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

The structure of Structure of the N-Terminal Domains of PHF1, PDB code: 5xfo 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)	29.34 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.467, 66.772, 76.165, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.7

The binding sites of Zinc atom in the Structure of the N-Terminal Domains of PHF1 (pdb code 5xfo). 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: 5xfo:
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:27.2 occ:1.00 SG A:CYS107 2.2 26.3 1.0 SG A:CYS110 2.4 31.5 1.0 SG A:CYS139 2.4 24.9 1.0 SG A:CYS136 2.5 22.4 1.0 CB A:CYS107 3.0 23.1 1.0 CB A:CYS139 3.3 22.8 1.0 CB A:CYS110 3.4 24.9 1.0 CB A:CYS136 3.4 18.4 1.0 N A:CYS110 3.7 33.7 1.0 N A:CYS136 3.9 15.5 1.0 CA A:CYS110 4.1 29.5 1.0 CA A:CYS136 4.2 15.5 1.0 N A:CYS139 4.3 19.3 1.0 CB A:LYS109 4.4 41.8 1.0 CA A:CYS139 4.4 20.2 1.0 CA A:CYS107 4.5 20.5 1.0 CG A:LYS109 4.7 53.0 1.0 O A:CYS136 4.7 13.8 1.0 CG1 A:VAL135 4.7 20.9 1.0 C A:CYS136 4.7 16.4 1.0 C A:LYS109 4.8 39.7 1.0 C A:CYS110 4.9 32.5 1.0 OH A:TYR114 4.9 28.1 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:26.9 occ:1.00 ND1 A:HIS115 2.2 27.2 1.0 SG A:CYS118 2.3 29.5 1.0 SG A:CYS90 2.3 27.4 1.0 SG A:CYS93 2.4 29.4 1.0 CB A:CYS90 3.0 24.6 1.0 CG A:HIS115 3.1 23.0 1.0 CB A:CYS93 3.2 28.6 1.0 CB A:CYS118 3.3 21.6 1.0 CE1 A:HIS115 3.3 34.9 1.0 CB A:HIS115 3.3 19.1 1.0 N A:CYS93 3.9 33.5 1.0 N A:HIS115 4.0 19.6 1.0 CA A:CYS93 4.1 30.4 1.0 CA A:HIS115 4.3 17.3 1.0 CD2 A:HIS115 4.3 26.7 1.0 O A:HOH620 4.4 34.6 1.0 NE2 A:HIS115 4.4 21.2 1.0 CA A:CYS90 4.4 28.2 1.0 CA A:CYS118 4.7 21.9 1.0 CB A:VAL92 4.7 24.6 1.0 C A:CYS93 4.8 28.4 1.0 C A:VAL92 4.9 31.7 1.0 C A:CYS90 5.0 31.0 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:12.1 occ:1.00 ND1 A:HIS212 2.1 10.7 1.0 SG A:CYS191 2.3 12.0 1.0 SG A:CYS215 2.3 13.7 1.0 SG A:CYS189 2.4 11.3 1.0 CE1 A:HIS212 3.1 17.6 1.0 CB A:CYS189 3.1 11.2 1.0 CG A:HIS212 3.1 9.3 1.0 CB A:CYS215 3.3 14.8 1.0 CB A:CYS191 3.3 15.1 1.0 CB A:HIS212 3.5 8.6 1.0 N A:CYS191 4.0 13.5 1.0 CA A:GLY44 4.2 9.5 1.0 N A:HIS212 4.2 10.1 1.0 NE2 A:HIS212 4.2 12.1 1.0 CD2 A:HIS212 4.3 10.2 1.0 CA A:CYS191 4.3 16.7 1.0 CA A:HIS212 4.4 8.8 1.0 N A:TYR190 4.5 11.6 1.0 CA A:CYS189 4.6 8.6 1.0 CA A:CYS215 4.7 10.8 1.0 C A:CYS189 4.9 12.5 1.0 N A:CYS215 4.9 12.6 1.0 O A:GLY44 5.0 13.8 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:17.9 occ:1.00 SG A:CYS207 2.3 17.0 1.0 SG A:CYS204 2.3 17.7 1.0 SG A:CYS237 2.3 20.2 1.0 SG A:CYS234 2.4 19.2 1.0 CB A:CYS204 3.2 13.3 1.0 CB A:CYS207 3.2 21.4 1.0 CB A:CYS237 3.3 17.4 1.0 CB A:CYS234 3.5 13.2 1.0 N A:CYS207 3.6 20.9 1.0 O A:HOH695 3.7 20.3 1.0 CA A:CYS207 4.0 18.9 1.0 N A:CYS234 4.1 16.3 1.0 N A:CYS237 4.2 21.8 1.0 O A:HOH685 4.2 39.2 1.0 CA A:CYS234 4.3 10.5 1.0 CA A:CYS237 4.3 22.8 1.0 CB A:SER206 4.4 20.8 1.0 CZ A:PHE211 4.5 9.8 1.0 CE2 A:PHE211 4.5 9.2 1.0 C A:SER206 4.6 26.3 1.0 CA A:CYS204 4.6 12.9 1.0 O A:CYS234 4.8 21.0 1.0 C A:CYS234 4.9 16.2 1.0 CA A:SER206 4.9 22.4 1.0 C A:CYS207 4.9 18.7 1.0 N A:SER206 4.9 14.2 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