Zinc in PDB 7m10: PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1

All present enzymatic activity of PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1:
2.7.11.1;

The structure of PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1, PDB code: 7m10 was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.50 / 1.15
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	34.24, 63.717, 103.152, 90, 90, 90
R / Rfree (%)	15.7 / 16.5

The binding sites of Zinc atom in the PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1 (pdb code 7m10). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1, PDB code: 7m10:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:13.8 occ:1.00 SG A:CYS53 2.3 15.4 1.0 SG A:CYS26 2.3 14.4 1.0 SG A:CYS23 2.3 12.4 1.0 SG A:CYS50 2.4 13.2 1.0 CB A:CYS23 3.1 12.3 1.0 CB A:CYS53 3.2 14.0 1.0 CB A:CYS26 3.3 15.3 1.0 CB A:CYS50 3.4 13.6 1.0 N A:CYS26 3.7 14.9 1.0 N A:CYS50 4.0 11.7 1.0 CA A:CYS26 4.1 15.0 1.0 N A:CYS53 4.2 14.1 1.0 O A:HOH217 4.2 35.7 1.0 CA A:CYS50 4.3 12.2 1.0 CA A:CYS53 4.3 14.7 1.0 CE1 A:PHE30 4.5 12.3 1.0 CB A:ALA25 4.6 14.9 1.0 CZ A:PHE30 4.6 13.9 1.0 CA A:CYS23 4.6 10.5 1.0 O A:HOH247 4.6 24.5 1.0 O A:HOH300 4.7 25.4 0.5 C A:ALA25 4.8 14.1 1.0 C A:CYS50 4.9 10.7 1.0 O A:CYS50 4.9 11.8 1.0 C A:CYS26 4.9 15.3 1.0 N A:ALA25 5.0 13.0 1.0

Zinc binding site 2 out of 2 in the PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PHF2 Phd Domain Complexed with Peptide From N-Terminus of VRK1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:12.3 occ:1.00 ND1 A:HIS31 2.1 11.8 1.0 SG A:CYS10 2.3 12.5 1.0 SG A:CYS34 2.3 13.2 1.0 SG A:CYS8 2.3 11.1 1.0 CE1 A:HIS31 3.0 13.0 1.0 CB A:CYS8 3.1 11.9 1.0 CG A:HIS31 3.1 10.8 1.0 CB A:CYS34 3.3 12.5 1.0 CB A:CYS10 3.5 12.9 1.0 CB A:HIS31 3.5 11.6 1.0 O A:HOH270 3.6 16.7 1.0 N A:CYS10 4.0 11.9 1.0 N A:HIS31 4.1 11.2 1.0 NE2 A:HIS31 4.2 12.3 1.0 CD2 A:HIS31 4.2 11.0 1.0 NH2 A:ARG18 4.4 15.6 1.0 CA A:CYS10 4.4 12.1 1.0 CA A:HIS31 4.5 10.7 1.0 CA A:CYS8 4.5 11.5 1.0 N A:VAL9 4.5 12.2 1.0 CG2 A:VAL9 4.6 14.8 1.0 CA A:CYS34 4.7 11.1 1.0 C A:CYS8 4.8 12.9 1.0 NH1 A:ARG18 4.9 15.0 1.0 CZ A:ARG18 4.9 14.8 1.0

J.Chen, J.Horton, C.Sagum, J.Zhou, X.Cheng, M.T.Bedford. Histone H3 N-Terminal Mimicry Drives A Novel Network of Methyl-Effector Interactions. Biochem.J. 2021.
ISSN: ESSN 1470-8728
PubMed: 33969871
DOI: 10.1042/BCJ20210203