Zinc in PDB 3sou: Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide

The structure of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide, PDB code: 3sou was solved by E.Rajakumara, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.218, 43.218, 184.347, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.3

The binding sites of Zinc atom in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide (pdb code 3sou). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide, PDB code: 3sou:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:35.2 occ:1.00 SG A:CYS326 2.3 25.4 1.0 SG A:CYS315 2.4 31.0 1.0 SG A:CYS329 2.4 27.6 1.0 SG A:CYS318 2.4 29.9 1.0 CB A:CYS315 3.1 34.1 1.0 CB A:CYS326 3.1 25.9 1.0 CB A:CYS329 3.3 27.7 1.0 CB A:CYS318 3.4 28.8 1.0 N A:CYS329 3.8 24.6 1.0 N A:CYS318 3.9 29.5 1.0 CA A:CYS329 4.2 28.4 1.0 CA A:CYS318 4.2 30.0 1.0 O A:HOH24 4.5 34.1 1.0 CA A:CYS315 4.5 35.5 1.0 CA A:CYS326 4.6 25.7 1.0 NH2 A:ARG337 4.6 32.5 1.0 CB A:HIS317 4.6 29.2 1.0 CB A:VAL328 4.7 27.0 1.0 C A:HIS317 4.8 30.5 1.0 C A:VAL328 4.9 25.0 1.0 NH1 A:ARG337 4.9 34.3 1.0 C A:CYS315 4.9 33.1 1.0 O A:CYS315 4.9 32.9 1.0 C A:CYS329 4.9 27.3 1.0

Zinc binding site 2 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:27.5 occ:1.00 ND1 A:HIS354 2.2 19.4 1.0 SG A:CYS357 2.3 20.6 1.0 SG A:CYS331 2.4 21.0 1.0 SG A:CYS334 2.4 19.8 1.0 CB A:CYS331 3.1 22.3 1.0 CE1 A:HIS354 3.1 21.9 1.0 CG A:HIS354 3.2 19.9 1.0 CB A:CYS334 3.2 23.5 1.0 CB A:CYS357 3.3 22.3 1.0 CB A:HIS354 3.4 19.9 1.0 N A:CYS334 3.8 20.1 1.0 CA A:CYS334 4.1 22.3 1.0 N A:HIS354 4.2 19.6 1.0 NE2 A:HIS354 4.3 21.6 1.0 CD2 A:HIS354 4.3 21.4 1.0 CA A:HIS354 4.4 18.7 1.0 CA A:CYS331 4.6 20.4 1.0 CE1 A:TYR356 4.6 21.3 1.0 CA A:CYS357 4.7 20.7 1.0 CB A:LEU333 4.8 22.2 1.0 C A:CYS334 4.8 24.2 1.0 C A:LEU333 4.8 23.9 1.0 N A:GLY335 4.9 21.1 1.0 N A:GLY336 5.0 22.5 1.0

Zinc binding site 3 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:35.5 occ:1.00 SG A:CYS349 2.3 29.6 1.0 SG A:CYS373 2.4 25.8 1.0 SG A:CYS346 2.4 25.8 1.0 SG A:CYS376 2.4 30.9 1.0 CB A:CYS346 3.2 25.4 1.0 CB A:CYS376 3.3 30.4 1.0 CB A:CYS349 3.3 34.4 1.0 CB A:CYS373 3.4 26.4 1.0 N A:CYS349 3.7 29.5 1.0 CA A:CYS349 4.1 31.0 1.0 N A:CYS373 4.1 25.8 1.0 N A:CYS376 4.2 31.6 1.0 CA A:CYS373 4.3 25.8 1.0 CA A:CYS376 4.3 31.9 1.0 O A:HOH52 4.5 36.0 1.0 CA A:CYS346 4.6 25.0 1.0 CB A:GLU348 4.6 34.7 1.0 C A:GLU348 4.7 33.5 1.0 CB A:GLU375 4.8 30.2 1.0 CE1 A:PHE353 4.8 25.0 1.0 C A:CYS373 4.8 28.9 1.0 C A:CYS349 4.9 28.8 1.0 C A:GLU375 4.9 31.6 1.0 CZ A:PHE353 4.9 25.2 1.0 N A:GLU348 5.0 31.7 1.0 O A:CYS373 5.0 28.6 1.0 CA A:GLU348 5.0 30.7 1.0

Zinc binding site 4 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:41.3 occ:1.00 OE2 A:GLU375 2.0 30.8 1.0 ND1 B:HIS317 2.0 33.0 1.0 NE2 A:HIS332 2.2 30.9 1.0 O B:HOH101 2.3 39.1 1.0 CD A:GLU375 2.8 29.9 1.0 OE1 A:GLU375 2.9 31.0 1.0 CD2 A:HIS332 3.0 28.1 1.0 CE1 B:HIS317 3.0 32.9 1.0 CG B:HIS317 3.0 31.8 1.0 CE1 A:HIS332 3.2 29.8 1.0 CB B:HIS317 3.4 29.4 1.0 O B:HOH120 3.8 40.6 1.0 CA B:HIS317 3.9 28.8 1.0 O A:HOH81 4.0 38.7 1.0 NE2 B:HIS317 4.1 33.2 1.0 CD2 B:HIS317 4.1 33.8 1.0 CG A:HIS332 4.2 25.5 1.0 CG A:GLU375 4.2 27.6 1.0 ND1 A:HIS332 4.3 27.0 1.0 O A:HOH52 4.3 36.0 1.0 O B:HIS317 4.8 29.9 1.0 C B:HIS317 4.8 28.2 1.0 N B:HIS317 4.8 31.1 1.0

Zinc binding site 5 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:29.1 occ:1.00 ND1 B:HIS354 2.2 19.6 1.0 SG B:CYS334 2.3 22.4 1.0 SG B:CYS331 2.3 19.5 1.0 SG B:CYS357 2.4 21.2 1.0 CB B:CYS331 3.0 23.2 1.0 CE1 B:HIS354 3.1 21.8 1.0 CG B:HIS354 3.1 20.5 1.0 CB B:CYS334 3.3 24.7 1.0 CB B:CYS357 3.4 22.0 1.0 CB B:HIS354 3.4 21.9 1.0 N B:CYS334 3.8 23.9 1.0 CA B:CYS334 4.1 24.2 1.0 N B:HIS354 4.2 18.6 1.0 NE2 B:HIS354 4.2 20.6 1.0 CD2 B:HIS354 4.3 21.7 1.0 CA B:HIS354 4.4 18.3 1.0 CA B:CYS331 4.5 22.5 1.0 CE1 B:TYR356 4.6 21.5 1.0 O B:HOH86 4.7 28.3 1.0 CA B:CYS357 4.8 22.6 1.0 C B:CYS334 4.8 24.8 1.0 CB B:LEU333 4.8 24.4 1.0 N B:GLY335 4.8 21.3 1.0 C B:LEU333 4.8 24.8 1.0 N B:GLY336 5.0 21.9 1.0

Zinc binding site 6 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5 b:33.9 occ:1.00 SG B:CYS329 2.3 26.3 1.0 SG B:CYS318 2.4 27.7 1.0 SG B:CYS326 2.4 25.2 1.0 SG B:CYS315 2.4 27.9 1.0 CB B:CYS326 3.1 28.1 1.0 CB B:CYS315 3.1 31.8 1.0 CB B:CYS329 3.3 27.1 1.0 CB B:CYS318 3.3 30.2 1.0 N B:CYS329 3.8 22.6 1.0 N B:CYS318 3.8 27.7 1.0 CA B:CYS329 4.1 25.7 1.0 CA B:CYS318 4.2 29.3 1.0 O B:HOH45 4.3 35.0 1.0 NH2 B:ARG337 4.4 34.0 1.0 CB B:HIS317 4.5 29.4 1.0 CA B:CYS326 4.6 26.2 1.0 CA B:CYS315 4.6 35.1 1.0 CB B:VAL328 4.7 27.7 1.0 NH1 B:ARG337 4.7 31.8 1.0 C B:HIS317 4.7 28.2 1.0 C B:VAL328 4.8 26.0 1.0 C B:CYS329 4.9 26.2 1.0 O B:CYS315 4.9 28.9 1.0 C B:CYS315 4.9 31.7 1.0 CA B:HIS317 5.0 28.8 1.0

Zinc binding site 7 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn6 b:33.0 occ:1.00 SG B:CYS376 2.3 28.4 1.0 SG B:CYS349 2.4 27.2 1.0 SG B:CYS373 2.4 25.1 1.0 SG B:CYS346 2.4 27.4 1.0 CB B:CYS376 3.2 28.8 1.0 CB B:CYS346 3.2 25.8 1.0 CB B:CYS349 3.3 29.5 1.0 CB B:CYS373 3.4 26.6 1.0 N B:CYS349 3.8 28.2 1.0 N B:CYS373 4.1 25.1 1.0 CA B:CYS349 4.1 24.9 1.0 N B:CYS376 4.1 29.7 1.0 CA B:CYS376 4.3 30.9 1.0 CA B:CYS373 4.3 25.8 1.0 CB B:GLU348 4.6 31.4 1.0 CA B:CYS346 4.7 24.9 1.0 C B:CYS373 4.8 28.6 1.0 O B:CYS373 4.8 30.3 1.0 C B:GLU348 4.8 30.9 1.0 CB B:GLU375 4.8 28.6 1.0 C B:GLU375 4.8 30.0 1.0 CE1 B:PHE353 4.9 24.1 1.0 C B:CYS349 4.9 29.0 1.0 N B:ASP350 5.0 25.9 1.0

Zinc binding site 8 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8 b:38.8 occ:1.00 ND1 A:HIS317 2.0 29.6 1.0 OE2 B:GLU375 2.0 28.5 1.0 NE2 B:HIS332 2.1 31.6 1.0 O B:HOH102 2.1 35.7 1.0 CD B:GLU375 2.7 30.5 1.0 OE1 B:GLU375 2.8 29.5 1.0 CE1 A:HIS317 3.0 31.5 1.0 CD2 B:HIS332 3.0 27.7 1.0 CG A:HIS317 3.0 29.5 1.0 CE1 B:HIS332 3.1 30.3 1.0 CB A:HIS317 3.4 29.2 1.0 O B:HOH108 3.7 25.8 1.0 CA A:HIS317 3.8 31.0 1.0 NE2 A:HIS317 4.1 28.7 1.0 O B:HOH66 4.1 35.0 1.0 CD2 A:HIS317 4.1 30.3 1.0 O B:HOH42 4.1 34.5 1.0 CG B:HIS332 4.2 27.6 1.0 ND1 B:HIS332 4.2 27.8 1.0 CG B:GLU375 4.2 29.2 1.0 N A:HIS317 4.7 31.5 1.0 C A:HIS317 4.9 30.5 1.0 O A:HIS317 4.9 31.6 1.0

E.Rajakumara, Z.Wang, H.Ma, L.Hu, H.Chen, Y.Lin, R.Guo, F.Wu, H.Li, F.Lan, Y.G.Shi, Y.Xu, D.J.Patel, Y.Shi. Phd Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression. Mol.Cell V. 43 275 2011.
ISSN: ISSN 1097-2765
PubMed: 21777816
DOI: 10.1016/J.MOLCEL.2011.07.006