Zinc in PDB 5xfp: Binary Complex of PHF1 and A Double Stranded Dna

The structure of Binary Complex of PHF1 and A Double Stranded Dna, PDB code: 5xfp 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)	49.77 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.601, 110.291, 118.853, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Binary Complex of PHF1 and A Double Stranded Dna (pdb code 5xfp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Binary Complex of PHF1 and A Double Stranded Dna, PDB code: 5xfp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:52.3 occ:1.00 SG A:CYS110 2.3 50.6 1.0 SG A:CYS139 2.3 50.8 1.0 SG A:CYS136 2.4 50.5 1.0 SG A:CYS107 2.4 56.0 1.0 CB A:CYS110 3.2 58.6 1.0 CB A:CYS107 3.3 56.2 1.0 CB A:CYS139 3.4 62.5 1.0 CB A:CYS136 3.5 44.9 1.0 N A:CYS110 3.7 56.0 1.0 CA A:CYS110 4.0 57.0 1.0 N A:CYS136 4.0 54.0 1.0 CA A:CYS136 4.3 43.9 1.0 N A:CYS139 4.4 48.2 1.0 CA A:CYS139 4.5 57.9 1.0 CA A:CYS107 4.7 57.4 1.0 C A:CYS136 4.8 52.3 1.0 C A:CYS110 4.8 56.7 1.0 O A:CYS136 4.8 53.5 1.0 C A:LYS109 4.9 64.5 1.0 CB A:LYS109 4.9 63.9 1.0 OH A:TYR114 4.9 60.5 1.0 N A:ARG111 5.0 56.5 1.0

Zinc binding site 2 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:42.5 occ:1.00 ND1 A:HIS212 2.3 33.7 1.0 SG A:CYS215 2.3 40.4 1.0 SG A:CYS189 2.4 35.4 1.0 SG A:CYS191 2.4 40.0 1.0 CB A:CYS189 3.0 34.0 1.0 CG A:HIS212 3.2 39.1 1.0 CE1 A:HIS212 3.3 33.1 1.0 CB A:CYS215 3.3 37.1 1.0 CB A:HIS212 3.4 33.8 1.0 CB A:CYS191 3.5 42.7 1.0 N A:CYS191 4.0 39.8 1.0 N A:HIS212 4.1 43.8 1.0 CA A:GLY44 4.2 37.7 1.0 CD2 A:HIS212 4.3 32.2 1.0 CA A:HIS212 4.3 40.7 1.0 CA A:CYS191 4.4 41.2 1.0 NE2 A:HIS212 4.4 38.4 1.0 N A:TYR190 4.4 39.5 1.0 CA A:CYS189 4.5 36.7 1.0 CA A:CYS215 4.7 39.8 1.0 C A:CYS189 4.8 39.2 1.0 N A:CYS215 5.0 43.9 1.0

Zinc binding site 3 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:61.7 occ:1.00 SG A:CYS118 2.3 58.4 1.0 ND1 A:HIS115 2.3 66.6 1.0 SG A:CYS93 2.4 60.0 1.0 SG A:CYS90 2.4 63.9 1.0 CB A:CYS90 2.9 52.3 1.0 CG A:HIS115 3.1 62.1 1.0 CB A:CYS118 3.2 48.6 1.0 CB A:CYS93 3.2 62.6 1.0 CB A:HIS115 3.3 56.9 1.0 CE1 A:HIS115 3.3 68.5 1.0 N A:CYS93 3.9 78.1 1.0 O A:HOH502 4.1 55.0 1.0 N A:HIS115 4.1 48.0 1.0 CA A:CYS93 4.1 69.4 1.0 CA A:HIS115 4.3 55.8 1.0 CD2 A:HIS115 4.3 67.0 1.0 NE2 A:HIS115 4.4 73.5 1.0 CA A:CYS90 4.5 60.1 1.0 CA A:CYS118 4.6 54.6 1.0 CB A:VAL92 4.8 60.5 1.0 C A:CYS93 4.9 72.4 1.0 C A:VAL92 5.0 75.4 1.0

Zinc binding site 4 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:45.3 occ:1.00 SG A:CYS234 2.3 37.4 1.0 SG A:CYS207 2.3 38.5 1.0 SG A:CYS204 2.4 44.6 1.0 SG A:CYS237 2.5 44.6 1.0 CB A:CYS204 3.2 39.1 1.0 CB A:CYS207 3.3 47.5 1.0 CB A:CYS237 3.4 30.0 1.0 CB A:CYS234 3.4 41.3 1.0 N A:CYS207 3.8 51.8 1.0 N A:CYS234 3.9 38.0 1.0 CA A:CYS207 4.1 41.4 1.0 CA A:CYS234 4.2 44.4 1.0 N A:CYS237 4.3 46.8 1.0 CA A:CYS237 4.4 48.4 1.0 CZ A:PHE211 4.5 37.2 1.0 CE2 A:PHE211 4.5 43.9 1.0 CB A:SER206 4.6 47.5 1.0 CA A:CYS204 4.7 39.2 1.0 C A:CYS234 4.8 45.6 1.0 C A:SER206 4.8 49.8 1.0 O A:CYS234 4.9 58.2 1.0 C A:CYS207 5.0 40.8 1.0

Zinc binding site 5 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:49.0 occ:1.00 SG B:CYS110 2.3 46.2 1.0 SG B:CYS139 2.3 50.1 1.0 SG B:CYS136 2.3 48.3 1.0 SG B:CYS107 2.4 48.0 1.0 CB B:CYS110 3.3 46.3 1.0 CB B:CYS139 3.3 44.5 1.0 CB B:CYS107 3.3 56.3 1.0 CB B:CYS136 3.4 52.6 1.0 N B:CYS110 3.7 56.4 1.0 N B:CYS136 4.0 58.5 1.0 CA B:CYS110 4.1 50.7 1.0 CA B:CYS136 4.2 53.5 1.0 N B:CYS139 4.2 47.2 1.0 CA B:CYS139 4.3 44.1 1.0 C B:CYS136 4.6 50.1 1.0 O B:CYS136 4.7 47.1 1.0 CA B:CYS107 4.8 55.3 1.0 OH B:TYR114 4.8 60.2 1.0 CB B:LYS109 4.8 75.6 1.0 C B:CYS110 4.9 45.1 1.0 CE2 B:TYR114 4.9 55.4 1.0 C B:LYS109 4.9 58.0 1.0

Zinc binding site 6 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:52.7 occ:1.00 SG B:CYS118 2.3 47.0 1.0 SG B:CYS93 2.3 48.0 1.0 ND1 B:HIS115 2.4 50.5 1.0 SG B:CYS90 2.4 49.7 1.0 CG B:HIS115 3.2 57.5 1.0 CB B:HIS115 3.2 58.5 1.0 CB B:CYS93 3.2 41.0 1.0 CB B:CYS90 3.3 57.1 1.0 CB B:CYS118 3.3 45.4 1.0 CE1 B:HIS115 3.5 61.8 1.0 N B:CYS93 3.8 49.5 1.0 CA B:CYS93 4.1 47.4 1.0 N B:HIS115 4.2 58.2 1.0 CA B:HIS115 4.3 57.3 1.0 CD2 B:HIS115 4.4 53.1 1.0 NE2 B:HIS115 4.5 58.1 1.0 CA B:CYS118 4.7 55.2 1.0 CB B:VAL92 4.7 56.2 1.0 CA B:CYS90 4.7 51.2 1.0 N B:ARG94 4.8 52.0 1.0 C B:CYS93 4.8 50.6 1.0 C B:VAL92 4.9 57.1 1.0 O B:SER95 4.9 59.1 1.0

Zinc binding site 7 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:48.5 occ:1.00 ND1 B:HIS212 2.3 36.8 1.0 SG B:CYS215 2.3 42.8 1.0 SG B:CYS189 2.4 47.4 1.0 SG B:CYS191 2.6 0.6 1.0 CB B:CYS189 3.0 34.4 1.0 CG B:HIS212 3.2 46.2 1.0 CB B:CYS191 3.2 58.8 1.0 CB B:HIS212 3.3 45.0 1.0 CB B:CYS215 3.3 36.0 1.0 CE1 B:HIS212 3.4 43.5 1.0 N B:CYS191 3.9 40.8 1.0 N B:HIS212 4.2 37.5 1.0 CA B:CYS191 4.2 47.1 1.0 CA B:GLY44 4.3 44.8 1.0 CD2 B:HIS212 4.4 43.4 1.0 CA B:HIS212 4.4 49.4 1.0 N B:TYR190 4.4 47.0 1.0 NE2 B:HIS212 4.4 49.9 1.0 CA B:CYS189 4.5 41.2 1.0 CA B:CYS215 4.7 39.4 1.0 C B:CYS189 4.8 43.9 1.0

Zinc binding site 8 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:52.3 occ:1.00 SG B:CYS234 2.3 49.0 1.0 SG B:CYS207 2.3 49.3 1.0 SG B:CYS204 2.3 48.3 1.0 SG B:CYS237 2.4 52.6 1.0 CB B:CYS204 3.2 50.8 1.0 CB B:CYS207 3.3 49.3 1.0 CB B:CYS237 3.5 54.9 1.0 CB B:CYS234 3.6 54.1 1.0 N B:CYS207 3.7 51.5 1.0 N B:CYS234 4.0 47.9 1.0 CA B:CYS207 4.1 49.5 1.0 CB B:SER206 4.3 53.5 1.0 N B:CYS237 4.3 56.2 1.0 CA B:CYS234 4.4 54.0 1.0 CZ B:PHE211 4.5 50.1 1.0 CE2 B:PHE211 4.5 57.0 1.0 CA B:CYS237 4.6 59.6 1.0 C B:SER206 4.6 59.5 1.0 CA B:CYS204 4.7 52.1 1.0 CA B:SER206 4.8 59.1 1.0 N B:SER206 4.9 61.2 1.0 O B:CYS234 4.9 54.9 1.0 C B:CYS207 4.9 48.4 1.0 C B:CYS234 4.9 59.6 1.0

Zinc binding site 9 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:77.2 occ:1.00 ND1 E:HIS115 2.1 68.6 1.0 SG E:CYS90 2.4 69.5 1.0 SG E:CYS118 2.6 74.6 1.0 CG E:HIS115 2.8 77.2 1.0 CB E:HIS115 2.9 79.8 1.0 SG E:CYS93 2.9 0.4 1.0 CB E:CYS93 3.1 69.5 1.0 CB E:CYS90 3.1 84.8 1.0 CE1 E:HIS115 3.2 64.9 1.0 CB E:CYS118 3.4 67.9 1.0 N E:CYS93 3.7 76.0 1.0 CA E:CYS93 4.0 84.1 1.0 CD2 E:HIS115 4.0 73.3 1.0 N E:HIS115 4.0 64.9 1.0 CA E:HIS115 4.1 70.8 1.0 NE2 E:HIS115 4.2 73.2 1.0 CA E:CYS90 4.6 84.4 1.0 CB E:VAL92 4.6 63.5 1.0 C E:VAL92 4.8 71.6 1.0 CA E:CYS118 4.8 60.8 1.0 C E:CYS90 4.9 72.8 1.0 O E:CYS90 5.0 64.0 1.0

Zinc binding site 10 out of 12 in the Binary Complex of PHF1 and A Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Binary Complex of PHF1 and A Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:50.6 occ:1.00 ND1 E:HIS212 2.2 60.0 1.0 SG E:CYS215 2.3 49.1 1.0 SG E:CYS191 2.4 51.5 1.0 SG E:CYS189 2.6 50.1 1.0 CB E:CYS189 3.1 40.0 1.0 CG E:HIS212 3.1 58.9 1.0 CE1 E:HIS212 3.2 56.3 1.0 CB E:CYS215 3.3 55.2 1.0 CB E:HIS212 3.4 54.1 1.0 CB E:CYS191 3.5 54.3 1.0 N E:CYS191 4.0 56.3 1.0 N E:HIS212 4.3 52.8 1.0 CD2 E:HIS212 4.3 46.7 1.0 NE2 E:HIS212 4.3 55.8 1.0 CA E:GLY44 4.3 62.0 1.0 CA E:CYS191 4.4 55.3 1.0 CA E:HIS212 4.4 51.8 1.0 N E:TYR190 4.5 44.6 1.0 CA E:CYS189 4.6 49.6 1.0 CA E:CYS215 4.8 58.5 1.0 C E:CYS189 4.9 46.0 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