Zinc in PDB 4up5: Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment

The structure of Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment, PDB code: 4up5 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)	39.52 / 1.65
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	54.270, 54.270, 57.655, 90.00, 90.00, 90.00
R / Rfree (%)	18.19 / 21.117

The binding sites of Zinc atom in the Crystal Structure of the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment (pdb code 4up5). 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 the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment, PDB code: 4up5:
Jump to Zinc binding site number: 1; 2;

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


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 the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1383 b:17.8 occ:1.00 ND1 A:HIS355 2.1 17.8 1.0 SG A:CYS358 2.3 20.2 1.0 SG A:CYS333 2.3 18.2 1.0 SG A:CYS330 2.4 17.3 1.0 CB A:CYS330 3.0 15.4 1.0 CE1 A:HIS355 3.0 15.3 1.0 CG A:HIS355 3.1 16.5 1.0 CB A:CYS333 3.2 20.5 1.0 CB A:CYS358 3.3 18.6 1.0 CB A:HIS355 3.5 16.5 1.0 N A:CYS333 3.8 19.9 1.0 N A:HIS355 4.1 17.1 1.0 CA A:CYS333 4.1 19.9 1.0 NE2 A:HIS355 4.2 19.6 1.0 O A:HOH2012 4.2 41.7 1.0 CD2 A:HIS355 4.2 19.9 1.0 CA A:HIS355 4.4 16.2 1.0 CA A:CYS330 4.5 15.5 1.0 CA A:CYS358 4.7 17.5 1.0 CB A:ALA332 4.8 20.0 1.0 C A:ALA332 4.9 21.3 1.0 C A:CYS333 4.9 20.2 1.0 N A:CYS358 4.9 18.7 1.0 N A:ARG334 5.0 18.3 1.0

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


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 the PYGO2 Phd Finger in Complex with the B9L HD1 Domain and A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1384 b:24.7 occ:1.00 SG A:CYS382 2.3 30.8 1.0 SG A:CYS346 2.3 22.3 1.0 SG A:CYS350 2.3 24.7 1.0 SG A:CYS379 2.4 24.3 1.0 CB A:CYS382 3.2 34.3 1.0 CB A:CYS346 3.2 19.6 1.0 CB A:CYS350 3.3 31.7 1.0 CB A:CYS379 3.5 23.4 1.0 O A:HOH2021 3.6 37.0 1.0 N A:CYS350 3.6 36.7 1.0 N A:CYS379 4.0 20.5 1.0 CA A:CYS350 4.0 31.9 1.0 N A:CYS382 4.1 32.0 1.0 CA A:CYS379 4.2 21.0 1.0 CA A:CYS382 4.3 35.1 1.0 CA A:CYS346 4.6 20.2 1.0 C A:CYS379 4.8 21.9 1.0 O A:CYS379 4.8 24.5 1.0 C A:SER349 4.8 43.5 1.0 CE1 A:PHE354 4.8 20.8 1.0 C A:CYS350 4.9 26.2 1.0 CB A:SER349 4.9 45.5 1.0 O A:CYS346 4.9 27.1 1.0 N A:GLN351 4.9 26.2 1.0 C A:LEU381 5.0 37.1 1.0 CZ A:PHE354 5.0 20.8 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