Zinc in PDB 3o7a: Crystal Structure of PHF13 in Complex with H3K4ME3

The structure of Crystal Structure of PHF13 in Complex with H3K4ME3, PDB code: 3o7a was solved by C.B.Bian, R.Lam, C.Xu, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, A.Bochkarev, J.Min, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.73 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	21.232, 44.334, 60.330, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.4

The binding sites of Zinc atom in the Crystal Structure of PHF13 in Complex with H3K4ME3 (pdb code 3o7a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PHF13 in Complex with H3K4ME3, PDB code: 3o7a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PHF13 in Complex with H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PHF13 in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.5 occ:1.00 ND1 A:HIS257 2.1 11.0 1.0 SG A:CYS260 2.3 10.7 1.0 SG A:CYS235 2.3 10.9 1.0 SG A:CYS237 2.3 10.8 1.0 CE1 A:HIS257 3.1 9.8 1.0 CB A:CYS235 3.1 10.1 1.0 CG A:HIS257 3.1 7.8 1.0 CB A:CYS237 3.2 10.2 1.0 CB A:CYS260 3.3 10.1 1.0 CB A:HIS257 3.5 9.4 1.0 O A:HOH402 3.7 11.9 1.0 N A:HIS257 4.0 9.5 1.0 N A:CYS237 4.0 11.5 1.0 NE2 A:HIS257 4.2 9.3 1.0 CA A:CYS237 4.2 9.8 1.0 CD2 A:HIS257 4.3 9.1 1.0 CA A:HIS257 4.4 8.5 1.0 CA A:CYS235 4.5 9.4 1.0 NH2 A:ARG244 4.6 11.6 1.0 CA A:CYS260 4.7 10.5 1.0 C A:CYS235 4.8 9.8 1.0 NH1 A:ARG244 4.9 13.7 1.0 N A:PHE236 4.9 10.5 1.0 N A:CYS260 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PHF13 in Complex with H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PHF13 in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.5 occ:1.00 SG A:CYS274 2.3 17.1 1.0 SG A:CYS252 2.3 14.4 1.0 SG A:CYS249 2.3 12.6 1.0 SG A:CYS277 2.3 19.1 1.0 CB A:CYS249 3.2 9.5 1.0 CB A:CYS252 3.2 13.3 1.0 CB A:CYS277 3.3 21.9 1.0 CB A:CYS274 3.4 15.6 1.0 N A:CYS252 3.7 13.0 1.0 N A:CYS274 3.9 15.2 1.0 CA A:CYS252 4.1 12.7 1.0 N A:CYS277 4.2 24.9 1.0 CA A:CYS274 4.2 17.4 1.0 CA A:CYS277 4.3 24.6 1.0 O A:CYS274 4.6 20.2 1.0 CA A:CYS249 4.6 10.4 1.0 C A:CYS274 4.7 19.5 1.0 C A:GLU251 4.7 16.2 1.0 C A:CYS252 4.8 10.7 1.0 CB A:GLU251 4.8 21.0 1.0 N A:GLU251 5.0 14.7 1.0

H.R.Chung, C.Xu, A.Fuchs, A.Mund, M.Lange, H.Staege, T.Schubert, C.Bian, I.Dunkel, A.Eberharter, C.Regnard, H.Klinker, D.Meierhofer, L.Cozzuto, A.Winterpacht, L.Di Croce, J.Min, H.Will, S.Kinkley. PHF13 Is A Molecular Reader and Transcriptional Co-Regulator of H3K4ME2/3. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27223324
DOI: 10.7554/ELIFE.10607