Fluorine in PDB 1k3c: Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate

All present enzymatic activity of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate:
4.1.1.49;

The structure of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate, PDB code: 1k3c was solved by A.M.Sudom, L.Prasad, H.Goldie, L.T.J.Delbaere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.738, 94.211, 46.336, 90.00, 96.05, 90.00
R / Rfree (%)	22.3 / 28.5

The structure of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate (pdb code 1k3c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate, PDB code: 1k3c:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:34.0 occ:1.00 F1 A:AF3999 0.0 34.0 1.0 AL A:AF3999 1.8 31.2 1.0 O3B A:ADP541 2.5 16.4 1.0 OG A:SER250 2.7 10.5 1.0 NH2 A:ARG333 2.9 12.1 1.0 F3 A:AF3999 3.1 41.5 1.0 F2 A:AF3999 3.1 45.4 1.0 CB A:SER250 3.2 14.3 1.0 CA A:SER250 3.4 14.1 1.0 N A:GLY251 3.7 10.3 1.0 CZ A:ARG333 3.7 9.9 1.0 NH1 A:ARG333 3.8 9.7 1.0 PB A:ADP541 4.0 10.4 1.0 C A:SER250 4.0 14.7 1.0 MG A:MG998 4.4 8.5 1.0 O3 A:PYR542 4.4 51.6 1.0 CD A:LYS288 4.5 9.2 1.0 N A:SER250 4.6 16.2 1.0 O A:HOH754 4.6 10.4 1.0 O A:HOH705 4.6 25.0 1.0 O2B A:ADP541 4.6 17.8 1.0 O3A A:ADP541 4.7 9.1 1.0 O1B A:ADP541 4.8 15.8 1.0 NZ A:LYS254 4.9 15.4 1.0 CA A:GLY251 4.9 9.4 1.0 O A:HOH663 4.9 16.1 1.0 NE A:ARG333 5.0 11.3 1.0

Fluorine binding site 2 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:45.4 occ:1.00 F2 A:AF3999 0.0 45.4 1.0 AL A:AF3999 1.8 31.2 1.0 NE2 A:HIS232 3.0 6.8 1.0 F3 A:AF3999 3.1 41.5 1.0 F1 A:AF3999 3.1 34.0 1.0 NZ A:LYS213 3.3 16.3 1.0 CE1 A:HIS232 3.5 5.6 1.0 OD2 A:ASP269 3.5 8.4 1.0 NZ A:LYS254 3.9 15.4 1.0 O A:HOH663 4.1 16.1 1.0 CA A:SER250 4.1 14.1 1.0 CB A:SER250 4.2 14.3 1.0 CE A:LYS254 4.2 14.0 1.0 O A:HOH656 4.3 27.4 1.0 CE A:LYS213 4.3 15.1 1.0 CD2 A:HIS232 4.3 7.3 1.0 N A:SER250 4.4 16.2 1.0 O3 A:PYR542 4.4 51.6 1.0 O3B A:ADP541 4.5 16.4 1.0 CG A:ASP269 4.5 13.5 1.0 OG A:SER250 4.6 10.5 1.0 OD1 A:ASP269 4.7 15.8 1.0 ND1 A:HIS232 4.8 4.3 1.0 C A:LEU249 4.9 17.2 1.0 O A:HOH662 5.0 11.2 1.0

Fluorine binding site 3 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Phosphoenolpyruvate Carboxykinase in Complex with Adp, ALF3 and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:41.5 occ:1.00 F3 A:AF3999 0.0 41.5 1.0 AL A:AF3999 1.8 31.2 1.0 MG A:MG998 2.1 8.5 1.0 O A:HOH662 2.5 11.2 1.0 O2B A:ADP541 2.8 17.8 1.0 O3B A:ADP541 2.8 16.4 1.0 F1 A:AF3999 3.1 34.0 1.0 PB A:ADP541 3.1 10.4 1.0 F2 A:AF3999 3.1 45.4 1.0 OD2 A:ASP269 3.2 8.4 1.0 O A:HOH753 3.3 8.6 1.0 CE A:LYS254 3.6 14.0 1.0 NZ A:LYS254 3.6 15.4 1.0 O A:HOH754 3.7 10.4 1.0 O A:HOH663 3.8 16.1 1.0 O1B A:ADP541 3.8 15.8 1.0 OG1 A:THR255 4.1 6.4 1.0 CG A:ASP269 4.2 13.5 1.0 O3A A:ADP541 4.4 9.1 1.0 NH1 A:ARG333 4.4 9.7 1.0 CB A:LYS254 4.8 9.8 1.0 CB A:ASP269 4.9 12.0 1.0 NE2 A:HIS232 4.9 6.8 1.0 O A:ASP268 4.9 11.8 1.0 CD A:LYS254 4.9 4.7 1.0

A.M.Sudom, L.Prasad, H.Goldie, L.T.Delbaere. The Phosphoryl-Transfer Mechanism of Escherichia Coli Phosphoenolpyruvate Carboxykinase From the Use of Alf(3). J.Mol.Biol. V. 314 83 2001.
ISSN: ISSN 0022-2836
PubMed: 11724534
DOI: 10.1006/JMBI.2001.5120