Zinc in PDB 3ql9: Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide

All present enzymatic activity of Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide:
3.6.4.12;

The structure of Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide, PDB code: 3ql9 was solved by B.Xiang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.95 / 0.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.719, 39.452, 41.057, 90.00, 111.24, 90.00
R / Rfree (%)	12.2 / 13.1

The binding sites of Zinc atom in the Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide (pdb code 3ql9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide, PDB code: 3ql9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:4.0 occ:1.00 SG A:CYS200 2.3 4.1 1.0 SG A:CYS174 2.3 5.1 1.0 SG A:CYS171 2.3 3.6 1.0 SG A:CYS197 2.3 3.9 1.0 CB A:CYS171 3.0 4.0 1.0 CB A:CYS200 3.2 3.8 1.0 CB A:CYS174 3.2 5.3 1.0 CB A:CYS197 3.4 3.7 1.0 N A:CYS174 3.6 4.5 1.0 CA A:CYS174 4.0 5.0 1.0 N A:CYS197 4.0 3.2 1.0 N A:CYS200 4.1 3.6 1.0 CA A:CYS200 4.2 3.5 1.0 CA A:CYS197 4.2 3.5 1.0 C A:ALA173 4.4 4.2 1.0 CB A:ALA173 4.5 4.3 1.0 CA A:CYS171 4.5 3.9 1.0 O A:HOH144 4.6 7.5 0.6 O A:CYS197 4.7 3.1 1.0 C A:CYS174 4.7 5.2 1.0 N A:ALA173 4.7 3.7 1.0 CA A:ALA173 4.8 4.0 1.0 C A:CYS197 4.8 3.2 1.0 N A:GLY175 4.9 5.3 1.0 C A:CYS171 4.9 3.5 1.0

Zinc binding site 2 out of 3 in the Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:3.3 occ:1.00 SG A:CYS243 2.3 3.3 1.0 SG A:CYS240 2.3 3.4 1.0 SG A:CYS223 2.3 3.6 1.0 SG A:CYS220 2.3 3.0 1.0 CB A:CYS220 3.1 3.1 1.0 CB A:CYS243 3.2 3.4 1.0 CB A:CYS223 3.3 3.7 1.0 CB A:CYS240 3.4 3.3 1.0 N A:CYS223 3.6 3.1 1.0 O A:HOH33 3.8 6.3 0.8 N A:CYS240 3.9 3.3 1.0 CA A:CYS223 4.0 3.3 1.0 O A:HOH29 4.1 5.5 0.8 N A:CYS243 4.1 3.4 1.0 CA A:CYS240 4.2 3.6 1.0 CB A:TRP222 4.2 3.0 1.0 CA A:CYS243 4.2 3.5 1.0 O A:HOH312 4.5 6.6 0.5 CA A:CYS220 4.5 3.0 1.0 O A:CYS240 4.5 3.5 1.0 C A:TRP222 4.6 2.9 1.0 C A:CYS240 4.7 3.4 1.0 CA A:TRP222 4.8 2.9 1.0 N A:TRP222 4.8 2.8 1.0 C A:CYS223 4.9 3.3 1.0 C A:CYS220 4.9 2.7 1.0

Zinc binding site 3 out of 3 in the Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Monoclinic Complex Structure of Atrx Add Bound to Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:4.0 occ:1.00 SG A:CYS268 2.3 5.1 1.0 SG A:CYS235 2.3 4.2 1.0 SG A:CYS232 2.3 4.0 1.0 SG A:CYS265 2.3 3.8 1.0 CB A:CYS232 3.1 4.0 1.0 CB A:CYS235 3.3 4.5 1.0 CB A:CYS265 3.3 4.1 1.0 CB A:CYS268 3.4 4.8 1.0 N A:CYS265 3.6 4.2 1.0 N A:CYS268 3.8 4.1 1.0 N A:CYS235 3.9 4.4 1.0 CA A:CYS265 4.0 4.0 1.0 CA A:CYS235 4.1 4.2 1.0 CA A:CYS268 4.2 4.5 1.0 O A:HOH145 4.3 14.3 0.7 C A:CYS265 4.4 3.8 1.0 CA A:CYS232 4.5 3.9 1.0 O A:CYS265 4.5 3.9 1.0 C A:PHE234 4.5 4.4 1.0 CB A:ILE267 4.6 4.5 1.0 C A:TYR264 4.7 4.5 1.0 C A:CYS235 4.7 3.9 1.0 ND2 A:ASN237 4.8 5.3 1.0 CB A:ASN237 4.8 3.9 1.0 C A:ILE267 4.8 4.2 1.0 N A:PHE234 4.8 4.5 1.0 CB A:PHE234 4.8 4.8 1.0 CA A:TYR264 4.9 4.9 1.0 O A:CYS235 4.9 4.1 1.0 CA A:PHE234 5.0 4.5 1.0 N A:ILE267 5.0 3.9 1.0

S.Iwase, B.Xiang, S.Ghosh, T.Ren, P.W.Lewis, J.C.Cochrane, C.D.Allis, D.J.Picketts, D.J.Patel, H.Li, Y.Shi. Atrx Add Domain Links An Atypical Histone Methylation Recognition Mechanism to Human Mental-Retardation Syndrome Nat.Struct.Mol.Biol. V. 18 769 2011.
ISSN: ISSN 1545-9993
PubMed: 21666679
DOI: 10.1038/NSMB.2062