Zinc in PDB 5xfn: Structure of the N-Terminal Domains of PHF1

The structure of Structure of the N-Terminal Domains of PHF1, PDB code: 5xfn was solved by Z.Wang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.48 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.025, 62.000, 135.368, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

The binding sites of Zinc atom in the Structure of the N-Terminal Domains of PHF1 (pdb code 5xfn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the N-Terminal Domains of PHF1, PDB code: 5xfn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the N-Terminal Domains of PHF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the N-Terminal Domains of PHF1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.6 occ:1.00 SG A:CYS107 2.3 21.0 1.0 SG A:CYS136 2.3 14.8 1.0 SG A:CYS139 2.3 18.6 1.0 SG A:CYS110 2.4 18.4 1.0 CB A:CYS107 3.1 18.2 1.0 CB A:CYS110 3.3 24.8 1.0 CB A:CYS139 3.3 17.9 1.0 CB A:CYS136 3.5 12.4 1.0 N A:CYS110 3.6 19.7 1.0 N A:CYS136 4.0 13.2 1.0 CA A:CYS110 4.0 21.1 1.0 CA A:CYS136 4.2 12.4 1.0 N A:CYS139 4.2 12.9 1.0 O A:HOH671 4.3 43.8 1.0 CA A:CYS139 4.4 13.8 1.0 CB A:LYS109 4.6 19.0 1.0 CA A:CYS107 4.6 15.2 1.0 O A:CYS136 4.6 12.0 1.0 C A:LYS109 4.7 29.2 1.0 C A:CYS136 4.7 15.1 1.0 OH A:TYR114 4.7 20.8 1.0 C A:CYS110 4.9 23.4 1.0 N A:LYS109 4.9 19.2 1.0 CA A:LYS109 5.0 21.3 1.0 N A:ARG111 5.0 18.8 1.0 CE2 A:TYR114 5.0 15.3 1.0

Zinc binding site 2 out of 4 in the Structure of the N-Terminal Domains of PHF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the N-Terminal Domains of PHF1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.1 occ:1.00 ND1 A:HIS115 2.1 18.5 1.0 SG A:CYS118 2.3 19.6 1.0 SG A:CYS93 2.4 20.1 1.0 SG A:CYS90 2.4 19.6 1.0 CB A:CYS90 3.1 17.1 1.0 CE1 A:HIS115 3.1 21.6 1.0 CG A:HIS115 3.1 18.2 1.0 CB A:CYS118 3.3 15.6 1.0 CB A:CYS93 3.4 22.1 1.0 CB A:HIS115 3.4 18.7 1.0 N A:CYS93 3.8 25.4 1.0 N A:HIS115 4.0 16.1 1.0 CA A:CYS93 4.2 21.3 1.0 NE2 A:HIS115 4.2 22.0 1.0 CD2 A:HIS115 4.2 21.8 1.0 O A:HOH627 4.3 27.9 1.0 CA A:HIS115 4.3 16.8 1.0 CA A:CYS90 4.5 20.2 1.0 CB A:VAL92 4.6 22.4 1.0 CA A:CYS118 4.7 15.5 1.0 C A:VAL92 4.9 25.8 1.0 C A:CYS93 4.9 23.4 1.0 C A:CYS90 5.0 19.5 1.0

Zinc binding site 3 out of 4 in the Structure of the N-Terminal Domains of PHF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the N-Terminal Domains of PHF1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.8 occ:1.00 ND1 A:HIS212 2.2 12.4 1.0 SG A:CYS189 2.3 12.2 1.0 SG A:CYS215 2.3 14.6 1.0 SG A:CYS191 2.4 14.1 1.0 CB A:CYS189 3.1 14.3 1.0 CG A:HIS212 3.1 11.3 1.0 CE1 A:HIS212 3.2 13.1 1.0 CB A:CYS215 3.3 11.1 1.0 CB A:HIS212 3.4 10.8 1.0 CB A:CYS191 3.5 12.8 1.0 N A:CYS191 4.0 12.4 1.0 N A:HIS212 4.2 14.0 1.0 CD2 A:HIS212 4.3 10.1 1.0 NE2 A:HIS212 4.3 11.1 1.0 CA A:GLY44 4.3 14.8 1.0 CA A:CYS191 4.4 11.7 1.0 CA A:HIS212 4.4 16.8 1.0 N A:TYR190 4.4 11.0 1.0 CA A:CYS189 4.5 10.9 1.0 CA A:CYS215 4.7 10.4 1.0 C A:CYS189 4.9 13.4 1.0 N A:CYS215 4.9 10.4 1.0

Zinc binding site 4 out of 4 in the Structure of the N-Terminal Domains of PHF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the N-Terminal Domains of PHF1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:19.5 occ:1.00 SG A:CYS237 2.3 18.6 1.0 SG A:CYS234 2.4 16.8 1.0 SG A:CYS204 2.4 18.3 1.0 SG A:CYS207 2.4 16.8 1.0 CB A:CYS204 3.2 19.9 1.0 CB A:CYS237 3.3 21.1 1.0 CB A:CYS207 3.4 19.5 1.0 CB A:CYS234 3.5 14.7 1.0 N A:CYS207 3.7 19.4 1.0 O A:HOH681 3.7 23.7 1.0 N A:CYS234 4.0 14.8 1.0 CA A:CYS207 4.1 23.2 1.0 N A:CYS237 4.2 18.4 1.0 CA A:CYS234 4.3 14.1 1.0 CA A:CYS237 4.3 17.0 1.0 CB A:SER206 4.5 21.8 1.0 CZ A:PHE211 4.5 14.8 1.0 CE2 A:PHE211 4.6 12.8 1.0 C A:SER206 4.7 21.4 1.0 CA A:CYS204 4.7 19.9 1.0 O A:CYS234 4.8 16.6 1.0 C A:CYS234 4.8 16.3 1.0 N A:SER206 4.9 19.8 1.0 CA A:SER206 4.9 18.3 1.0

H.Li, R.Liefke, J.Jiang, J.V.Kurland, W.Tian, P.Deng, W.Zhang, Q.He, D.J.Patel, M.L.Bulyk, Y.Shi, Z.Wang. Polycomb-Like Proteins Link the PRC2 Complex to Cpg Islands Nature V. 549 287 2017.
ISSN: ESSN 1476-4687
PubMed: 28869966
DOI: 10.1038/NATURE23881