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Fluorine in PDB 4c4r: Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride

Enzymatic activity of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride

All present enzymatic activity of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride:
5.4.2.6;

Protein crystallography data

The structure of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride, PDB code: 4c4r was solved by E.Pellegrini, M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.648 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.012, 54.201, 105.407, 90.00, 90.00, 90.00
R / Rfree (%) 14.92 / 17.26

Other elements in 4c4r:

The structure of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride (pdb code 4c4r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride, PDB code: 4c4r:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4c4r

Go back to Fluorine Binding Sites List in 4c4r
Fluorine binding site 1 out of 3 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:3.5
occ:1.00
 F1 A:MGF1221 0.0 3.5 1.0
MG A:MGF1221 1.8 3.2 1.0
MG A:MG1219 2.0 3.1 1.0
O A:HOH2021 2.7 3.6 1.0
O6 A:YO51220 2.8 3.4 1.0
OD1 A:ASP8 2.9 3.1 1.0
O A:HOH2031 2.9 3.8 1.0
OD2 A:ASP8 2.9 3.4 1.0
C6 A:YO51220 3.0 3.8 1.0
O A:ASP10 3.0 2.6 1.0
F2 A:MGF1221 3.1 3.4 1.0
F3 A:MGF1221 3.2 4.1 1.0
CG A:ASP8 3.3 2.9 1.0
CB A:ASP10 3.3 2.9 1.0
N A:ASP10 3.7 2.3 1.0
CA A:ASP10 3.8 2.9 1.0
C A:ASP10 3.8 2.6 1.0
N A:GLY46 3.9 3.8 1.0
O A:HOH2566 3.9 3.4 1.0
OD2 A:ASP10 4.0 3.3 1.0
OD1 A:ASP170 4.0 3.4 1.0
CA A:GLY46 4.0 3.8 1.0
CG A:ASP10 4.1 2.7 1.0
C5 A:YO51220 4.3 3.4 1.0
O4 A:YO51220 4.7 3.4 1.0
C A:LEU9 4.7 2.7 1.0
CB A:ASP8 4.8 3.3 1.0
N A:LEU9 4.8 2.9 1.0
CG A:ASP170 4.9 2.7 1.0
C A:LYS45 5.0 3.9 1.0
NZ A:LYS145 5.0 3.7 1.0

Fluorine binding site 2 out of 3 in 4c4r

Go back to Fluorine Binding Sites List in 4c4r
Fluorine binding site 2 out of 3 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:3.4
occ:1.00
 F2 A:MGF1221 0.0 3.4 1.0
MG A:MGF1221 1.9 3.2 1.0
OG A:SER114 2.6 4.3 1.0
OD1 A:ASP8 2.7 3.1 1.0
N A:ASP10 2.8 2.3 1.0
O6 A:YO51220 2.8 3.4 1.0
N A:LEU9 3.0 2.9 1.0
F1 A:MGF1221 3.1 3.5 1.0
CB A:SER114 3.2 4.5 1.0
F3 A:MGF1221 3.3 4.1 1.0
CB A:LEU9 3.3 2.8 1.0
OD2 A:ASP10 3.4 3.3 1.0
CA A:LEU9 3.4 2.6 1.0
C A:LEU9 3.5 2.7 1.0
CG A:ASP10 3.5 2.7 1.0
CG A:ASP8 3.6 2.9 1.0
CB A:ASP10 3.7 2.9 1.0
CA A:SER114 3.7 3.9 1.0
CA A:ASP10 3.8 2.9 1.0
OD2 A:ASP8 4.0 3.4 1.0
C6 A:YO51220 4.1 3.8 1.0
C A:ASP8 4.1 3.1 1.0
OD1 A:ASP10 4.2 3.2 1.0
N A:ALA115 4.2 4.1 1.0
C A:SER114 4.4 4.3 1.0
MG A:MG1219 4.5 3.1 1.0
CA A:ASP8 4.5 2.9 1.0
O A:ASP10 4.6 2.6 1.0
CB A:ASP8 4.6 3.3 1.0
CB A:SER116 4.6 4.9 1.0
CG A:LEU9 4.7 3.3 1.0
C A:ASP10 4.7 2.6 1.0
O A:LEU9 4.7 2.8 1.0
N A:SER116 4.7 4.7 1.0
N A:SER114 5.0 4.5 1.0

Fluorine binding site 3 out of 3 in 4c4r

Go back to Fluorine Binding Sites List in 4c4r
Fluorine binding site 3 out of 3 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:4.1
occ:1.00
 F3 A:MGF1221 0.0 4.1 1.0
MG A:MGF1221 1.8 3.2 1.0
NZ A:LYS145 2.7 3.7 1.0
OD1 A:ASP8 2.7 3.1 1.0
N A:ALA115 2.8 4.1 1.0
O6 A:YO51220 2.8 3.4 1.0
F1 A:MGF1221 3.2 3.5 1.0
F2 A:MGF1221 3.3 3.4 1.0
C6 A:YO51220 3.3 3.8 1.0
CB A:ALA115 3.3 5.5 1.0
CE A:LYS145 3.6 4.7 1.0
CA A:ALA115 3.6 4.7 1.0
CA A:GLY46 3.7 3.8 1.0
C A:SER114 3.7 4.3 1.0
CA A:SER114 3.7 3.9 1.0
CG A:ASP8 3.9 2.9 1.0
O A:GLY46 3.9 5.5 1.0
O A:HOH2021 4.0 3.6 1.0
CD A:LYS145 4.0 5.6 1.0
OG A:SER114 4.1 4.3 1.0
C A:GLY46 4.1 4.5 1.0
O A:ALA113 4.5 6.1 1.0
CB A:SER114 4.5 4.5 1.0
OD2 A:ASP8 4.5 3.4 1.0
OE2 A:GLU169 4.5 5.7 1.0
N A:GLY46 4.6 3.8 1.0
C A:ALA115 4.7 4.4 1.0
N A:SER116 4.7 4.7 1.0
C5 A:YO51220 4.7 3.4 1.0
MG A:MG1219 4.7 3.1 1.0
O5 A:YO51220 4.9 3.2 1.0
O A:SER114 4.9 5.3 1.0
N A:SER114 4.9 4.5 1.0
CB A:ASP8 5.0 3.3 1.0

Reference:

Y.Jin, D.Bhattasali, E.Pellegrini, S.M.Forget, N.J.Baxter, M.J.Cliff, M.W.Bowler, D.L.Jakeman, G.M.Blackburn, J.P.Waltho. Alpha-Fluorophosphonates Reveal How A Phosphomutase Conserves Transition State Conformation Over Hexose Recognition in Its Two-Step Reaction. Proc.Natl.Acad.Sci.Usa V. 111 12384 2014.
ISSN: ISSN 0027-8424
PubMed: 25104750
DOI: 10.1073/PNAS.1402850111
Page generated: Thu Aug 1 00:29:57 2024

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