Zinc in PDB 2vnf: Molecular Basis of Histone H3K4ME3 Recognition By ING4

The structure of Molecular Basis of Histone H3K4ME3 Recognition By ING4, PDB code: 2vnf was solved by A.Palacios, I.G.Munoz, D.Pantoja-Uceda, M.J.Marcaida, D.Torres, J.M.Martin-Garcia, I.Luque, G.Montoya, F.J.Blanco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.51 / 1.76
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	68.516, 68.516, 28.174, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 22.7

The structure of Molecular Basis of Histone H3K4ME3 Recognition By ING4 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Molecular Basis of Histone H3K4ME3 Recognition By ING4 (pdb code 2vnf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Molecular Basis of Histone H3K4ME3 Recognition By ING4, PDB code: 2vnf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Molecular Basis of Histone H3K4ME3 Recognition By ING4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Molecular Basis of Histone H3K4ME3 Recognition By ING4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1246 b:18.5 occ:1.00 ND1 A:HIS223 2.1 13.7 1.0 SG A:CYS226 2.3 17.9 1.0 SG A:CYS199 2.3 17.6 1.0 SG A:CYS201 2.4 17.6 1.0 CB A:CYS199 3.0 15.7 1.0 CE1 A:HIS223 3.0 15.3 1.0 CG A:HIS223 3.1 16.4 1.0 CB A:CYS226 3.2 16.5 1.0 CB A:CYS201 3.4 17.7 1.0 CB A:HIS223 3.5 12.0 1.0 N A:HIS223 4.1 15.3 1.0 N A:CYS201 4.1 16.8 1.0 O A:HOH2015 4.1 22.4 1.0 NE2 A:HIS223 4.2 16.6 1.0 CD2 A:HIS223 4.2 18.1 1.0 CA A:CYS201 4.3 16.6 1.0 CA A:HIS223 4.4 14.1 1.0 CA A:CYS199 4.5 16.3 1.0 O A:HOH2013 4.6 24.0 1.0 CA A:CYS226 4.6 18.6 1.0 OH A:TYR206 4.6 21.4 1.0 N A:LEU200 4.7 18.5 1.0 C A:CYS199 4.9 18.2 1.0 O A:HIS223 4.9 17.4 1.0 N A:CYS226 5.0 18.4 1.0

Zinc binding site 2 out of 4 in the Molecular Basis of Histone H3K4ME3 Recognition By ING4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Molecular Basis of Histone H3K4ME3 Recognition By ING4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1247 b:21.2 occ:1.00 SG A:CYS239 2.3 22.9 1.0 SG A:CYS242 2.3 25.2 1.0 SG A:CYS212 2.3 18.8 1.0 SG A:CYS217 2.4 22.4 1.0 CB A:CYS212 3.2 18.3 1.0 CB A:CYS217 3.2 17.9 1.0 CB A:CYS242 3.2 25.7 1.0 CB A:CYS239 3.3 20.1 1.0 N A:CYS239 3.9 20.8 1.0 CA A:CYS217 4.1 22.2 1.0 N A:CYS242 4.1 30.3 1.0 CA A:CYS239 4.2 22.7 1.0 CA A:CYS242 4.3 28.8 1.0 CZ A:PHE222 4.4 19.4 1.0 CE1 A:PHE222 4.5 17.7 1.0 CB A:ASN214 4.6 17.5 1.0 CA A:CYS212 4.6 16.4 1.0 C A:CYS239 4.8 24.8 1.0 ND2 A:ASN214 4.9 22.3 1.0

Zinc binding site 3 out of 4 in the Molecular Basis of Histone H3K4ME3 Recognition By ING4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Molecular Basis of Histone H3K4ME3 Recognition By ING4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1247 b:25.1 occ:1.00 ND1 C:HIS223 2.2 20.8 1.0 SG C:CYS201 2.3 24.9 1.0 SG C:CYS199 2.3 23.0 1.0 SG C:CYS226 2.3 27.4 1.0 CB C:CYS199 3.0 21.4 1.0 CB C:CYS226 3.2 24.1 1.0 CE1 C:HIS223 3.2 21.3 1.0 CG C:HIS223 3.2 20.2 1.0 CB C:CYS201 3.4 30.0 1.0 CB C:HIS223 3.5 22.3 1.0 N C:CYS201 4.0 29.9 1.0 N C:HIS223 4.0 20.1 1.0 NE2 C:HIS223 4.3 24.1 1.0 CA C:CYS201 4.3 29.0 1.0 CD2 C:HIS223 4.4 19.5 1.0 CA C:HIS223 4.4 19.3 1.0 CA C:CYS199 4.4 24.6 1.0 N C:LEU200 4.5 27.9 1.0 CA C:CYS226 4.6 23.6 1.0 OH C:TYR206 4.6 30.3 1.0 O C:HOH2011 4.6 31.9 1.0 C C:CYS199 4.7 27.4 1.0 O C:HIS223 4.9 21.4 1.0 O C:TYR198 4.9 28.5 1.0

Zinc binding site 4 out of 4 in the Molecular Basis of Histone H3K4ME3 Recognition By ING4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Molecular Basis of Histone H3K4ME3 Recognition By ING4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1248 b:33.3 occ:1.00 SG C:CYS239 2.3 36.7 1.0 SG C:CYS217 2.3 33.1 1.0 SG C:CYS242 2.3 37.7 1.0 SG C:CYS212 2.3 28.8 1.0 CB C:CYS212 3.2 26.2 1.0 CB C:CYS217 3.2 34.3 1.0 CB C:CYS242 3.2 44.2 1.0 CB C:CYS239 3.3 34.7 1.0 N C:CYS239 3.8 31.4 1.0 CA C:CYS217 4.1 37.6 1.0 CA C:CYS239 4.2 34.8 1.0 N C:CYS242 4.2 44.9 1.0 CA C:CYS242 4.3 42.5 1.0 CB C:ASN214 4.5 27.9 1.0 CE1 C:PHE222 4.6 24.6 1.0 CA C:CYS212 4.6 24.8 1.0 CZ C:PHE222 4.7 26.7 1.0 C C:CYS239 4.8 38.6 1.0 O C:CYS239 4.8 36.5 1.0 ND2 C:ASN214 4.8 33.0 1.0

A.Palacios, I.G.Munoz, D.Pantoja-Uceda, M.J.Marcaida, D.Torres, J.M.Martin-Garcia, I.Luque, G.Montoya, F.J.Blanco. Molecular Basis of Histone H3K4ME3 Recognition By ING4 J.Biol.Chem. V. 283 15956 2008.
ISSN: ISSN 0021-9258
PubMed: 18381289
DOI: 10.1074/JBC.M710020200