Zinc in PDB 6ds6: Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide

All present enzymatic activity of Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide:
2.3.1.48;

The structure of Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide, PDB code: 6ds6 was solved by Y.Zhang, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.32 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.026, 44.026, 85.904, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.3

The structure of Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide (pdb code 6ds6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of P300 Zz Domain in Complex with Histone H3 Peptide, PDB code: 6ds6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of P300 Zz Domain in Complex with Histone H3 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 P300 Zz Domain in Complex with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5001 b:54.9 occ:1.00 SG A:CYS36 2.1 42.1 1.0 SG A:CYS17 2.3 52.1 1.0 SG A:CYS39 2.4 46.5 1.0 SG A:CYS14 2.5 48.1 1.0 CB A:CYS39 3.1 44.7 1.0 CB A:CYS14 3.2 39.9 1.0 CB A:CYS36 3.3 43.1 1.0 CB A:CYS17 3.4 48.8 1.0 N A:CYS17 3.7 49.6 1.0 N A:CYS36 3.8 35.1 1.0 CA A:CYS17 4.1 51.8 1.0 CA A:CYS36 4.1 38.3 1.0 N A:CYS39 4.2 42.1 1.0 CA A:CYS39 4.3 40.2 1.0 CB A:GLU16 4.5 48.8 1.0 CA A:CYS14 4.7 42.3 1.0 C A:CYS36 4.7 38.5 1.0 O A:CYS36 4.8 40.1 1.0 C A:GLU16 4.8 47.8 1.0 C A:CYS17 4.9 58.4 1.0 C A:LEU35 5.0 34.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of P300 Zz Domain in Complex with Histone H3 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 P300 Zz Domain in Complex with Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5002 b:52.4 occ:1.00 NE2 A:HIS45 1.9 44.8 1.0 SG A:CYS27 2.3 39.9 1.0 ND1 A:HIS47 2.3 50.5 1.0 SG A:CYS30 2.3 45.0 1.0 CD2 A:HIS45 2.7 37.3 1.0 CE1 A:HIS45 3.1 51.6 1.0 CE1 A:HIS47 3.2 44.4 1.0 CG A:HIS47 3.3 47.2 1.0 CB A:CYS30 3.3 37.9 1.0 CB A:CYS27 3.4 40.2 1.0 CB A:HIS47 3.5 42.2 1.0 N A:CYS30 3.6 43.4 1.0 CG A:HIS45 3.9 39.8 1.0 CA A:CYS30 4.0 38.8 1.0 ND1 A:HIS45 4.1 40.7 1.0 NE2 A:HIS47 4.4 45.7 1.0 CD2 A:HIS47 4.4 49.1 1.0 CB A:VAL29 4.4 44.1 1.0 CB A:TYR33 4.5 45.9 1.0 C A:VAL29 4.6 40.6 1.0 CG A:TYR33 4.7 42.8 1.0 CD2 A:TYR33 4.7 43.0 1.0 CA A:CYS27 4.7 35.7 1.0 CA A:HIS47 4.9 44.1 1.0 CA A:VAL29 4.9 48.1 1.0 CG1 A:VAL29 4.9 47.2 1.0 N A:VAL29 4.9 41.1 1.0 O A:HOH5146 5.0 64.7 1.0

Y.Zhang, Y.Xue, J.Shi, J.Ahn, W.Mi, M.Ali, X.Wang, B.J.Klein, H.Wen, W.Li, X.Shi, T.G.Kutateladze. The Zz Domain of P300 Mediates Specificity of the Adjacent Hat Domain For Histone H3. Nat. Struct. Mol. Biol. V. 25 841 2018.
ISSN: ESSN 1545-9985
PubMed: 30150647
DOI: 10.1038/S41594-018-0114-9