Magnesium in PDB 8fvd: E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)

All present enzymatic activity of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2):
6.3.4.2;

The structure of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2), PDB code: 8fvd was solved by T.Holyoak, M.J.Mcleod, N.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.93 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	161.069, 110.013, 129.511, 90, 90, 90
R / Rfree (%)	20.9 / 23.2

The structure of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) (pdb code 8fvd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2), PDB code: 8fvd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:62.1 occ:1.00 O1B A:GTF602 2.4 65.3 1.0 O3G A:GTF602 2.4 64.2 1.0 O2A A:GTF602 2.5 63.6 1.0 PB A:GTF602 3.5 50.4 1.0 PA A:GTF602 3.7 48.1 1.0 PG A:GTF602 3.7 50.5 1.0 O3A A:GTF602 3.9 55.9 1.0 O3B A:GTF602 4.0 58.7 1.0 NZ A:LYS187 4.0 66.0 1.0 NZ A:LYS223 4.1 76.1 1.0 OE2 A:GLU185 4.3 71.2 0.5 O1A A:GTF602 4.4 63.9 1.0 O1G A:GTF602 4.4 54.4 1.0 OE1 A:GLU185 4.8 75.7 0.5 O2B A:GTF602 4.8 59.7 1.0 O2G A:GTF602 4.8 41.2 1.0 CD A:GLU185 4.9 74.4 0.5

Magnesium binding site 2 out of 2 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:67.0 occ:1.00 O B:HOH813 2.4 56.3 1.0 O2G B:GTF701 2.5 63.8 1.0 O1A B:GTF701 2.6 62.2 1.0 O2B B:GTF701 2.7 64.0 1.0 O B:HOH823 3.4 69.8 1.0 PG B:GTF701 3.8 49.4 1.0 O B:HOH830 3.9 64.4 1.0 PA B:GTF701 3.9 48.9 1.0 PB B:GTF701 3.9 50.6 1.0 NZ B:LYS223 4.0 85.1 1.0 OE2 B:GLU185 4.0 88.1 1.0 NZ B:LYS187 4.1 69.6 1.0 O3A B:GTF701 4.3 55.9 1.0 O3B B:GTF701 4.3 59.5 1.0 OE1 B:GLU185 4.4 99.3 1.0 O1G B:GTF701 4.4 61.2 1.0 O2A B:GTF701 4.5 65.6 1.0 CD B:GLU185 4.6 92.7 1.0 O3G B:GTF701 5.0 44.9 1.0

M.J.Mcleod, N.Tran, G.D.Mccluskey, T.D.Gillis, S.L.Bearne, T.Holyoak. A Metal Dependent Conformational Change Provides A Structural Basis For the Inhibition of Ctp Synthase By Gemcitabine-5'-Triphosphate. Protein Sci. E4648 2023.
ISSN: ESSN 1469-896X
PubMed: 37106216
DOI: 10.1002/PRO.4648