Zinc in PDB 5vab: Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3

The structure of Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3, PDB code: 5vab was solved by E.Bergamin, S.Sarvan, J.Malette, M.Eram, S.Yeung, V.Mongeon, M.Joshi, J.S.Brunzelle, S.D.Michaels, A.Blais, M.Vedadi, J.-F.Couture, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.54 / 1.70
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.010, 44.010, 71.948, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.9

The binding sites of Zinc atom in the Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3 (pdb code 5vab). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3, PDB code: 5vab:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:15.0 occ:1.00 ND1 A:HIS48 2.1 14.2 1.0 SG A:CYS51 2.3 13.5 1.0 SG A:CYS25 2.3 12.5 1.0 SG A:CYS28 2.3 16.2 1.0 CB A:CYS25 3.0 13.7 1.0 CG A:HIS48 3.1 13.3 1.0 CE1 A:HIS48 3.1 14.2 1.0 CB A:CYS28 3.3 17.1 1.0 CB A:CYS51 3.3 12.5 1.0 CB A:HIS48 3.4 12.4 1.0 N A:CYS28 3.8 15.8 1.0 CA A:CYS28 4.1 17.0 1.0 N A:HIS48 4.2 10.9 1.0 NE2 A:HIS48 4.2 14.0 1.0 CD2 A:HIS48 4.2 13.2 1.0 O A:HOH229 4.3 29.2 1.0 CE1 A:PHE50 4.3 13.7 1.0 CA A:HIS48 4.4 11.1 1.0 CA A:CYS25 4.5 14.6 1.0 CB A:GLU27 4.6 15.7 1.0 CA A:CYS51 4.7 11.6 1.0 C A:GLU27 4.8 16.4 1.0 CD1 A:PHE50 4.9 12.8 1.0 C A:CYS28 4.9 18.0 1.0 O A:HOH234 4.9 24.8 1.0 C A:CYS25 5.0 14.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ATXR5 Phd Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:14.9 occ:1.00 SG A:CYS69 2.3 15.7 1.0 SG A:CYS66 2.3 13.0 1.0 SG A:CYS40 2.3 12.7 1.0 SG A:CYS43 2.4 13.9 1.0 CB A:CYS69 3.1 15.3 1.0 CB A:CYS40 3.2 12.2 1.0 CB A:CYS43 3.4 14.6 1.0 CB A:CYS66 3.4 13.3 1.0 OG A:SER68 3.7 23.2 1.0 N A:CYS43 3.7 14.2 1.0 N A:CYS66 4.0 12.6 1.0 CA A:CYS43 4.1 13.8 1.0 CA A:CYS66 4.2 12.2 1.0 N A:CYS69 4.2 16.7 1.0 CA A:CYS69 4.3 16.4 1.0 O A:CYS66 4.6 13.1 1.0 C A:CYS66 4.6 12.8 1.0 CA A:CYS40 4.6 11.6 1.0 CB A:LYS42 4.8 17.5 1.0 C A:SER68 4.9 17.4 1.0 C A:LYS42 4.9 15.4 1.0 N A:ASP44 4.9 13.0 1.0 C A:CYS43 4.9 13.3 1.0 CB A:SER68 4.9 20.8 1.0

E.Bergamin, S.Sarvan, J.Malette, M.S.Eram, S.Yeung, V.Mongeon, M.Joshi, J.S.Brunzelle, S.D.Michaels, A.Blais, M.Vedadi, J.F.Couture. Molecular Basis For the Methylation Specificity of ATXR5 For Histone H3. Nucleic Acids Res. V. 45 6375 2017.
ISSN: ESSN 1362-4962
PubMed: 28383693
DOI: 10.1093/NAR/GKX224