Zinc in PDB 3pur: CEKDM7A From C.Elegans, Complex with D-2-Hg

All present enzymatic activity of CEKDM7A From C.Elegans, Complex with D-2-Hg:
1.14.11.27;

The structure of CEKDM7A From C.Elegans, Complex with D-2-Hg, PDB code: 3pur 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.009, 144.086, 78.087, 90.00, 106.22, 90.00
R / Rfree (%)	21.4 / 25.1

The structure of CEKDM7A From C.Elegans, Complex with D-2-Hg also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the CEKDM7A From C.Elegans, Complex with D-2-Hg (pdb code 3pur). 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 D-2-Hg, PDB code: 3pur:
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 D-2-Hg


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 D-2-Hg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:65.6 occ:1.00 ND1 A:HIS252 2.3 64.3 1.0 SG A:CYS255 2.4 70.7 1.0 SG A:CYS198 2.4 62.7 1.0 SG A:CYS201 2.4 74.8 1.0 CB A:CYS201 3.1 70.6 1.0 CG A:HIS252 3.2 67.3 1.0 CB A:CYS198 3.2 65.6 1.0 CE1 A:HIS252 3.3 69.3 1.0 CB A:CYS255 3.3 65.3 1.0 CB A:HIS252 3.3 60.8 1.0 N A:CYS201 3.5 68.7 1.0 CA A:CYS201 3.8 69.3 1.0 N A:HIS252 4.1 59.1 1.0 CD2 A:HIS252 4.3 66.9 1.0 NE2 A:HIS252 4.4 68.9 1.0 CA A:HIS252 4.4 60.4 1.0 C A:GLY200 4.6 67.0 1.0 CA A:CYS198 4.7 66.7 1.0 C A:CYS201 4.7 72.8 1.0 CA A:CYS255 4.7 61.9 1.0 CA A:GLY200 4.9 64.4 1.0 N A:GLY202 4.9 72.8 1.0 O A:CYS198 4.9 67.2 1.0 N A:GLY200 5.0 62.9 1.0 C A:CYS198 5.0 65.1 1.0

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


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 D-2-Hg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:55.5 occ:1.00 SG A:CYS271 2.2 56.4 1.0 SG A:CYS244 2.4 50.7 1.0 SG A:CYS247 2.4 55.8 1.0 SG A:CYS274 2.5 54.7 1.0 CB A:CYS244 3.0 50.6 1.0 CB A:CYS271 3.4 56.5 1.0 CB A:CYS247 3.4 51.7 1.0 CB A:CYS274 3.5 57.8 1.0 N A:CYS247 3.7 51.7 1.0 N A:CYS271 3.8 54.0 1.0 CA A:CYS247 4.1 53.0 1.0 CA A:CYS271 4.1 56.8 1.0 N A:CYS274 4.2 58.6 1.0 CA A:CYS274 4.5 60.0 1.0 CA A:CYS244 4.5 52.8 1.0 CB A:SER246 4.6 55.2 1.0 C A:CYS271 4.7 57.3 1.0 O A:CYS271 4.7 53.4 1.0 C A:CYS247 4.8 56.7 1.0 C A:SER246 4.8 54.4 1.0 C A:LYS273 4.8 62.9 1.0 N A:GLN248 4.9 54.2 1.0 CB A:LYS273 4.9 65.2 1.0 OH A:TYR251 4.9 62.5 1.0 N A:SER246 4.9 56.9 1.0 C A:PHE270 4.9 53.8 1.0 C A:CYS244 5.0 54.8 1.0

Zinc binding site 3 out of 4 in the CEKDM7A From C.Elegans, Complex with D-2-Hg


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 D-2-Hg within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:72.2 occ:1.00 ND1 C:HIS252 2.3 76.4 1.0 SG C:CYS198 2.3 69.5 1.0 SG C:CYS201 2.4 80.3 1.0 SG C:CYS255 2.5 69.6 1.0 CB C:CYS198 3.0 72.4 1.0 CG C:HIS252 3.2 76.7 1.0 CB C:HIS252 3.3 68.9 1.0 CB C:CYS201 3.3 73.8 1.0 CE1 C:HIS252 3.3 77.4 1.0 CB C:CYS255 3.5 64.7 1.0 N C:CYS201 3.7 74.1 1.0 N C:HIS252 4.1 67.2 1.0 CA C:CYS201 4.1 76.3 1.0 CD2 C:HIS252 4.3 76.2 1.0 CA C:HIS252 4.3 67.5 1.0 NE2 C:HIS252 4.4 79.2 1.0 CA C:CYS198 4.5 74.3 1.0 C C:GLY200 4.8 71.7 1.0 C C:CYS201 4.9 79.0 1.0 CA C:CYS255 4.9 65.6 1.0

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


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 D-2-Hg within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:58.2 occ:1.00 SG C:CYS274 2.2 60.0 1.0 SG C:CYS247 2.3 54.8 1.0 SG C:CYS271 2.4 61.8 1.0 SG C:CYS244 2.5 55.5 1.0 CB C:CYS247 3.2 57.9 1.0 CB C:CYS244 3.2 53.9 1.0 CB C:CYS274 3.3 59.4 1.0 CB C:CYS271 3.6 52.1 1.0 N C:CYS247 3.6 61.3 1.0 CA C:CYS247 4.0 60.5 1.0 N C:CYS271 4.0 55.9 1.0 N C:CYS274 4.2 60.8 1.0 CA C:CYS271 4.3 54.3 1.0 CA C:CYS274 4.3 59.6 1.0 OH C:TYR251 4.5 60.6 1.0 CB C:SER246 4.6 59.0 1.0 O C:CYS271 4.7 58.8 1.0 CA C:CYS244 4.7 56.9 1.0 C C:CYS247 4.7 60.1 1.0 C C:CYS271 4.7 58.9 1.0 C C:SER246 4.8 60.4 1.0 N C:GLN248 4.8 55.3 1.0 C C:LYS273 4.9 62.9 1.0 CB C:LYS273 4.9 61.0 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