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Fluorine in PDB 1k3d: Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3

Enzymatic activity of Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3

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

Protein crystallography data

The structure of Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3, PDB code: 1k3d 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 (°) 126.033, 95.844, 46.608, 90.00, 95.59, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 1k3d:

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

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3 (pdb code 1k3d). 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 and ALF3, PDB code: 1k3d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1k3d

Go back to Fluorine Binding Sites List in 1k3d
Fluorine binding site 1 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3


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 and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:33.2
occ:1.00
F1 A:AF3999 0.0 33.2 1.0
AL A:AF3999 1.8 33.3 1.0
OG A:SER250 2.5 26.1 1.0
O3B A:ADP541 2.7 29.7 1.0
CB A:SER250 2.8 20.7 1.0
NH2 A:ARG333 3.0 24.0 1.0
CA A:SER250 3.0 20.2 1.0
F3 A:AF3999 3.1 38.4 1.0
F2 A:AF3999 3.1 31.0 1.0
O A:HOH750 3.4 27.2 1.0
N A:GLY251 3.9 17.4 1.0
CZ A:ARG333 3.9 24.6 1.0
NH1 A:ARG333 4.0 19.4 1.0
C A:SER250 4.0 18.0 1.0
N A:SER250 4.1 22.0 1.0
O A:HOH702 4.1 24.3 1.0
PB A:ADP541 4.2 21.9 1.0
O A:HOH749 4.4 70.1 1.0
O2B A:ADP541 4.8 28.5 1.0
NZ A:LYS254 4.9 16.9 1.0
O A:HOH769 4.9 24.9 1.0
C A:LEU249 4.9 21.7 1.0
O3A A:ADP541 4.9 20.7 1.0
O1B A:ADP541 4.9 25.3 1.0
O A:LEU249 5.0 21.3 1.0
O A:HOH854 5.0 44.1 1.0

Fluorine binding site 2 out of 3 in 1k3d

Go back to Fluorine Binding Sites List in 1k3d
Fluorine binding site 2 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3


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 and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:31.0
occ:1.00
F2 A:AF3999 0.0 31.0 1.0
AL A:AF3999 1.8 33.3 1.0
O A:HOH750 2.5 27.2 1.0
OD2 A:ASP269 2.5 16.7 1.0
NE2 A:HIS232 2.7 14.7 1.0
O A:HOH749 2.9 70.1 1.0
F3 A:AF3999 3.1 38.4 1.0
F1 A:AF3999 3.1 33.2 1.0
NZ A:LYS213 3.2 19.8 1.0
CG A:ASP269 3.4 15.3 1.0
CE1 A:HIS232 3.4 8.5 1.0
OD1 A:ASP269 3.7 18.5 1.0
CD2 A:HIS232 3.8 14.4 1.0
CE A:LYS213 3.8 14.0 1.0
NZ A:LYS254 3.9 16.9 1.0
O A:HOH708 4.1 23.0 1.0
CE A:LYS254 4.3 14.2 1.0
O3B A:ADP541 4.4 29.7 1.0
ND1 A:HIS232 4.7 12.8 1.0
O A:HOH702 4.7 24.3 1.0
O A:HOH751 4.7 25.4 1.0
CB A:ASP269 4.7 15.8 1.0
MG A:MG998 4.8 30.6 1.0
O A:HOH706 4.9 36.0 1.0
CG A:HIS232 4.9 10.0 1.0

Fluorine binding site 3 out of 3 in 1k3d

Go back to Fluorine Binding Sites List in 1k3d
Fluorine binding site 3 out of 3 in the Phosphoenolpyruvate Carboxykinase in Complex with Adp and ALF3


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 and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:38.4
occ:1.00
F3 A:AF3999 0.0 38.4 1.0
AL A:AF3999 1.8 33.3 1.0
MG A:MG998 2.0 30.6 1.0
O2B A:ADP541 2.7 28.5 1.0
O3B A:ADP541 2.7 29.7 1.0
O A:HOH708 2.8 23.0 1.0
O A:HOH707 3.0 23.4 1.0
F1 A:AF3999 3.1 33.2 1.0
PB A:ADP541 3.1 21.9 1.0
F2 A:AF3999 3.1 31.0 1.0
O A:HOH706 3.3 36.0 1.0
NH1 A:ARG333 3.5 19.4 1.0
OD2 A:ASP269 3.7 16.7 1.0
O A:HOH749 3.8 70.1 1.0
OG1 A:THR255 4.1 18.6 1.0
O3A A:ADP541 4.2 20.7 1.0
O1B A:ADP541 4.2 25.3 1.0
O2A A:ADP541 4.3 26.4 1.0
NZ A:LYS254 4.4 16.9 1.0
NH2 A:ARG333 4.4 24.0 1.0
O A:TYR286 4.4 16.8 1.0
CZ A:ARG333 4.4 24.6 1.0
CG A:ASP269 4.6 15.3 1.0
PA A:ADP541 4.8 27.6 1.0
CE A:LYS254 4.8 14.2 1.0

Reference:

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
Page generated: Sun Dec 13 11:30:35 2020

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