Zinc in PDB 7zdd: Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide.

The structure of Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide., PDB code: 7zdd was solved by S.Caria, S.Duclos, S.Crespillo, J.Errey, J.J.Barker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.38 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.13, 52.893, 105.698, 90, 90, 90
R / Rfree (%)	20.8 / 25

The binding sites of Zinc atom in the Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide. (pdb code 7zdd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide., PDB code: 7zdd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:17.6 occ:1.00 SG A:CYS902 2.3 17.3 1.0 SG A:CYS931 2.3 18.9 1.0 SG A:CYS928 2.3 19.3 1.0 SG A:CYS905 2.3 19.0 1.0 CB A:CYS905 3.3 17.1 1.0 CB A:CYS902 3.3 12.8 1.0 CB A:CYS931 3.3 17.9 1.0 CB A:CYS928 3.4 17.1 1.0 N A:CYS905 3.6 17.7 1.0 N A:CYS928 3.8 15.1 1.0 CA A:CYS905 4.0 17.0 1.0 CA A:CYS928 4.1 16.1 1.0 N A:CYS931 4.1 17.4 1.0 CA A:CYS931 4.3 18.7 1.0 O A:HOH1331 4.5 29.1 1.0 C A:CYS905 4.6 16.9 1.0 C A:CYS928 4.6 15.8 1.0 O A:CYS928 4.7 15.9 1.0 O A:CYS905 4.7 16.7 1.0 C A:LYS904 4.7 18.8 1.0 CA A:CYS902 4.7 13.0 1.0 CB A:PHE930 4.8 16.6 1.0 CB A:LYS904 4.8 20.6 1.0 C A:PHE930 4.9 17.1 1.0 C A:ILE927 4.9 15.6 1.0 N A:LYS904 5.0 16.8 1.0 CB A:LYS907 5.0 16.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:16.2 occ:1.00 ND1 A:HIS910 2.1 16.3 1.0 SG A:CYS913 2.3 14.7 1.0 SG A:CYS893 2.4 18.2 1.0 SG A:CYS890 2.4 16.1 1.0 CB A:CYS890 3.0 17.1 1.0 CE1 A:HIS910 3.1 16.9 1.0 CB A:CYS913 3.1 15.4 1.0 CG A:HIS910 3.2 14.7 1.0 CB A:CYS893 3.3 14.9 1.0 CB A:HIS910 3.5 13.2 1.0 N A:CYS893 3.7 15.2 1.0 N A:HIS910 4.1 13.3 1.0 CA A:CYS893 4.1 15.2 1.0 NE2 A:HIS910 4.2 16.8 1.0 CD2 A:HIS910 4.3 15.2 1.0 CA A:HIS910 4.4 13.3 1.0 CA A:CYS890 4.5 16.5 1.0 CA A:CYS913 4.6 15.4 1.0 CB A:VAL892 4.8 15.0 1.0 C A:VAL892 4.9 16.1 1.0 C A:CYS893 4.9 15.5 1.0 O A:HOH1352 4.9 18.6 1.0 O A:HOH1241 5.0 23.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TRIM33 Phd-Bromodomain Isoform B in Complex with H3K10AC Histone Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:70.6 occ:1.00 O D:HOH201 2.7 34.0 1.0 N D:ALY10 4.3 32.0 1.0 CG D:LYS9 4.4 37.1 1.0 OXT D:ALY10 4.7 36.6 1.0 CB D:ALY10 4.9 32.8 1.0

A.R.Sekirnik, J.K.Reynolds, L.See, J.P.Bluck, A.R.Scorah, C.Tallant, B.Lee, K.B.Leszczynska, R.L.Grimley, R.I.Storer, M.Malattia, S.Crespillo, S.Caria, S.Duclos, E.M.Hammond, S.Knapp, G.M.Morris, F.Duarte, P.C.Biggin, S.J.Conway. Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands For the TRIM33 Alpha and TRIM33 Beta Bromodomains. Acs Chem.Biol. V. 17 2753 2022.
ISSN: ESSN 1554-8937
PubMed: 36098557
DOI: 10.1021/ACSCHEMBIO.2C00266