Zinc in PDB 3n9m: CEKDM7A From C.Elegans, Alone

All present enzymatic activity of CEKDM7A From C.Elegans, Alone:
1.14.11.27;

The structure of CEKDM7A From C.Elegans, Alone, PDB code: 3n9m 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)	32.69 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.004, 144.515, 78.413, 90.00, 106.69, 90.00
R / Rfree (%)	20.1 / 24.7

The structure of CEKDM7A From C.Elegans, Alone also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the CEKDM7A From C.Elegans, Alone (pdb code 3n9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the CEKDM7A From C.Elegans, Alone, PDB code: 3n9m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the CEKDM7A From C.Elegans, Alone


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, Alone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:86.2 occ:1.00 SG A:CYS201 2.3 99.9 1.0 ND1 A:HIS252 2.3 85.9 1.0 SG A:CYS198 2.3 82.0 1.0 SG A:CYS255 2.3 90.9 1.0 CG A:HIS252 3.1 86.2 1.0 CB A:HIS252 3.2 82.3 1.0 CB A:CYS198 3.3 80.9 1.0 CE1 A:HIS252 3.4 89.3 1.0 CB A:CYS255 3.4 79.1 1.0 N A:CYS201 3.5 81.5 1.0 CB A:CYS201 3.5 84.0 1.0 N A:HIS252 4.0 71.3 1.0 CA A:CYS201 4.0 86.4 1.0 CA A:HIS252 4.2 79.2 1.0 CD2 A:HIS252 4.3 87.3 1.0 NE2 A:HIS252 4.4 87.5 1.0 C A:GLY200 4.5 82.1 1.0 CA A:GLY200 4.6 80.2 1.0 CA A:CYS198 4.7 83.8 1.0 N A:GLY200 4.8 74.2 1.0 CA A:CYS255 4.8 78.1 1.0 C A:CYS201 4.8 89.3 1.0 N A:GLY202 5.0 86.3 1.0

Zinc binding site 2 out of 4 in the CEKDM7A From C.Elegans, Alone


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, Alone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:65.0 occ:1.00 SG A:CYS274 2.3 60.6 1.0 SG A:CYS244 2.3 63.1 1.0 SG A:CYS247 2.3 67.0 1.0 SG A:CYS271 2.4 54.9 1.0 CB A:CYS274 3.2 66.5 1.0 CB A:CYS244 3.2 61.9 1.0 CB A:CYS247 3.2 56.4 1.0 N A:CYS247 3.5 65.2 1.0 CB A:CYS271 3.9 65.8 1.0 CA A:CYS247 3.9 65.9 1.0 N A:CYS271 4.1 61.9 1.0 OG1 A:THR249 4.2 71.3 1.0 N A:CYS274 4.3 70.0 1.0 CA A:CYS274 4.3 67.2 1.0 CB A:SER246 4.4 63.0 1.0 CA A:CYS271 4.5 62.8 1.0 O A:CYS271 4.7 64.6 1.0 C A:SER246 4.7 66.4 1.0 CA A:CYS244 4.7 64.1 1.0 C A:CYS247 4.7 62.9 1.0 OH A:TYR251 4.8 69.4 1.0 C A:CYS271 4.9 64.3 1.0 CA A:SER246 4.9 69.4 1.0 N A:GLN248 4.9 60.6 1.0 N A:SER246 5.0 65.6 1.0 C A:LYS273 5.0 68.5 1.0

Zinc binding site 3 out of 4 in the CEKDM7A From C.Elegans, Alone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CEKDM7A From C.Elegans, Alone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:73.7 occ:1.00 ND1 C:HIS252 2.3 63.0 1.0 SG C:CYS201 2.3 85.6 1.0 SG C:CYS198 2.3 67.3 1.0 SG C:CYS255 2.4 77.4 1.0 CG C:HIS252 3.1 76.4 1.0 CB C:CYS198 3.1 71.4 1.0 CB C:CYS201 3.2 74.0 1.0 CB C:HIS252 3.2 69.8 1.0 CB C:CYS255 3.3 66.8 1.0 CE1 C:HIS252 3.3 75.3 1.0 N C:CYS201 3.9 74.1 1.0 N C:HIS252 4.0 63.5 1.0 CA C:CYS201 4.1 71.5 1.0 CA C:HIS252 4.2 68.9 1.0 CD2 C:HIS252 4.3 78.4 1.0 NE2 C:HIS252 4.4 78.1 1.0 C C:GLY200 4.5 74.7 1.0 CA C:CYS198 4.6 70.1 1.0 CA C:CYS255 4.7 65.7 1.0 C C:CYS201 4.9 74.6 1.0

Zinc binding site 4 out of 4 in the CEKDM7A From C.Elegans, Alone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CEKDM7A From C.Elegans, Alone within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:55.9 occ:1.00 SG C:CYS244 2.3 51.1 1.0 SG C:CYS274 2.3 62.0 1.0 SG C:CYS247 2.3 55.1 1.0 SG C:CYS271 2.5 58.6 1.0 CB C:CYS244 3.2 46.3 1.0 CB C:CYS247 3.4 45.4 1.0 CB C:CYS274 3.5 61.1 1.0 N C:CYS247 3.6 48.4 1.0 CB C:CYS271 3.7 58.7 1.0 N C:CYS271 4.0 51.8 1.0 CA C:CYS247 4.1 49.4 1.0 CA C:CYS271 4.3 53.2 1.0 N C:CYS274 4.3 60.2 1.0 CB C:SER246 4.4 57.9 1.0 CA C:CYS274 4.5 58.8 1.0 O C:CYS271 4.6 62.9 1.0 CA C:CYS244 4.6 44.4 1.0 C C:SER246 4.8 50.0 1.0 C C:CYS271 4.8 58.0 1.0 OH C:TYR251 4.8 56.6 1.0 C C:CYS247 4.8 49.2 1.0 CB C:LYS273 4.9 62.7 1.0 N C:GLN248 4.9 48.6 1.0 N C:SER246 5.0 54.4 1.0 CA C:SER246 5.0 51.3 1.0 C C:LYS273 5.0 66.0 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