Zinc in PDB 8f8y: PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide

All present enzymatic activity of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide:
2.7.11.1;

The structure of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide, PDB code: 8f8y 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)	38.87 / 3.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.406, 84.065, 105.215, 90, 103.99, 90
R / Rfree (%)	19.5 / 24.9

The binding sites of Zinc atom in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide (pdb code 8f8y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide, PDB code: 8f8y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:40.9 occ:1.00 SG A:CYS50 2.3 47.8 1.0 SG A:CYS53 2.3 68.2 1.0 SG A:CYS26 2.3 38.0 1.0 SG A:CYS23 2.3 54.5 1.0 CB A:CYS53 3.1 52.1 1.0 CB A:CYS23 3.1 40.9 1.0 CB A:CYS26 3.3 36.7 1.0 CB A:CYS50 3.6 44.2 1.0 N A:CYS26 3.7 45.8 1.0 N A:CYS50 3.9 48.3 1.0 CA A:CYS26 4.1 40.7 1.0 CE1 A:PHE30 4.2 55.4 1.0 CA A:CYS53 4.3 55.2 1.0 N A:CYS53 4.3 65.6 1.0 CZ A:PHE30 4.3 48.0 1.0 CA A:CYS50 4.3 41.7 1.0 CB A:ALA25 4.5 42.5 1.0 CA A:CYS23 4.6 43.1 1.0 O A:CYS50 4.8 68.0 1.0 C A:ALA25 4.8 52.5 1.0 N A:ALA25 4.9 46.6 1.0 C A:CYS50 4.9 60.7 1.0 CA A:ALA25 5.0 44.5 1.0

Zinc binding site 2 out of 4 in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:53.9 occ:1.00 ND1 A:HIS31 2.1 53.9 1.0 SG A:CYS8 2.3 80.2 1.0 SG A:CYS34 2.3 53.3 1.0 SG A:CYS10 2.3 65.0 1.0 CG A:HIS31 3.0 47.0 1.0 CB A:CYS8 3.1 55.0 1.0 CE1 A:HIS31 3.1 57.2 1.0 CB A:CYS34 3.2 43.1 1.0 CB A:HIS31 3.2 41.0 1.0 CB A:CYS10 3.8 55.3 1.0 N A:HIS31 4.0 51.7 1.0 N A:CYS10 4.1 68.2 1.0 NH2 A:ARG18 4.1 50.1 1.0 CD2 A:HIS31 4.2 42.3 1.0 CA A:HIS31 4.2 43.4 1.0 NE2 A:HIS31 4.2 48.2 1.0 N A:VAL9 4.4 53.0 1.0 CA A:CYS8 4.5 55.5 1.0 CA A:CYS10 4.6 66.7 1.0 CG2 A:VAL9 4.6 59.9 1.0 CA A:CYS34 4.6 55.8 1.0 CZ A:ARG18 4.7 53.2 1.0 NH1 A:ARG18 4.8 65.0 1.0 C A:CYS8 4.8 56.6 1.0

Zinc binding site 3 out of 4 in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:62.2 occ:1.00 SG B:CYS53 2.3 47.9 1.0 SG B:CYS26 2.3 50.6 1.0 SG B:CYS50 2.3 64.3 1.0 SG B:CYS23 2.3 65.5 1.0 CB B:CYS53 3.1 64.0 1.0 CB B:CYS23 3.2 41.0 1.0 CB B:CYS26 3.2 49.9 1.0 CB B:CYS50 3.5 54.7 1.0 N B:CYS26 3.6 56.4 1.0 N B:CYS50 3.9 56.8 1.0 CA B:CYS26 4.0 51.6 1.0 N B:CYS53 4.2 74.7 1.0 CA B:CYS50 4.2 60.3 1.0 CA B:CYS53 4.2 76.6 1.0 CE1 B:PHE30 4.4 44.5 1.0 CB B:ALA25 4.5 59.5 1.0 CZ B:PHE30 4.5 48.7 1.0 CA B:CYS23 4.6 55.1 1.0 O B:CYS50 4.7 73.4 1.0 C B:ALA25 4.7 58.1 1.0 C B:CYS50 4.8 71.7 1.0 N B:ALA25 4.8 47.7 1.0 C B:CYS26 4.9 53.1 1.0 CA B:ALA25 4.9 55.6 1.0 C B:HIS49 5.0 72.1 1.0

Zinc binding site 4 out of 4 in the PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PHF2 (Phd+Jmj) in Complex with VRK1 N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:67.8 occ:1.00 ND1 B:HIS31 2.1 71.0 1.0 SG B:CYS8 2.3 70.5 1.0 SG B:CYS34 2.3 73.5 1.0 SG B:CYS10 2.3 74.8 1.0 CG B:HIS31 3.0 66.6 1.0 CE1 B:HIS31 3.1 74.9 1.0 CB B:CYS8 3.2 73.1 1.0 CB B:HIS31 3.3 72.6 1.0 CB B:CYS34 3.4 68.3 1.0 CB B:CYS10 3.6 83.5 1.0 N B:HIS31 3.9 68.9 1.0 N B:CYS10 4.0 74.9 1.0 CD2 B:HIS31 4.2 64.1 1.0 NE2 B:HIS31 4.2 68.6 1.0 CA B:HIS31 4.2 71.0 1.0 CA B:CYS10 4.5 75.5 1.0 NH2 B:ARG18 4.5 71.6 1.0 N B:VAL9 4.5 64.8 1.0 CA B:CYS8 4.6 67.4 1.0 CG2 B:VAL9 4.6 61.0 1.0 CA B:CYS34 4.8 72.4 1.0 C B:CYS8 4.8 63.8 1.0 NH1 B:ARG18 5.0 64.0 1.0

J.R.Horton, J.Zhou, Q.Chen, X.Zhang, M.T.Bedford, X.Cheng. A Complete Methyl-Lysine Binding Aromatic Cage Constructed By Two Domains of PHF2. J.Biol.Chem. 02862 2022.
ISSN: ESSN 1083-351X
PubMed: 36596360
DOI: 10.1016/J.JBC.2022.102862