Zinc in PDB 4up0: Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide

The structure of Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide, PDB code: 4up0 was solved by T.C.R.Miller, M.Fiedler, T.J.Rutherford, K.Birchall, J.Chugh, M.Bienz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.47 / 1.28
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.910, 53.910, 57.940, 90.00, 90.00, 90.00
R / Rfree (%)	13.797 / 16.611

The binding sites of Zinc atom in the Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide (pdb code 4up0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide, PDB code: 4up0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1383 b:11.9 occ:1.00 ND1 A:HIS355 2.1 11.0 1.0 SG A:CYS358 2.3 13.4 1.0 SG A:CYS333 2.3 12.9 1.0 SG A:CYS330 2.3 11.6 1.0 CB A:CYS330 3.0 11.8 1.0 CE1 A:HIS355 3.0 11.6 1.0 CG A:HIS355 3.1 10.5 1.0 CB A:CYS333 3.3 15.3 1.0 CB A:CYS358 3.3 12.4 1.0 CB A:HIS355 3.5 10.5 1.0 N A:CYS333 3.7 14.4 1.0 CA A:CYS333 4.1 13.3 1.0 N A:HIS355 4.1 9.8 1.0 NE2 A:HIS355 4.2 12.7 1.0 CD2 A:HIS355 4.2 13.0 1.0 O A:HOH2023 4.3 41.0 1.0 CA A:HIS355 4.4 10.1 1.0 O A:HOH2054 4.4 35.3 1.0 CA A:CYS330 4.5 11.1 1.0 CA A:CYS358 4.7 11.6 1.0 C A:CYS333 4.8 12.9 1.0 CB A:ALA332 4.8 15.1 1.0 C A:ALA332 4.9 15.2 1.0 O A:HOH2053 4.9 42.3 1.0 N A:ARG334 5.0 12.7 1.0

Zinc binding site 2 out of 2 in the Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1384 b:16.2 occ:1.00 SG A:CYS350 2.3 17.0 1.0 SG A:CYS379 2.3 15.4 1.0 SG A:CYS382 2.3 21.8 1.0 SG A:CYS346 2.4 15.2 1.0 CB A:CYS346 3.2 12.9 1.0 CB A:CYS350 3.3 17.4 1.0 CB A:CYS382 3.3 23.9 1.0 CB A:CYS379 3.5 13.5 1.0 N A:CYS350 3.6 17.0 1.0 N A:CYS379 3.9 12.8 1.0 CA A:CYS350 4.1 18.2 1.0 CA A:CYS379 4.3 13.3 1.0 N A:CYS382 4.3 24.5 1.0 CB A:SER349 4.4 24.5 1.0 O A:HOH2048 4.4 35.5 1.0 CA A:CYS382 4.4 26.8 1.0 CE1 A:PHE354 4.5 14.1 1.0 OG A:SER349 4.6 31.3 1.0 CA A:CYS346 4.6 12.3 1.0 O A:HOH2068 4.7 39.0 1.0 C A:SER349 4.7 19.5 1.0 CZ A:PHE354 4.8 17.0 1.0 C A:CYS379 4.8 15.2 1.0 C A:CYS350 4.9 16.6 1.0 O A:CYS379 4.9 17.5 1.0 O A:CYS346 5.0 17.5 1.0 N A:GLN351 5.0 16.1 1.0

T.C.R.Miller, T.J.Rutherford, K.Birchall, J.Chugh, M.Fiedler, M.Bienz. Competitive Binding of A Benzimidazole to the Histone- Binding Pocket of the Pygo Phd Finger. Acs Chem.Biol. 2014.
ISSN: ESSN 1554-8937
PubMed: 25323450
DOI: 10.1021/CB500585S