Zinc in PDB 3kv4: Structure of PHF8 in Complex with Histone H3

The structure of Structure of PHF8 in Complex with Histone H3, PDB code: 3kv4 was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.72 / 2.19
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.500, 73.500, 210.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.5

The structure of Structure of PHF8 in Complex with Histone H3 also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Iron	(Fe)	1 atom

The binding sites of Zinc atom in the Structure of PHF8 in Complex with Histone H3 (pdb code 3kv4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of PHF8 in Complex with Histone H3, PDB code: 3kv4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of PHF8 in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PHF8 in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn448 b:13.7 occ:1.00 ND1 A:HIS31 2.1 8.0 1.0 SG A:CYS34 2.3 15.7 1.0 SG A:CYS10 2.4 14.7 1.0 SG A:CYS8 2.4 16.2 1.0 CE1 A:HIS31 3.1 10.1 1.0 CG A:HIS31 3.1 9.8 1.0 CB A:CYS8 3.1 13.8 1.0 CB A:CYS34 3.2 17.4 1.0 O1 A:EDO452 3.3 14.3 1.0 CB A:HIS31 3.4 10.5 1.0 CB A:CYS10 3.4 16.0 1.0 N A:CYS10 4.0 16.3 1.0 C1 A:EDO452 4.2 13.1 1.0 N A:HIS31 4.2 12.4 1.0 NH2 A:ARG18 4.2 13.5 1.0 NE2 A:HIS31 4.2 9.8 1.0 CD2 A:HIS31 4.2 9.2 1.0 CA A:CYS10 4.3 16.0 1.0 CA A:HIS31 4.4 10.8 1.0 N A:LEU9 4.5 14.8 1.0 CA A:CYS8 4.6 14.7 1.0 CA A:CYS34 4.6 16.7 1.0 NH1 A:ARG18 4.7 15.8 1.0 CZ A:ARG18 4.8 13.2 1.0 C A:CYS8 4.9 15.7 1.0

Zinc binding site 2 out of 2 in the Structure of PHF8 in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PHF8 in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn449 b:37.0 occ:1.00 SG A:CYS26 1.9 47.5 1.0 SG A:CYS50 2.3 39.4 1.0 SG A:CYS23 2.3 36.8 1.0 SG A:CYS53 2.5 42.4 1.0 CB A:CYS26 2.6 43.1 1.0 CB A:CYS23 3.1 34.1 1.0 N A:CYS26 3.3 44.2 1.0 CB A:CYS53 3.4 43.6 1.0 CA A:CYS26 3.5 43.6 1.0 CB A:CYS50 3.6 39.6 1.0 N A:CYS50 4.2 39.9 1.0 CE1 A:PHE30 4.2 22.5 1.0 CZ A:PHE30 4.3 20.0 1.0 CB A:MET25 4.3 49.0 1.0 C A:MET25 4.4 45.4 1.0 CA A:CYS50 4.5 41.8 1.0 N A:CYS53 4.5 46.8 1.0 CA A:CYS23 4.6 33.4 1.0 CA A:CYS53 4.6 46.3 1.0 C A:CYS26 4.7 41.5 1.0 CA A:MET25 4.8 45.5 1.0 C A:CYS23 4.9 34.4 1.0 N A:GLN27 5.0 40.0 1.0 N A:MET25 5.0 44.8 1.0 O A:CYS23 5.0 34.6 1.0

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753