 1.0 HB3 B:CYS1258 3.7 60.9 1.0 C B:CYS1163 3.9 62.3 1.0 CA B:CYS1164 3.9 66.6 1.0 HB3 B:CYS1163 3.9 64.2 1.0 HB3 B:HIS1255 4.1 64.5 1.0 CA B:CYS1163 4.1 62.2 1.0 NE2 B:HIS1255 4.1 69.0 1.0 N B:HIS1255 4.1 62.5 1.0 CD2 B:HIS1255 4.2 67.4 1.0 HB2 B:CYS1164 4.3 67.4 1.0 C B:CYS1164 4.4 66.6 1.0 CA B:HIS1255 4.4 62.9 1.0 HH2 B:TRP1115 4.6 58.4 1.0 O B:CYS1164 4.6 65.2 1.0 O B:CYS1163 4.6 61.5 1.0 H B:CYS1163 4.6 59.9 1.0 HH22 B:ARG1166 4.7 92.1 1.0 HZ2 B:TRP1115 4.7 57.6 1.0 H B:CYS1258 4.7 58.5 1.0 HA B:CYS1164 4.8 66.6 1.0 HB2 B:ARG1166 4.8 74.1 1.0 CA B:CYS1258 4.8 59.5 1.0 N B:CYS1163 4.8 59.9 1.0 HA B:CYS1163 4.9 62.2 1.0 HE2 B:HIS1255 4.9 69.0 1.0 NH2 B:ARG1166 4.9 92.1 1.0

Zinc binding site 4 out of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:72.8 occ:1.00 SG B:CYS1247 2.3 61.6 1.0 SG B:CYS1250 2.3 66.7 1.0 SG B:CYS1272 2.3 50.2 1.0 SG B:CYS1275 2.4 63.3 1.0 H B:CYS1250 2.8 63.5 1.0 HB2 B:CYS1275 3.2 60.6 1.0 HB3 B:CYS1247 3.2 64.0 1.0 H B:CYS1272 3.3 54.9 1.0 CB B:CYS1247 3.3 64.0 1.0 HB3 B:CYS1272 3.3 55.3 1.0 HB3 B:CYS1250 3.3 66.0 1.0 CB B:CYS1275 3.4 60.6 1.0 CB B:CYS1250 3.4 66.0 1.0 HB2 B:CYS1247 3.4 64.0 1.0 CB B:CYS1272 3.5 55.3 1.0 HB2 B:GLU1249 3.6 69.0 1.0 N B:CYS1250 3.6 63.5 1.0 H B:CYS1275 3.6 57.3 1.0 N B:CYS1272 4.0 54.9 1.0 CA B:CYS1250 4.0 64.0 1.0 HB3 B:CYS1275 4.1 60.6 1.0 HB2 B:CYS1272 4.2 55.3 1.0 HB2 B:CYS1250 4.2 66.0 1.0 N B:CYS1275 4.3 57.3 1.0 HB2 B:ARG1252 4.3 58.2 1.0 HG13 B:VAL1271 4.3 53.5 1.0 HH11 B:ARG1252 4.3 58.5 1.0 CA B:CYS1272 4.3 55.8 1.0 HB3 B:GLU1249 4.4 69.0 1.0 H B:GLU1249 4.4 63.9 1.0 CB B:GLU1249 4.4 69.0 1.0 CA B:CYS1275 4.4 59.2 1.0 HD2 B:ARG1252 4.4 59.6 1.0 H B:GLY1251 4.5 60.6 1.0 H B:ARG1252 4.5 57.9 1.0 HA B:VAL1271 4.7 52.8 1.0 C B:GLU1249 4.7 66.0 1.0 HE2 B:MET1254 4.7 64.3 1.0 CA B:CYS1247 4.7 63.2 1.0 O B:CYS1272 4.8 56.8 1.0 HA B:CYS1275 4.8 59.2 1.0 HA B:CYS1250 4.8 64.0 1.0 C B:CYS1272 4.9 57.2 1.0 C B:CYS1250 4.9 62.6 1.0 N B:GLY1251 4.9 60.6 1.0 HG12 B:VAL1271 4.9 53.5 1.0 CA B:GLU1249 5.0 66.1 1.0 N B:GLU1249 5.0 63.9 1.0 NH1 B:ARG1252 5.0 58.5 1.0

E.Ortega, S.Rengachari, Z.Ibrahim, N.Hoghoughi, J.Gaucher, A.S.Holehouse, S.Khochbin, D.Panne. Transcription Factor Dimerization Activates the P300 Acetyltransferase. Nature V. 562 538 2018.
ISSN: ESSN 1476-4687
PubMed: 30323286
DOI: 10.1038/S41586-018-0621-1