Zinc in PDB 2xb1: Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain

The structure of Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain, PDB code: 2xb1 was solved by T.C.Miller, T.J.Rutherford, C.M.Johnson, M.Fiedler, M.Bienz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.31 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.750, 69.730, 82.070, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.7

The binding sites of Zinc atom in the Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain (pdb code 2xb1). 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 the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain, PDB code: 2xb1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain


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 Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.2 occ:1.00 ND1 A:HIS355 2.0 17.4 1.0 SG A:CYS358 2.3 19.1 1.0 SG A:CYS330 2.4 14.6 1.0 SG A:CYS333 2.4 17.1 1.0 CE1 A:HIS355 2.9 19.5 1.0 CB A:CYS330 3.0 15.0 1.0 CG A:HIS355 3.1 17.4 1.0 CB A:CYS333 3.3 19.0 1.0 CB A:CYS358 3.4 18.7 1.0 CB A:HIS355 3.6 16.0 1.0 N A:CYS333 3.8 17.1 1.0 CA A:CYS333 4.1 18.4 1.0 N A:HIS355 4.1 14.0 1.0 NE2 A:HIS355 4.1 19.3 1.0 CD2 A:HIS355 4.2 17.7 1.0 CA A:HIS355 4.4 14.7 1.0 CA A:CYS330 4.5 14.0 1.0 CA A:CYS358 4.8 18.1 1.0 C A:CYS333 4.8 18.8 1.0 N A:ARG334 4.9 17.0 1.0 C A:ALA332 4.9 18.7 1.0 OG A:SER335 5.0 22.7 1.0 CB A:ALA332 5.0 18.1 1.0 O A:HIS355 5.0 14.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain


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 Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.8 occ:1.00 SG A:CYS382 2.3 17.8 1.0 SG A:CYS379 2.4 15.2 1.0 SG A:CYS350 2.4 15.7 1.0 SG A:CYS346 2.4 19.0 1.0 CB A:CYS346 3.2 14.9 1.0 CB A:CYS350 3.2 15.2 1.0 CB A:CYS382 3.3 16.4 1.0 CB A:CYS379 3.5 15.3 1.0 N A:CYS350 3.7 16.0 1.0 N A:CYS379 4.0 13.6 1.0 CA A:CYS350 4.0 15.4 1.0 O A:HOH2074 4.1 9.8 1.0 N A:CYS382 4.2 17.0 1.0 O A:HOH2083 4.2 20.9 1.0 CA A:CYS379 4.3 14.3 1.0 CA A:CYS382 4.3 16.7 1.0 CB A:SER349 4.3 21.0 1.0 CA A:CYS346 4.7 15.6 1.0 CE2 A:PHE354 4.7 13.7 1.0 OG A:SER349 4.8 25.7 1.0 C A:CYS379 4.8 14.0 1.0 O A:CYS379 4.8 13.5 1.0 CZ A:PHE354 4.9 16.5 1.0 C A:CYS350 4.9 14.2 1.0 C A:SER349 4.9 18.1 1.0 O A:CYS346 5.0 18.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain


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 the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:15.4 occ:1.00 ND1 C:HIS355 2.1 14.6 1.0 SG C:CYS358 2.3 17.6 1.0 SG C:CYS333 2.4 18.8 1.0 SG C:CYS330 2.4 15.0 1.0 CB C:CYS330 3.0 16.1 1.0 CE1 C:HIS355 3.1 18.6 1.0 CG C:HIS355 3.1 14.9 1.0 CB C:CYS358 3.4 16.3 1.0 CB C:CYS333 3.4 18.9 1.0 CB C:HIS355 3.4 13.0 1.0 N C:CYS333 3.9 18.1 1.0 N C:HIS355 4.0 14.1 1.0 CA C:CYS333 4.2 19.4 1.0 NE2 C:HIS355 4.2 16.1 1.0 CD2 C:HIS355 4.2 15.1 1.0 CA C:HIS355 4.3 12.8 1.0 C3 C:PEG403 4.4 44.2 1.0 C4 C:PEG403 4.5 43.2 1.0 CA C:CYS330 4.5 15.7 1.0 O4 C:PEG403 4.7 40.7 1.0 CA C:CYS358 4.8 17.1 1.0 C C:CYS333 4.9 19.9 1.0 CB C:ALA332 4.9 16.6 1.0 C C:ALA332 5.0 18.4 1.0 O C:HIS355 5.0 12.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain


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 the Human PYGO2 Phd Finger in Complex with the B9L HD1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:13.8 occ:1.00 SG C:CYS379 2.3 14.1 1.0 SG C:CYS382 2.3 16.2 1.0 SG C:CYS350 2.4 12.4 1.0 SG C:CYS346 2.4 18.8 1.0 CB C:CYS346 3.2 13.2 1.0 CB C:CYS350 3.3 14.5 1.0 CB C:CYS382 3.3 14.2 1.0 CB C:CYS379 3.5 13.3 1.0 N C:CYS350 3.7 14.8 1.0 O C:HOH574 3.8 7.7 1.0 N C:CYS379 4.0 12.1 1.0 CA C:CYS350 4.0 14.5 1.0 O C:HOH591 4.2 11.9 1.0 N C:CYS382 4.2 15.0 1.0 CA C:CYS379 4.3 12.6 1.0 CA C:CYS382 4.4 15.1 1.0 CB C:SER349 4.4 16.2 1.0 CA C:CYS346 4.7 14.9 1.0 OG C:SER349 4.7 19.6 1.0 CE2 C:PHE354 4.8 13.0 1.0 C C:CYS379 4.8 13.0 1.0 O C:CYS379 4.8 12.6 1.0 C C:CYS350 4.8 13.1 1.0 C C:SER349 4.9 15.8 1.0 CZ C:PHE354 4.9 13.0 1.0 O C:CYS346 4.9 16.9 1.0

T.C.Miller, T.J.Rutherford, C.M.Johnson, M.Fiedler, M.Bienz. Allosteric Remodeling of the Histone H3 Binding Pocket in the PYGO2 Phd Finger Triggered By Its Binding to the B9L/BCL9 Co-Factor. J.Mol.Biol. V. 401 969 2010.
ISSN: ISSN 0022-2836
PubMed: 20637214
DOI: 10.1016/J.JMB.2010.07.007