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Fluorine in PDB 4c4t: Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride

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

All present enzymatic activity of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride:
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 Aluminium Tetrafluoride, PDB code: 4c4t 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) 48.172 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.191, 54.284, 104.496, 90.00, 90.00, 90.00
R / Rfree (%) 15.91 / 19.94

Other elements in 4c4t:

The structure of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride 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 Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride (pdb code 4c4t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride, PDB code: 4c4t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4c4t

Go back to Fluorine Binding Sites List in 4c4t
Fluorine binding site 1 out of 5 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride


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 Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1218

b:7.3
occ:1.00
 F1 A:GRX1218 0.0 7.3 1.0
C7 A:GRX1218 1.4 4.8 1.0
C1 A:GRX1218 2.4 5.2 1.0
P A:GRX1218 2.6 7.3 1.0
C2 A:GRX1218 2.9 8.4 1.0
O1P A:GRX1218 3.0 7.2 1.0
O5 A:GRX1218 3.0 5.0 1.0
N A:ARG49 3.1 8.2 1.0
O3P A:GRX1218 3.1 7.8 1.0
O2 A:GRX1218 3.2 7.2 1.0
O A:HOH2153 3.4 16.0 1.0
O A:HOH2154 3.6 13.3 1.0
CB A:ARG49 3.6 7.6 1.0
CA A:ARG49 3.6 7.6 1.0
C A:SER48 3.7 8.5 1.0
O A:ALA115 3.7 8.2 1.0
O2P A:GRX1218 3.9 8.0 1.0
CA A:SER48 3.9 9.7 1.0
O A:VAL47 4.2 10.2 1.0
C3 A:GRX1218 4.2 5.0 1.0
O A:HOH2311 4.2 19.8 1.0
C A:ALA115 4.3 7.6 1.0
CB A:ALA115 4.4 10.1 1.0
C5 A:GRX1218 4.4 5.3 1.0
CA A:SER116 4.5 6.3 1.0
CG A:ARG49 4.6 6.8 1.0
C4 A:GRX1218 4.7 8.5 1.0
O A:SER48 4.7 7.9 1.0
NE A:ARG49 4.7 7.5 1.0
N A:SER116 4.7 7.0 1.0
O A:HOH2310 4.8 19.2 1.0
CB A:SER48 4.9 12.1 1.0
N A:SER48 4.9 9.1 1.0
C A:VAL47 5.0 9.5 1.0

Fluorine binding site 2 out of 5 in 4c4t

Go back to Fluorine Binding Sites List in 4c4t
Fluorine binding site 2 out of 5 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride


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 Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1219

b:6.7
occ:1.00
 F1 A:ALF1219 0.0 6.7 1.0
AL A:ALF1219 1.8 6.8 1.0
F3 A:ALF1219 2.5 7.5 1.0
OD1 A:ASP8 2.6 6.8 1.0
O6 A:GRX1218 2.6 5.8 1.0
F2 A:ALF1219 2.6 6.0 1.0
N A:ASP10 2.8 5.3 1.0
OG A:SER114 2.9 7.0 1.0
N A:LEU9 3.0 6.3 1.0
OD2 A:ASP10 3.2 7.3 1.0
CB A:LEU9 3.3 6.0 1.0
CA A:LEU9 3.4 7.0 1.0
CG A:ASP8 3.5 5.5 1.0
CG A:ASP10 3.5 5.8 1.0
C A:LEU9 3.5 6.6 1.0
F4 A:ALF1219 3.6 6.6 1.0
CB A:SER114 3.6 5.2 1.0
CB A:ASP10 3.7 5.9 1.0
CA A:ASP10 3.8 5.0 1.0
OD2 A:ASP8 3.9 7.0 1.0
C6 A:GRX1218 4.0 6.6 1.0
CA A:SER114 4.1 5.9 1.0
C A:ASP8 4.2 7.2 1.0
OD1 A:ASP10 4.2 7.8 1.0
MG A:MG2833 4.3 5.7 1.0
CA A:ASP8 4.5 6.9 1.0
O A:ASP10 4.5 5.4 1.0
N A:ALA115 4.5 5.5 1.0
CB A:ASP8 4.6 5.3 1.0
C A:ASP10 4.7 4.8 1.0
O A:LEU9 4.7 5.8 1.0
CG A:LEU9 4.7 10.7 1.0
NZ A:LYS145 4.8 7.4 1.0
C A:SER114 4.9 8.3 1.0
CB A:SER116 4.9 5.2 1.0
C5 A:GRX1218 4.9 5.3 1.0
O A:HOH2014 5.0 6.6 1.0

Fluorine binding site 3 out of 5 in 4c4t

Go back to Fluorine Binding Sites List in 4c4t
Fluorine binding site 3 out of 5 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride


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 Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1219

b:6.0
occ:1.00
 F2 A:ALF1219 0.0 6.0 1.0
AL A:ALF1219 1.8 6.8 1.0
MG A:MG2833 1.9 5.7 1.0
F4 A:ALF1219 2.5 6.6 1.0
O6 A:GRX1218 2.6 5.8 1.0
F1 A:ALF1219 2.6 6.7 1.0
OD1 A:ASP8 2.7 6.8 1.0
O A:HOH2014 2.8 6.6 1.0
OD2 A:ASP8 2.8 7.0 1.0
O A:ASP10 2.9 5.4 1.0
O A:HOH2016 3.0 6.4 1.0
CB A:ASP10 3.1 5.9 1.0
CG A:ASP8 3.1 5.5 1.0
C6 A:GRX1218 3.1 6.6 1.0
N A:ASP10 3.2 5.3 1.0
CA A:ASP10 3.5 5.0 1.0
F3 A:ALF1219 3.6 7.5 1.0
OD2 A:ASP10 3.6 7.3 1.0
C A:ASP10 3.6 4.8 1.0
CG A:ASP10 3.8 5.8 1.0
OD1 A:ASP170 3.9 6.7 1.0
O A:HOH2440 4.2 6.7 1.0
C A:LEU9 4.3 6.6 1.0
C5 A:GRX1218 4.3 5.3 1.0
N A:LEU9 4.4 6.3 1.0
N A:GLY46 4.6 6.3 1.0
CB A:ASP8 4.6 5.3 1.0
CA A:GLY46 4.7 10.5 1.0
OD1 A:ASP10 4.9 7.8 1.0
CA A:LEU9 4.9 7.0 1.0
N A:GLY11 4.9 5.5 1.0
CG A:ASP170 4.9 7.3 1.0
NZ A:LYS145 5.0 7.4 1.0

Fluorine binding site 4 out of 5 in 4c4t

Go back to Fluorine Binding Sites List in 4c4t
Fluorine binding site 4 out of 5 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1219

b:7.5
occ:1.00
 F3 A:ALF1219 0.0 7.5 1.0
AL A:ALF1219 1.8 6.8 1.0
F4 A:ALF1219 2.4 6.6 1.0
F1 A:ALF1219 2.5 6.7 1.0
OD1 A:ASP8 2.6 6.8 1.0
N A:ALA115 2.6 5.5 1.0
O6 A:GRX1218 2.8 5.8 1.0
NZ A:LYS145 2.8 7.4 1.0
CA A:SER114 3.0 5.9 1.0
OG A:SER114 3.1 7.0 1.0
C A:SER114 3.3 8.3 1.0
CB A:SER114 3.5 5.2 1.0
F2 A:ALF1219 3.6 6.0 1.0
CB A:ALA115 3.7 10.1 1.0
CA A:ALA115 3.7 6.3 1.0
C6 A:GRX1218 3.7 6.6 1.0
CE A:LYS145 3.8 8.0 1.0
CG A:ASP8 3.8 5.5 1.0
O A:ALA113 3.9 8.2 1.0
N A:SER114 4.2 7.1 1.0
N A:SER116 4.4 7.0 1.0
N A:LEU9 4.5 6.3 1.0
C A:ALA113 4.5 8.3 1.0
O A:SER114 4.5 8.2 1.0
C A:ALA115 4.6 7.6 1.0
CD A:LYS145 4.6 11.5 1.0
OD2 A:ASP8 4.7 7.0 1.0
CB A:ASP8 4.7 5.3 1.0
O A:HOH2014 4.8 6.6 1.0
CA A:ASP8 4.8 6.9 1.0
OD2 A:ASP10 4.8 7.3 1.0
OE2 A:GLU169 4.9 7.7 1.0
C5 A:GRX1218 4.9 5.3 1.0
O5 A:GRX1218 4.9 5.0 1.0

Fluorine binding site 5 out of 5 in 4c4t

Go back to Fluorine Binding Sites List in 4c4t
Fluorine binding site 5 out of 5 in the Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Beta-Phosphoglucomutase in Complex with A Phosphonate Analogue of Beta-Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1219

b:6.6
occ:1.00
 F4 A:ALF1219 0.0 6.6 1.0
AL A:ALF1219 1.8 6.8 1.0
F3 A:ALF1219 2.4 7.5 1.0
F2 A:ALF1219 2.5 6.0 1.0
O A:HOH2014 2.6 6.6 1.0
OD1 A:ASP8 2.7 6.8 1.0
O6 A:GRX1218 2.7 5.8 1.0
C6 A:GRX1218 2.9 6.6 1.0
CA A:GLY46 3.0 10.5 1.0
NZ A:LYS145 3.0 7.4 1.0
CG A:ASP8 3.5 5.5 1.0
F1 A:ALF1219 3.6 6.7 1.0
MG A:MG2833 3.6 5.7 1.0
N A:GLY46 3.7 6.3 1.0
OD2 A:ASP8 3.9 7.0 1.0
C A:GLY46 3.9 9.9 1.0
OE2 A:GLU169 3.9 7.7 1.0
CE A:LYS145 4.0 8.0 1.0
CD A:LYS145 4.0 11.5 1.0
O A:GLY46 4.0 10.5 1.0
C5 A:GRX1218 4.3 5.3 1.0
O A:HOH2016 4.5 6.4 1.0
OE1 A:GLU169 4.5 7.3 1.0
CB A:ALA115 4.6 10.1 1.0
CD A:GLU169 4.6 7.6 1.0
N A:ALA115 4.7 5.5 1.0
CB A:ASP8 4.8 5.3 1.0
OG A:SER171 4.8 6.9 1.0
C A:LYS45 4.9 7.3 1.0
O5 A:GRX1218 4.9 5.0 1.0
N A:VAL47 5.0 10.2 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 00:30:42 2024

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