Zinc in PDB 3puq: CEKDM7A From C.Elegans, Complex with Alpha-Kg

All present enzymatic activity of CEKDM7A From C.Elegans, Complex with Alpha-Kg:
1.14.11.27;

The structure of CEKDM7A From C.Elegans, Complex with Alpha-Kg, PDB code: 3puq was solved by Y.Yang, P.Wang, W.Xu, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.592, 78.138, 102.930, 90.00, 92.07, 90.00
R / Rfree (%)	18.8 / 22.4

The structure of CEKDM7A From C.Elegans, Complex with Alpha-Kg also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the CEKDM7A From C.Elegans, Complex with Alpha-Kg (pdb code 3puq). 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, Complex with Alpha-Kg, PDB code: 3puq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


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 Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:45.6 occ:1.00 ND1 A:HIS252 2.0 36.9 1.0 SG A:CYS198 2.3 41.7 1.0 SG A:CYS255 2.4 45.4 1.0 SG A:CYS201 2.5 44.6 1.0 CE1 A:HIS252 3.0 47.8 1.0 CG A:HIS252 3.0 44.2 1.0 CB A:CYS198 3.2 48.4 1.0 CB A:CYS255 3.2 40.1 1.0 CB A:HIS252 3.4 39.4 1.0 CB A:CYS201 3.4 49.8 1.0 N A:CYS201 3.7 51.1 1.0 N A:HIS252 4.1 38.2 1.0 NE2 A:HIS252 4.1 45.5 1.0 CA A:CYS201 4.1 53.9 1.0 CD2 A:HIS252 4.1 43.8 1.0 CA A:HIS252 4.4 37.1 1.0 CA A:CYS198 4.6 46.4 1.0 CA A:CYS255 4.7 35.9 1.0 C A:GLY200 4.7 51.1 1.0 C A:CYS201 4.9 54.9 1.0 CA A:GLY200 4.9 45.1 1.0 N A:GLY202 4.9 52.8 1.0 N A:GLY200 5.0 47.6 1.0

Zinc binding site 2 out of 4 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


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 Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:34.3 occ:1.00 SG A:CYS274 2.3 36.6 1.0 SG A:CYS244 2.3 27.2 1.0 SG A:CYS271 2.4 33.3 1.0 CB A:CYS247 2.5 33.9 1.0 SG A:CYS247 2.8 52.4 1.0 CB A:CYS244 3.2 28.8 1.0 CB A:CYS274 3.3 34.4 1.0 CB A:CYS271 3.4 31.5 1.0 N A:CYS247 3.6 34.2 1.0 CA A:CYS247 3.6 38.5 1.0 N A:CYS271 3.8 28.9 1.0 CA A:CYS271 4.1 29.1 1.0 N A:CYS274 4.2 33.1 1.0 O A:CYS271 4.4 34.6 1.0 CA A:CYS274 4.4 35.0 1.0 C A:CYS271 4.5 31.3 1.0 CA A:CYS244 4.7 30.4 1.0 OH A:TYR251 4.7 38.3 1.0 C A:CYS247 4.8 32.0 1.0 C A:SER246 4.8 37.8 1.0 CB A:SER246 4.9 35.4 1.0 C A:PHE270 4.9 30.8 1.0 N A:GLN248 5.0 33.5 1.0 CB A:LYS273 5.0 40.3 1.0

Zinc binding site 3 out of 4 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


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, Complex with Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:46.2 occ:1.00 CD2 C:HIS252 2.2 41.5 1.0 SG C:CYS255 2.3 48.1 1.0 SG C:CYS198 2.4 45.7 1.0 SG C:CYS201 2.5 50.4 1.0 CG C:HIS252 2.9 46.1 1.0 CB C:CYS198 3.1 50.1 1.0 CB C:HIS252 3.2 42.5 1.0 CB C:CYS255 3.3 44.0 1.0 CB C:CYS201 3.3 54.1 1.0 NE2 C:HIS252 3.4 50.4 1.0 N C:CYS201 3.9 54.0 1.0 N C:HIS252 4.0 41.5 1.0 ND1 C:HIS252 4.2 47.2 1.0 CA C:CYS201 4.2 60.4 1.0 CA C:HIS252 4.2 42.5 1.0 CE1 C:HIS252 4.4 49.3 1.0 CA C:CYS198 4.6 49.9 1.0 CA C:CYS255 4.7 40.8 1.0 O C:HOH1676 4.9 61.3 1.0 C C:GLY200 4.9 50.1 1.0 N C:CYS255 5.0 42.7 1.0

Zinc binding site 4 out of 4 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


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, Complex with Alpha-Kg within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:38.7 occ:1.00 SG C:CYS274 2.3 40.3 1.0 SG C:CYS244 2.3 31.1 1.0 SG C:CYS271 2.5 43.4 1.0 SG C:CYS247 2.5 39.6 1.0 CB C:CYS244 3.1 30.2 1.0 CB C:CYS247 3.2 35.8 1.0 CB C:CYS274 3.3 38.2 1.0 CB C:CYS271 3.5 40.1 1.0 N C:CYS247 3.6 37.2 1.0 N C:CYS271 3.8 32.4 1.0 CA C:CYS247 4.0 36.2 1.0 CA C:CYS271 4.1 36.9 1.0 N C:CYS274 4.3 38.8 1.0 CA C:CYS274 4.4 39.0 1.0 CA C:CYS244 4.6 34.2 1.0 C C:CYS271 4.6 35.1 1.0 O C:CYS271 4.6 38.1 1.0 CB C:SER246 4.7 41.2 1.0 C C:CYS247 4.7 38.1 1.0 C C:SER246 4.8 40.0 1.0 CB C:LYS273 4.8 44.5 1.0 OH C:TYR251 4.8 43.3 1.0 N C:GLN248 4.9 37.3 1.0 C C:PHE270 4.9 36.2 1.0 C C:LYS273 4.9 44.1 1.0

W.Xu, H.Yang, Y.Liu, Y.Yang, P.Wang, S.-H.Kim, S.Ito, C.Yang, P.Wang, M.-T.Xiao, L.-X.Liu, W.-Q.Jiang, J.Liu, J.-Y.Zhang, B.Wang, S.Frye, Y.Zhang, Y.-H.Xu, Q.-Y.Lei, K.-L.Guan, S.-M.Zhao, Y.Xiong. Oncometabolite 2-Hydroxyglutarate Is A Competitive Inhibitor of Alpha-Ketoglutarate-Dependent Dioxygenases Cancer Cell V. 19 17 2011.
ISSN: ISSN 1535-6108
PubMed: 21251613
DOI: 10.1016/J.CCR.2010.12.014