Zinc in PDB 8f8z: PHF2 (Phd+Jmj) in Complex with H3 Histone N-Terminal Peptide

The structure of PHF2 (Phd+Jmj) in Complex with H3 Histone N-Terminal Peptide, PDB code: 8f8z 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)	54.50 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.854, 83.756, 104.128, 90, 103.67, 90
R / Rfree (%)	21.3 / 25.6

The binding sites of Zinc atom in the PHF2 (Phd+Jmj) in Complex with H3 Histone N-Terminal Peptide (pdb code 8f8z). 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 H3 Histone N-Terminal Peptide, PDB code: 8f8z:
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 H3 Histone 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 H3 Histone N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.0 occ:1.00 SG A:CYS50 2.2 59.6 1.0 SG A:CYS23 2.3 59.8 1.0 SG A:CYS26 2.3 53.3 1.0 SG A:CYS53 2.4 59.4 1.0 CB A:CYS23 3.1 50.6 1.0 CB A:CYS50 3.3 57.7 1.0 CB A:CYS53 3.3 59.1 1.0 CB A:CYS26 3.5 56.1 1.0 N A:CYS50 3.7 58.3 1.0 N A:CYS26 3.8 59.4 1.0 CE1 A:PHE30 4.0 56.6 1.0 CA A:CYS50 4.1 60.9 1.0 CZ A:PHE30 4.1 56.6 1.0 CA A:CYS26 4.3 57.7 1.0 N A:CYS53 4.4 62.1 1.0 CA A:CYS53 4.5 59.0 1.0 CB A:ALA25 4.5 57.4 1.0 CA A:CYS23 4.5 52.5 1.0 O A:CYS50 4.7 77.2 1.0 C A:CYS50 4.7 72.5 1.0 C A:ALA25 4.9 59.2 1.0 C A:HIS49 4.9 58.2 1.0 C A:CYS23 4.9 57.0 1.0 N A:ALA25 4.9 61.0 1.0

Zinc binding site 2 out of 4 in the PHF2 (Phd+Jmj) in Complex with H3 Histone 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 H3 Histone N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:76.5 occ:1.00 ND1 A:HIS31 2.1 70.9 1.0 SG A:CYS34 2.1 51.8 1.0 SG A:CYS8 2.3 60.2 1.0 SG A:CYS10 2.3 60.9 1.0 CG A:HIS31 2.7 64.7 1.0 CB A:HIS31 2.9 62.4 1.0 CB A:CYS8 3.1 65.3 1.0 CE1 A:HIS31 3.1 64.5 1.0 CB A:CYS34 3.4 61.7 1.0 N A:HIS31 3.7 57.7 1.0 CB A:CYS10 3.8 68.9 1.0 CD2 A:HIS31 3.9 66.4 1.0 CA A:HIS31 3.9 60.2 1.0 NE2 A:HIS31 4.1 63.2 1.0 NH2 A:ARG18 4.3 66.8 1.0 N A:CYS10 4.5 79.5 1.0 NH1 A:ARG18 4.5 66.6 1.0 CA A:CYS8 4.6 62.1 1.0 CZ A:ARG18 4.6 65.9 1.0 CA A:CYS34 4.6 67.2 1.0 N A:CYS34 4.7 65.3 1.0 CA A:CYS10 4.8 73.5 1.0 N A:VAL9 4.9 72.5 1.0 C A:HIS31 4.9 62.6 1.0 C A:PHE30 5.0 54.4 1.0

Zinc binding site 3 out of 4 in the PHF2 (Phd+Jmj) in Complex with H3 Histone 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 H3 Histone N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:61.6 occ:1.00 SG B:CYS53 2.2 66.0 1.0 SG B:CYS26 2.2 53.5 1.0 SG B:CYS50 2.3 65.3 1.0 SG B:CYS23 2.4 60.3 1.0 CB B:CYS23 3.1 58.7 1.0 CB B:CYS53 3.3 66.3 1.0 CB B:CYS50 3.4 62.3 1.0 CB B:CYS26 3.4 53.6 1.0 N B:CYS26 3.8 61.0 1.0 N B:CYS50 3.9 66.0 1.0 CE1 B:PHE30 4.0 54.5 1.0 CZ B:PHE30 4.1 56.9 1.0 CA B:CYS50 4.2 66.7 1.0 CA B:CYS26 4.2 57.2 1.0 N B:CYS53 4.3 72.7 1.0 CA B:CYS53 4.4 70.5 1.0 CB B:ALA25 4.5 67.1 1.0 CA B:CYS23 4.6 55.8 1.0 O B:CYS50 4.8 71.3 1.0 C B:CYS50 4.8 69.2 1.0 C B:ALA25 4.8 61.5 1.0 C B:CYS23 4.9 59.1 1.0 C B:CYS26 5.0 55.9 1.0 N B:ALA25 5.0 60.6 1.0

Zinc binding site 4 out of 4 in the PHF2 (Phd+Jmj) in Complex with H3 Histone 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 H3 Histone N-Terminal Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:66.2 occ:1.00 ND1 B:HIS31 2.1 67.5 1.0 SG B:CYS34 2.2 65.6 1.0 SG B:CYS10 2.4 66.8 1.0 SG B:CYS8 2.4 57.8 1.0 CG B:HIS31 2.9 64.2 1.0 CB B:HIS31 3.0 62.9 1.0 CE1 B:HIS31 3.1 71.2 1.0 CB B:CYS34 3.2 61.4 1.0 CB B:CYS8 3.3 60.8 1.0 CB B:CYS10 3.7 65.8 1.0 N B:HIS31 3.8 57.5 1.0 CA B:HIS31 4.0 61.0 1.0 CD2 B:HIS31 4.0 64.7 1.0 NE2 B:HIS31 4.1 66.5 1.0 N B:CYS10 4.2 76.9 1.0 NH2 B:ARG18 4.3 68.2 1.0 NH1 B:ARG18 4.5 70.2 1.0 CA B:CYS10 4.6 68.2 1.0 CA B:CYS34 4.6 64.2 1.0 CZ B:ARG18 4.6 70.7 1.0 N B:VAL9 4.7 75.6 1.0 CA B:CYS8 4.7 63.3 1.0 CG2 B:VAL9 4.8 81.5 1.0 N B:CYS34 4.9 68.0 1.0 O B:HIS31 4.9 62.7 1.0 C B:HIS31 4.9 62.4 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