Zinc in PDB 5xfq: Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide

The structure of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide, PDB code: 5xfq 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)	47.41 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.243, 62.550, 97.338, 90.00, 103.04, 90.00
R / Rfree (%)	22.2 / 25.8

The binding sites of Zinc atom in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide (pdb code 5xfq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide, PDB code: 5xfq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:48.9 occ:1.00 ND1 A:HIS115 2.1 45.4 1.0 SG A:CYS118 2.3 43.5 1.0 SG A:CYS93 2.4 48.6 1.0 SG A:CYS90 2.5 42.5 1.0 CG A:HIS115 3.0 48.7 1.0 CE1 A:HIS115 3.1 42.8 1.0 CB A:CYS90 3.2 42.9 1.0 CB A:HIS115 3.3 40.7 1.0 CB A:CYS93 3.3 49.7 1.0 CB A:CYS118 3.3 43.9 1.0 N A:CYS93 3.8 44.8 1.0 CD2 A:HIS115 4.2 47.1 1.0 CA A:CYS93 4.2 50.5 1.0 NE2 A:HIS115 4.2 44.4 1.0 N A:HIS115 4.3 40.5 1.0 CA A:HIS115 4.4 44.3 1.0 CB A:VAL92 4.6 49.3 1.0 CA A:CYS90 4.7 41.4 1.0 CA A:CYS118 4.7 47.6 1.0 C A:VAL92 4.9 53.2 1.0 C A:CYS93 5.0 51.6 1.0 N A:ARG94 5.0 49.3 1.0

Zinc binding site 2 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:41.0 occ:1.00 SG A:CYS107 2.3 41.9 1.0 SG A:CYS139 2.4 43.4 1.0 SG A:CYS136 2.4 42.0 1.0 SG A:CYS110 2.5 45.2 1.0 CB A:CYS107 3.0 42.0 1.0 CB A:CYS139 3.3 47.3 1.0 CB A:CYS110 3.5 48.7 1.0 CB A:CYS136 3.6 37.8 1.0 N A:CYS110 3.8 42.9 1.0 N A:CYS136 4.0 39.3 1.0 N A:CYS139 4.1 46.5 1.0 CA A:CYS110 4.2 47.6 1.0 CA A:CYS139 4.3 47.4 1.0 CA A:CYS136 4.3 40.3 1.0 CB A:LYS109 4.4 52.0 1.0 CA A:CYS107 4.5 41.8 1.0 C A:CYS136 4.8 46.9 1.0 O A:CYS136 4.8 44.9 1.0 C A:LYS109 4.8 43.8 1.0 CG1 A:VAL135 4.8 42.1 1.0 N A:LYS109 4.9 47.2 1.0 CA A:LYS109 5.0 45.6 1.0 C A:CYS107 5.0 37.1 1.0 C A:CYS110 5.0 44.4 1.0 CE2 A:TYR114 5.0 50.1 1.0

Zinc binding site 3 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:40.9 occ:1.00 ND1 A:HIS212 2.3 39.6 1.0 SG A:CYS215 2.4 34.5 1.0 SG A:CYS191 2.4 44.1 1.0 SG A:CYS189 2.5 39.7 1.0 CB A:CYS189 3.0 32.6 1.0 CG A:HIS212 3.1 41.6 1.0 CB A:HIS212 3.2 41.0 1.0 CB A:CYS215 3.3 39.8 1.0 CE1 A:HIS212 3.4 40.6 1.0 CB A:CYS191 3.5 39.6 1.0 N A:HIS212 4.0 37.3 1.0 N A:CYS191 4.1 44.2 1.0 CA A:HIS212 4.2 38.8 1.0 CA A:GLY44 4.3 38.1 1.0 CD2 A:HIS212 4.3 40.0 1.0 N A:TYR190 4.4 35.5 1.0 NE2 A:HIS212 4.4 45.5 1.0 CA A:CYS191 4.4 45.4 1.0 CA A:CYS189 4.5 37.1 1.0 CA A:CYS215 4.7 37.6 1.0 C A:CYS189 4.8 39.0 1.0 O A:GLY44 4.9 43.5 1.0 N A:CYS215 5.0 37.2 1.0

Zinc binding site 4 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:44.7 occ:1.00 SG A:CYS234 2.3 44.5 1.0 SG A:CYS207 2.3 41.1 1.0 SG A:CYS237 2.4 44.5 1.0 SG A:CYS204 2.4 46.0 1.0 CB A:CYS204 3.3 41.5 1.0 CB A:CYS207 3.4 51.3 1.0 CB A:CYS237 3.4 45.3 1.0 CB A:CYS234 3.6 47.0 1.0 N A:CYS207 3.8 51.8 1.0 N A:CYS234 4.0 51.2 1.0 CA A:CYS207 4.2 52.1 1.0 N A:CYS237 4.2 46.3 1.0 CA A:CYS234 4.3 49.5 1.0 CA A:CYS237 4.4 46.6 1.0 CZ A:PHE211 4.4 41.1 1.0 CB A:SER206 4.5 51.3 1.0 CE1 A:PHE211 4.6 38.8 1.0 CA A:CYS204 4.8 51.0 1.0 C A:SER206 4.8 52.0 1.0 O A:CYS234 4.8 47.3 1.0 C A:CYS234 4.8 46.5 1.0 N A:SER206 5.0 53.8 1.0 CA A:SER206 5.0 54.3 1.0

Zinc binding site 5 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:43.0 occ:1.00 ND1 B:HIS212 2.1 33.0 1.0 SG B:CYS191 2.3 49.7 1.0 SG B:CYS215 2.4 38.6 1.0 SG B:CYS189 2.4 42.3 1.0 CB B:CYS189 2.9 37.3 1.0 CG B:HIS212 3.1 40.0 1.0 CE1 B:HIS212 3.1 38.7 1.0 CB B:CYS215 3.4 43.7 1.0 CB B:HIS212 3.4 37.4 1.0 CB B:CYS191 3.6 47.6 1.0 N B:CYS191 4.0 50.6 1.0 N B:HIS212 4.2 44.0 1.0 CA B:GLY44 4.2 40.6 1.0 NE2 B:HIS212 4.2 40.2 1.0 CD2 B:HIS212 4.3 37.7 1.0 N B:TYR190 4.4 48.7 1.0 CA B:CYS189 4.4 42.8 1.0 CA B:HIS212 4.4 41.3 1.0 CA B:CYS191 4.4 50.3 1.0 C B:CYS189 4.8 46.2 1.0 CA B:CYS215 4.8 41.9 1.0 O B:TYR188 5.0 49.6 1.0

Zinc binding site 6 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:58.2 occ:1.00 SG B:CYS207 2.3 48.3 1.0 SG B:CYS234 2.3 53.9 1.0 SG B:CYS204 2.4 49.4 1.0 SG B:CYS237 2.5 59.6 1.0 CB B:CYS207 3.1 55.9 1.0 CB B:CYS204 3.2 51.1 1.0 CB B:CYS237 3.5 52.0 1.0 CB B:CYS234 3.6 49.7 1.0 N B:CYS207 3.6 53.8 1.0 CA B:CYS207 4.0 49.6 1.0 N B:CYS234 4.1 48.1 1.0 N B:CYS237 4.4 50.6 1.0 CA B:CYS234 4.4 50.8 1.0 CB B:SER206 4.5 59.4 1.0 CZ B:PHE211 4.5 50.2 1.0 CA B:CYS237 4.6 60.2 1.0 CE2 B:PHE211 4.6 42.8 1.0 C B:SER206 4.7 58.0 1.0 CA B:CYS204 4.7 49.5 1.0 C B:CYS207 4.8 48.2 1.0 CA B:SER206 4.9 54.5 1.0 N B:SER206 5.0 57.5 1.0

Zinc binding site 7 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:0.6 occ:1.00 ND1 B:HIS115 2.3 0.3 1.0 SG B:CYS93 2.4 0.6 1.0 SG B:CYS90 2.4 0.1 1.0 CB B:HIS115 2.7 0.9 1.0 CG B:HIS115 2.8 0.8 1.0 SG B:CYS118 2.9 0.8 1.0 CB B:CYS93 3.0 0.8 1.0 CB B:CYS118 3.4 0.6 1.0 CB B:CYS90 3.4 0.6 1.0 CE1 B:HIS115 3.5 0.8 1.0 N B:CYS93 3.7 0.6 1.0 CA B:HIS115 3.9 0.9 1.0 CA B:CYS93 4.0 0.8 1.0 N B:HIS115 4.0 99.3 1.0 CD2 B:HIS115 4.0 0.8 1.0 NE2 B:HIS115 4.4 0.0 1.0 CB B:VAL92 4.4 1.0 1.0 C B:VAL92 4.7 0.4 1.0 O B:SER95 4.8 0.6 1.0 CA B:CYS118 4.8 0.7 1.0 CA B:CYS90 4.8 0.5 1.0 C B:CYS93 4.9 0.5 1.0 CA B:VAL92 5.0 0.0 1.0

Zinc binding site 8 out of 8 in the Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ternary Complex of PHF1, A Dna Duplex and A Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:68.7 occ:1.00 SG B:CYS107 2.3 76.4 1.0 SG B:CYS139 2.5 67.9 1.0 SG B:CYS110 2.5 75.7 1.0 SG B:CYS136 2.6 72.2 1.0 CB B:CYS139 3.2 66.7 1.0 CB B:CYS110 3.2 74.5 1.0 CB B:CYS107 3.2 81.0 1.0 N B:CYS110 3.6 74.5 1.0 CB B:CYS136 3.6 70.4 1.0 N B:CYS136 3.9 68.3 1.0 CA B:CYS110 4.0 78.3 1.0 N B:CYS139 4.3 52.8 1.0 CA B:CYS136 4.3 66.7 1.0 CA B:CYS139 4.4 57.5 1.0 CB B:LYS109 4.5 74.7 1.0 C B:LYS109 4.6 75.2 1.0 CA B:CYS107 4.7 82.1 1.0 C B:CYS110 4.8 81.2 1.0 C B:CYS136 4.8 65.7 1.0 N B:LYS109 4.8 78.8 1.0 O B:CYS136 4.8 63.9 1.0 CG1 B:VAL135 4.9 63.6 1.0 CA B:LYS109 4.9 75.5 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