Zinc in PDB 3n9o: CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog

All present enzymatic activity of CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog:
1.14.11.27;

The structure of CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog, PDB code: 3n9o was solved by Y.Yang, L.Hu, P.Wang, H.Hou, C.D.Chen, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.28 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.090, 87.379, 102.727, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.2

The structure of CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog (pdb code 3n9o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog, PDB code: 3n9o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:75.9 occ:1.00 ND1 A:HIS252 2.3 58.9 1.0 SG A:CYS255 2.3 64.2 1.0 SG A:CYS201 2.3 56.0 1.0 SG A:CYS198 2.4 47.3 1.0 CB A:CYS198 3.1 50.8 1.0 CE1 A:HIS252 3.1 58.2 1.0 CB A:CYS201 3.2 49.8 1.0 CB A:CYS255 3.2 58.9 1.0 CG A:HIS252 3.2 58.7 1.0 N A:CYS201 3.4 57.1 1.0 CB A:HIS252 3.6 56.0 1.0 CA A:CYS201 3.9 58.0 1.0 CD2 A:HIS206 3.9 67.8 1.0 NE2 A:HIS252 4.2 61.4 1.0 N A:HIS252 4.2 58.6 1.0 CD2 A:HIS252 4.3 61.6 1.0 C A:GLY200 4.5 56.3 1.0 CA A:HIS252 4.5 60.0 1.0 CA A:CYS198 4.5 52.6 1.0 CA A:CYS255 4.7 58.2 1.0 C A:CYS201 4.7 57.7 1.0 CA A:GLY200 4.7 59.8 1.0 NE2 A:HIS206 4.8 67.0 1.0 N A:GLY200 4.8 60.3 1.0 N A:GLY202 4.8 59.2 1.0 CG A:HIS206 4.9 73.2 1.0 C A:CYS198 4.9 51.8 1.0

Zinc binding site 2 out of 2 in the CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CEKDM7A From C.Elegans, Complex with H3K4ME3 Peptide, H3K9ME2 Peptide and Nog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:80.4 occ:1.00 SG A:CYS247 2.3 64.5 1.0 SG A:CYS244 2.4 57.8 1.0 SG A:CYS274 2.4 67.8 1.0 SG A:CYS271 2.6 68.0 1.0 CB A:CYS244 3.2 57.7 1.0 CB A:CYS247 3.3 62.4 1.0 CB A:CYS271 3.5 64.2 1.0 N A:CYS247 3.7 65.2 1.0 CB A:CYS274 3.7 73.2 1.0 N A:CYS271 4.0 55.1 1.0 N A:CYS274 4.0 74.3 1.0 CA A:CYS247 4.0 60.6 1.0 CA A:CYS271 4.2 59.7 1.0 CB A:SER246 4.4 66.2 1.0 CA A:CYS274 4.5 76.6 1.0 OG1 A:THR249 4.7 60.7 1.0 CA A:CYS244 4.7 58.5 1.0 O A:CYS271 4.7 66.2 1.0 C A:CYS271 4.7 64.6 1.0 C A:SER246 4.8 66.6 1.0 CB A:LYS273 4.8 74.6 1.0 C A:CYS247 4.8 60.7 1.0 OH A:TYR251 4.8 70.3 1.0 N A:GLN248 4.9 59.5 1.0 OG A:SER246 4.9 71.7 1.0 CA A:SER246 5.0 64.2 1.0 CE2 A:TYR251 5.0 61.8 1.0 N A:SER246 5.0 61.4 1.0

Y.Yang, L.Hu, P.Wang, H.Hou, Y.Lin, Y.Liu, Z.Li, R.Gong, X.Feng, L.Zhou, W.Zhang, Y.Dong, H.Yang, H.Lin, Y.Wang, C.D.Chen, Y.Xu. Structural Insights Into A Dual-Specificity Histone Demethylase CEKDM7A From Caenorhabditis Elegans Cell Res. V. 20 886 2010.
ISSN: ISSN 1001-0602
PubMed: 20567261
DOI: 10.1038/CR.2010.86