Zinc in PDB 5xfr: Ternary Complex of MTF2, Dna and Histone

The structure of Ternary Complex of MTF2, Dna and Histone, PDB code: 5xfr 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)	46.59 / 2.25
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.743, 137.743, 101.226, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.1

The binding sites of Zinc atom in the Ternary Complex of MTF2, Dna and Histone (pdb code 5xfr). 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 MTF2, Dna and Histone, PDB code: 5xfr:
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 MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.6 occ:1.00 ND1 A:HIS130 2.0 33.0 1.0 SG A:CYS133 2.4 43.5 1.0 SG A:CYS105 2.4 42.9 1.0 SG A:CYS108 2.4 45.9 1.0 CE1 A:HIS130 3.0 47.4 1.0 CG A:HIS130 3.0 42.3 1.0 CB A:CYS105 3.1 47.3 1.0 CB A:CYS133 3.3 36.0 1.0 CB A:HIS130 3.3 37.6 1.0 CB A:CYS108 3.4 40.2 1.0 N A:CYS108 3.9 42.8 1.0 O B:HOH542 4.0 35.1 1.0 NE2 A:HIS130 4.1 48.9 1.0 N A:HIS130 4.1 37.1 1.0 CD2 A:HIS130 4.1 42.8 1.0 CA A:CYS108 4.2 46.0 1.0 CA A:HIS130 4.3 38.6 1.0 CB A:ILE107 4.6 45.4 1.0 CA A:CYS105 4.6 49.7 1.0 OH A:TYR112 4.7 56.5 1.0 CA A:CYS133 4.7 34.8 1.0 CG B:LYS328 4.8 36.6 1.0 C A:ILE107 4.9 44.3 1.0 C A:CYS108 5.0 52.1 1.0

Zinc binding site 2 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:38.1 occ:1.00 SG A:CYS122 2.3 35.1 1.0 SG A:CYS154 2.3 40.9 1.0 SG A:CYS151 2.4 34.9 1.0 SG A:CYS125 2.4 43.2 1.0 CB A:CYS122 3.2 40.9 1.0 CB A:CYS154 3.3 30.5 1.0 CB A:CYS125 3.3 35.1 1.0 CB A:CYS151 3.6 35.5 1.0 N A:CYS125 3.8 44.1 1.0 N A:CYS151 3.9 35.3 1.0 CA A:CYS125 4.1 45.0 1.0 N A:CYS154 4.2 34.6 1.0 CA A:CYS151 4.3 35.8 1.0 CA A:CYS154 4.3 33.7 1.0 OE1 A:GLN153 4.5 56.8 1.0 CA A:CYS122 4.7 40.5 1.0 CB A:LYS124 4.8 49.0 1.0 O A:CYS151 4.8 31.9 1.0 C A:CYS151 4.9 33.8 1.0 C A:CYS125 4.9 42.0 1.0 C A:LYS124 4.9 44.8 1.0 C A:LEU150 5.0 36.5 1.0 N A:GLY126 5.0 41.5 1.0

Zinc binding site 3 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:26.2 occ:1.00 SG A:CYS222 2.3 23.1 1.0 SG A:CYS249 2.3 24.6 1.0 SG A:CYS252 2.4 26.9 1.0 SG A:CYS219 2.4 25.4 1.0 CB A:CYS219 3.2 22.5 1.0 CB A:CYS222 3.3 30.4 1.0 CB A:CYS252 3.4 23.2 1.0 CB A:CYS249 3.5 25.6 1.0 O A:HOH651 3.6 31.8 1.0 N A:CYS222 3.7 28.7 1.0 N A:CYS249 4.0 25.4 1.0 CA A:CYS222 4.1 27.7 1.0 N A:CYS252 4.2 35.2 1.0 CA A:CYS249 4.3 25.6 1.0 CA A:CYS252 4.4 33.2 1.0 CE2 A:PHE226 4.4 30.7 1.0 CZ A:PHE226 4.4 24.8 1.0 CB A:LYS221 4.5 28.1 1.0 CA A:CYS219 4.7 24.1 1.0 O A:CYS249 4.7 26.6 1.0 C A:CYS249 4.8 31.3 1.0 C A:LYS221 4.8 31.1 1.0 C A:CYS222 5.0 27.4 1.0

Zinc binding site 4 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:25.1 occ:1.00 ND1 A:HIS227 2.2 18.9 1.0 SG A:CYS230 2.3 24.4 1.0 SG A:CYS206 2.4 26.4 1.0 SG A:CYS204 2.5 25.7 1.0 CB A:CYS204 3.1 18.8 1.0 CG A:HIS227 3.1 22.8 1.0 CE1 A:HIS227 3.2 22.7 1.0 CB A:CYS230 3.3 20.1 1.0 CB A:HIS227 3.3 22.4 1.0 CB A:CYS206 3.5 24.6 1.0 N A:CYS206 4.1 30.6 1.0 N A:HIS227 4.2 23.0 1.0 CD2 A:HIS227 4.2 19.8 1.0 NE2 A:HIS227 4.2 25.0 1.0 CA A:GLY59 4.3 22.1 1.0 O A:HOH553 4.3 39.0 1.0 CA A:HIS227 4.4 24.4 1.0 CA A:CYS206 4.4 26.3 1.0 N A:TYR205 4.4 25.3 1.0 CA A:CYS204 4.5 22.2 1.0 CA A:CYS230 4.7 21.0 1.0 C A:CYS204 4.9 25.9 1.0 N A:CYS230 4.9 21.2 1.0

Zinc binding site 5 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:54.2 occ:1.00 SG B:CYS125 2.3 64.2 1.0 SG B:CYS154 2.4 61.2 1.0 SG B:CYS151 2.5 51.6 1.0 SG B:CYS122 2.5 54.7 1.0 CB B:CYS122 3.1 60.0 1.0 CB B:CYS154 3.1 55.6 1.0 O B:HOH622 3.3 41.2 1.0 CB B:CYS125 3.4 55.9 1.0 CB B:CYS151 3.6 44.9 1.0 O B:HOH626 3.6 46.4 1.0 N B:CYS125 4.0 61.7 1.0 N B:CYS151 4.0 47.2 1.0 CA B:CYS125 4.2 58.1 1.0 CA B:CYS151 4.3 47.3 1.0 CA B:CYS154 4.4 52.4 1.0 N B:CYS154 4.5 50.7 1.0 CA B:CYS122 4.6 65.1 1.0 N B:GLY126 4.8 54.4 1.0 C B:CYS125 4.9 57.9 1.0 C B:CYS151 4.9 50.9 1.0 O B:CYS151 4.9 52.5 1.0

Zinc binding site 6 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:75.8 occ:1.00 ND1 B:HIS130 2.5 67.6 1.0 SG B:CYS133 2.5 62.0 1.0 CB B:CYS108 2.6 81.5 1.0 CB B:CYS105 2.6 74.0 1.0 SG B:CYS105 2.9 73.9 1.0 CG B:HIS130 3.2 72.2 1.0 CB B:CYS133 3.2 56.6 1.0 CB B:HIS130 3.3 68.6 1.0 CE1 B:HIS130 3.5 77.6 1.0 SG B:CYS108 3.6 87.7 1.0 CA B:CYS108 3.8 82.4 1.0 N B:CYS108 3.9 76.7 1.0 N B:HIS130 4.0 69.2 1.0 CA B:CYS105 4.1 77.2 1.0 CA B:HIS130 4.3 70.3 1.0 CD2 B:HIS130 4.4 74.3 1.0 NE2 B:HIS130 4.5 82.4 1.0 O B:HOH619 4.5 55.5 1.0 C B:ILE107 4.5 75.1 1.0 N B:CYS105 4.6 84.3 1.0 CA B:CYS133 4.7 60.7 1.0 C B:CYS108 4.7 88.7 1.0 C B:CYS105 4.9 79.5 1.0 CB B:ILE107 5.0 75.1 1.0

Zinc binding site 7 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:24.8 occ:1.00 ND1 B:HIS227 2.2 17.9 1.0 SG B:CYS206 2.4 26.4 1.0 SG B:CYS204 2.4 23.5 1.0 SG B:CYS230 2.4 27.3 1.0 CB B:CYS204 3.0 18.7 1.0 CG B:HIS227 3.1 26.8 1.0 CE1 B:HIS227 3.2 23.4 1.0 CB B:CYS230 3.3 23.6 1.0 CB B:HIS227 3.4 18.6 1.0 CB B:CYS206 3.5 23.4 1.0 N B:CYS206 4.0 26.1 1.0 N B:HIS227 4.2 20.1 1.0 NE2 B:HIS227 4.3 20.9 1.0 CA B:GLY59 4.3 25.6 1.0 CD2 B:HIS227 4.3 21.7 1.0 CA B:CYS206 4.4 30.5 1.0 N B:TYR205 4.4 22.9 1.0 CA B:HIS227 4.4 20.0 1.0 CA B:CYS204 4.5 24.6 1.0 CA B:CYS230 4.7 21.8 1.0 C B:CYS204 4.8 25.7 1.0 N B:CYS230 5.0 28.2 1.0

Zinc binding site 8 out of 8 in the Ternary Complex of MTF2, Dna and Histone


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 MTF2, Dna and Histone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:22.8 occ:1.00 SG B:CYS249 2.3 21.3 1.0 SG B:CYS252 2.3 23.4 1.0 SG B:CYS222 2.4 23.4 1.0 SG B:CYS219 2.4 20.4 1.0 CB B:CYS219 3.2 22.9 1.0 CB B:CYS222 3.3 20.8 1.0 CB B:CYS252 3.4 20.6 1.0 CB B:CYS249 3.5 23.0 1.0 N B:CYS222 3.7 24.3 1.0 N B:CYS249 3.9 18.7 1.0 O B:HOH644 3.9 37.1 1.0 CA B:CYS222 4.1 29.0 1.0 N B:CYS252 4.2 23.8 1.0 CA B:CYS249 4.2 22.2 1.0 CB B:LYS221 4.4 24.1 1.0 CA B:CYS252 4.4 23.9 1.0 CZ B:PHE226 4.4 19.7 1.0 CE2 B:PHE226 4.5 18.7 1.0 CA B:CYS219 4.6 21.5 1.0 O B:HOH629 4.8 34.0 1.0 C B:CYS249 4.8 23.4 1.0 C B:LYS221 4.8 27.9 1.0 O B:CYS249 4.9 20.2 1.0 C B:CYS222 4.9 19.5 1.0 CA B:LYS221 5.0 24.9 1.0 C B:ILE248 5.0 24.1 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