Iron 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:

Zinc

(Zn)

4 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the CEKDM7A From C.Elegans, Complex with D-2-Hg, PDB code: 3pur:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the CEKDM7A From C.Elegans, Complex with D-2-Hg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe1 b:40.0 occ:1.00 NE2 A:HIS567 2.0 41.6 1.0 O3 A:2HG1000 2.1 42.2 1.0 O2 A:2HG1000 2.1 38.4 1.0 OD2 A:ASP497 2.2 36.4 1.0 NE2 A:HIS495 2.2 40.4 1.0 O A:HOH1065 2.4 42.5 1.0 C2 A:2HG1000 2.7 50.2 1.0 C1 A:2HG1000 2.7 53.4 1.0 CE1 A:HIS567 2.8 36.7 1.0 CD2 A:HIS495 3.1 40.0 1.0 CG A:ASP497 3.1 40.1 1.0 CD2 A:HIS567 3.2 39.7 1.0 CE1 A:HIS495 3.2 43.6 1.0 OD1 A:ASP497 3.4 47.4 1.0 ND1 A:HIS567 4.0 37.9 1.0 O1 A:2HG1000 4.0 59.3 1.0 O A:HOH1072 4.1 55.8 1.0 C3 A:2HG1000 4.2 47.6 0.5 CG A:HIS567 4.2 37.5 1.0 O A:HOH1279 4.2 57.3 1.0 CG A:HIS495 4.3 39.8 1.0 ND1 A:HIS495 4.3 44.5 1.0 CB A:ASP497 4.5 38.4 1.0 CA A:ASP497 4.8 42.0 1.0 N A:ASP497 4.9 33.4 1.0 C4 A:2HG1000 5.0 45.4 0.5

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 C:Fe1 b:39.5 occ:1.00 NE2 C:HIS567 2.1 41.2 1.0 O2 C:2HG1000 2.1 51.3 1.0 OD2 C:ASP497 2.1 41.7 1.0 NE2 C:HIS495 2.2 42.0 1.0 O3 C:2HG1000 2.2 43.2 1.0 O C:HOH1041 2.3 43.9 1.0 C2 C:2HG1000 2.8 52.5 1.0 C1 C:2HG1000 2.8 55.8 1.0 CE1 C:HIS567 2.8 36.5 1.0 CG C:ASP497 3.1 43.2 1.0 CE1 C:HIS495 3.2 42.5 1.0 CD2 C:HIS495 3.2 39.2 1.0 CD2 C:HIS567 3.2 42.8 1.0 OD1 C:ASP497 3.3 49.5 1.0 ND1 C:HIS567 4.0 35.1 1.0 O1 C:2HG1000 4.0 60.1 1.0 O C:HOH1282 4.0 56.0 1.0 O C:HOH1280 4.1 55.1 1.0 CG C:HIS567 4.2 36.2 1.0 ND1 C:HIS495 4.2 44.1 1.0 C3 C:2HG1000 4.3 49.5 0.5 CG C:HIS495 4.3 40.1 1.0 CB C:ASP497 4.5 37.2 1.0 CA C:ASP497 4.8 38.0 1.0 C4 C:2HG1000 4.9 47.4 0.5 N C:ASP497 5.0 34.4 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