Zinc in PDB 6lsb: Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide

All present enzymatic activity of Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide:
2.3.1.48;

The structure of Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide, PDB code: 6lsb was solved by H.T.Li, X.L.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.30 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.187, 48.187, 116.848, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 20.5

The binding sites of Zinc atom in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide (pdb code 6lsb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide, PDB code: 6lsb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ 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 Dpf Domain of Moz in Complex with H3K14BZ Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.7 occ:1.00 ND1 A:HIS238 2.2 33.1 1.0 SG A:CYS209 2.3 25.7 1.0 SG A:CYS241 2.3 25.5 1.0 SG A:CYS212 2.4 27.2 1.0 CB A:CYS209 3.1 22.4 1.0 CE1 A:HIS238 3.1 27.5 1.0 CG A:HIS238 3.1 27.2 1.0 CB A:CYS212 3.3 24.2 1.0 CB A:CYS241 3.3 25.8 1.0 CB A:HIS238 3.4 24.6 1.0 N A:CYS212 3.7 24.3 1.0 N A:HIS238 4.0 24.3 1.0 CA A:CYS212 4.1 28.0 1.0 O A:HOH514 4.2 32.2 1.0 NE2 A:HIS238 4.2 28.8 1.0 CD2 A:HIS238 4.3 30.6 1.0 CA A:HIS238 4.3 23.6 1.0 CA A:CYS209 4.6 22.4 1.0 CA A:CYS241 4.7 23.8 1.0 CB A:PHE211 4.7 24.7 1.0 C A:PHE211 4.8 27.9 1.0 C A:CYS212 4.8 30.6 1.0 N A:CYS241 4.9 24.1 1.0 N A:GLY214 4.9 26.5 1.0 N A:LEU213 5.0 27.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ 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 Dpf Domain of Moz in Complex with H3K14BZ Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:25.4 occ:1.00 SG A:CYS310 2.3 27.2 1.0 SG A:CYS281 2.4 26.2 1.0 SG A:CYS307 2.4 27.6 1.0 SG A:CYS284 2.4 23.1 1.0 CB A:CYS281 3.2 24.3 1.0 CB A:CYS284 3.3 28.5 1.0 CB A:CYS310 3.4 27.4 1.0 CB A:CYS307 3.5 23.4 1.0 N A:CYS284 3.8 26.7 1.0 N A:CYS307 3.9 24.8 1.0 CA A:CYS284 4.1 26.8 1.0 N A:CYS310 4.1 27.0 1.0 CA A:CYS307 4.2 22.3 1.0 CA A:CYS310 4.4 28.9 1.0 CB A:SER283 4.5 28.2 1.0 NH1 A:ARG286 4.5 26.7 1.0 O A:HOH543 4.6 49.0 1.0 CA A:CYS281 4.6 23.4 1.0 C A:CYS307 4.7 24.3 1.0 C A:SER283 4.7 25.8 1.0 O A:CYS307 4.8 27.8 1.0 C A:CYS284 4.8 25.8 1.0 CB A:ILE309 4.9 30.3 1.0 NH1 A:ARG251 4.9 42.7 1.0 N A:SER283 4.9 22.6 1.0 CA A:SER283 5.0 26.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ 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 Dpf Domain of Moz in Complex with H3K14BZ Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:29.6 occ:1.00 SG A:CYS262 2.2 28.4 1.0 SG A:CYS233 2.4 30.2 1.0 SG A:CYS259 2.4 26.2 1.0 SG A:CYS230 2.4 25.0 1.0 CB A:CYS262 3.1 20.6 1.0 CB A:CYS230 3.1 25.4 1.0 CB A:CYS233 3.2 27.4 1.0 CB A:CYS259 3.5 23.0 1.0 N A:CYS233 3.8 30.9 1.0 O A:HOH547 4.0 57.9 1.0 N A:CYS259 4.0 23.4 1.0 CA A:CYS233 4.1 27.4 1.0 N A:CYS262 4.1 28.6 1.0 CA A:CYS262 4.2 26.4 1.0 CA A:CYS259 4.3 25.9 1.0 O A:HOH569 4.5 69.0 1.0 CB A:ASP232 4.6 28.5 1.0 CA A:CYS230 4.6 23.0 1.0 O A:HOH560 4.8 65.0 1.0 C A:ASP232 4.8 33.4 1.0 C A:CYS233 4.8 29.2 1.0 N A:GLY234 4.9 24.9 1.0 C A:CYS259 4.9 29.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dpf Domain of Moz in Complex with H3K14BZ Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:33.4 occ:1.00 ND1 A:HIS289 2.1 39.8 1.0 SG A:CYS268 2.2 34.5 1.0 SG A:CYS292 2.3 32.8 1.0 SG A:CYS265 2.4 27.5 1.0 CB A:CYS265 3.0 25.7 1.0 CG A:HIS289 3.1 40.9 1.0 CE1 A:HIS289 3.1 38.8 1.0 CB A:CYS292 3.1 30.6 1.0 CB A:CYS268 3.2 39.4 1.0 CB A:HIS289 3.4 36.1 1.0 N A:CYS268 3.7 28.1 1.0 CA A:CYS268 4.0 32.7 1.0 N A:HIS289 4.0 29.9 1.0 NE2 A:HIS289 4.2 36.8 1.0 CD2 A:HIS289 4.2 39.6 1.0 CA A:HIS289 4.3 33.2 1.0 CA A:CYS265 4.5 21.7 1.0 CA A:CYS292 4.6 38.4 1.0 CB A:SER267 4.7 25.2 1.0 C A:CYS268 4.8 36.9 1.0 C A:SER267 4.8 30.0 1.0 N A:ARG269 4.9 32.4 1.0 N A:CYS292 5.0 36.7 1.0

X.L.Ren, Y.Zhou, Z.Y.Xue, N.Hao, Y.Y.Li, X.H.Guo, D.L.Wang, X.B.Shi, H.T.Li. Histone Benzoylation Serves As An Epigenetic Mark For Dpf and Yeats Family Proteins. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA1130