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Fluorine in PDB 4c4s: Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride

Enzymatic activity of Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride

All present enzymatic activity of Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride, PDB code: 4c4s 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) 37.634 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.541, 54.337, 104.346, 90.00, 90.00, 90.00
R / Rfree (%) 17.25 / 19.84

Other elements in 4c4s:

The structure of Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride (pdb code 4c4s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride, PDB code: 4c4s:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4c4s

Go back to Fluorine Binding Sites List in 4c4s
Fluorine binding site 1 out of 4 in the Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1219

b:9.7
occ:1.00
 F1 A:GRX1219 0.0 9.7 1.0
C7 A:GRX1219 1.4 8.5 1.0
C1 A:GRX1219 2.4 6.1 1.0
P A:GRX1219 2.7 8.5 1.0
C2 A:GRX1219 2.8 8.0 1.0
O3P A:GRX1219 2.9 7.6 1.0
N A:ARG49 3.0 10.2 1.0
O1P A:GRX1219 3.0 8.9 1.0
O5 A:GRX1219 3.1 8.5 1.0
O2 A:GRX1219 3.2 8.7 1.0
O A:HOH2104 3.3 16.4 1.0
CB A:ARG49 3.5 12.5 1.0
CA A:ARG49 3.5 11.6 1.0
O A:HOH2109 3.6 15.4 1.0
C A:SER48 3.6 10.3 1.0
O A:ALA115 3.8 13.1 1.0
CA A:SER48 3.8 13.2 1.0
O2P A:GRX1219 3.9 7.9 1.0
O A:VAL47 4.1 12.7 1.0
C3 A:GRX1219 4.2 6.6 1.0
O A:HOH2212 4.2 18.4 1.0
C A:ALA115 4.4 10.7 1.0
C5 A:GRX1219 4.4 8.0 1.0
CB A:ALA115 4.5 8.3 1.0
CA A:SER116 4.5 8.4 1.0
O A:SER48 4.5 9.7 1.0
CG A:ARG49 4.6 9.1 1.0
C4 A:GRX1219 4.6 8.9 1.0
NE A:ARG49 4.7 9.3 1.0
O A:HOH2211 4.8 25.8 1.0
N A:SER116 4.8 9.8 1.0
N A:SER48 4.8 11.7 1.0
CB A:SER48 4.8 14.3 1.0
C A:VAL47 4.9 8.5 1.0

Fluorine binding site 2 out of 4 in 4c4s

Go back to Fluorine Binding Sites List in 4c4s
Fluorine binding site 2 out of 4 in the Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1220

b:8.1
occ:1.00
 F1 A:MGF1220 0.0 8.1 1.0
MG A:MGF1220 1.8 7.4 1.0
MG A:MG2833 2.0 7.4 1.0
O A:HOH2009 2.7 8.3 1.0
O6 A:GRX1219 2.7 7.3 1.0
OD1 A:ASP8 2.9 8.5 1.0
O A:HOH2011 2.9 7.1 1.0
OD2 A:ASP8 2.9 7.1 1.0
C6 A:GRX1219 3.0 9.4 1.0
F2 A:MGF1220 3.0 9.2 1.0
O A:ASP10 3.0 6.3 1.0
F3 A:MGF1220 3.1 9.6 1.0
CG A:ASP8 3.3 6.7 1.0
CB A:ASP10 3.3 8.2 1.0
N A:ASP10 3.6 6.0 1.0
CA A:ASP10 3.8 6.7 1.0
C A:ASP10 3.8 5.5 1.0
OD2 A:ASP10 3.9 8.1 1.0
O A:HOH2296 4.0 7.2 1.0
OD1 A:ASP170 4.0 7.7 1.0
N A:GLY46 4.0 8.2 1.0
CG A:ASP10 4.1 7.2 1.0
CA A:GLY46 4.1 8.4 1.0
C5 A:GRX1219 4.3 8.0 1.0
C A:LEU9 4.7 6.6 1.0
N A:LEU9 4.7 6.4 1.0
CB A:ASP8 4.8 8.0 1.0
O4 A:GRX1219 4.8 10.9 1.0
CG A:ASP170 4.9 8.9 1.0

Fluorine binding site 3 out of 4 in 4c4s

Go back to Fluorine Binding Sites List in 4c4s
Fluorine binding site 3 out of 4 in the Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1220

b:9.2
occ:1.00
 F2 A:MGF1220 0.0 9.2 1.0
MG A:MGF1220 1.8 7.4 1.0
OG A:SER114 2.6 9.1 1.0
OD1 A:ASP8 2.8 8.5 1.0
O6 A:GRX1219 2.8 7.3 1.0
N A:ASP10 2.8 6.0 1.0
N A:LEU9 3.0 6.4 1.0
F1 A:MGF1220 3.0 8.1 1.0
F3 A:MGF1220 3.1 9.6 1.0
CB A:SER114 3.3 8.5 1.0
OD2 A:ASP10 3.4 8.1 1.0
CB A:LEU9 3.4 4.9 1.0
CA A:LEU9 3.4 7.1 1.0
CG A:ASP10 3.6 7.2 1.0
C A:LEU9 3.6 6.6 1.0
CG A:ASP8 3.6 6.7 1.0
CA A:SER114 3.8 7.0 1.0
CB A:ASP10 3.8 8.2 1.0
CA A:ASP10 3.9 6.7 1.0
OD2 A:ASP8 4.1 7.1 1.0
C6 A:GRX1219 4.1 9.4 1.0
C A:ASP8 4.2 7.4 1.0
N A:ALA115 4.2 8.3 1.0
OD1 A:ASP10 4.2 8.8 1.0
C A:SER114 4.5 9.9 1.0
MG A:MG2833 4.5 7.4 1.0
CA A:ASP8 4.5 6.5 1.0
O A:ASP10 4.6 6.3 1.0
CB A:ASP8 4.7 8.0 1.0
CB A:SER116 4.7 8.0 1.0
CG A:LEU9 4.7 6.5 1.0
C A:ASP10 4.7 5.5 1.0
O A:LEU9 4.8 7.4 1.0
N A:SER116 4.8 9.8 1.0
N A:SER114 5.0 8.5 1.0

Fluorine binding site 4 out of 4 in 4c4s

Go back to Fluorine Binding Sites List in 4c4s
Fluorine binding site 4 out of 4 in the Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate 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 4 of Structure of Beta-Phosphoglucomutase in Complex with An Alpha-Fluorophosphonate Analogue of Beta-Glucose-1-Phosphate and Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1220

b:9.6
occ:1.00
 F3 A:MGF1220 0.0 9.6 1.0
MG A:MGF1220 1.8 7.4 1.0
OD1 A:ASP8 2.6 8.5 1.0
NZ A:LYS145 2.7 8.4 1.0
O6 A:GRX1219 2.8 7.3 1.0
N A:ALA115 2.9 8.3 1.0
F2 A:MGF1220 3.1 9.2 1.0
F1 A:MGF1220 3.1 8.1 1.0
C6 A:GRX1219 3.3 9.4 1.0
CB A:ALA115 3.4 8.3 1.0
CE A:LYS145 3.6 10.9 1.0
CA A:ALA115 3.8 8.3 1.0
CA A:SER114 3.8 7.0 1.0
C A:SER114 3.8 9.9 1.0
CG A:ASP8 3.8 6.7 1.0
CA A:GLY46 3.8 8.4 1.0
O A:HOH2009 4.0 8.3 1.0
OG A:SER114 4.0 9.1 1.0
O A:GLY46 4.1 10.6 1.0
CD A:LYS145 4.1 11.5 1.0
C A:GLY46 4.3 10.1 1.0
O A:ALA113 4.4 9.6 1.0
OD2 A:ASP8 4.5 7.1 1.0
CB A:SER114 4.5 8.5 1.0
OE2 A:GLU169 4.5 11.8 1.0
MG A:MG2833 4.6 7.4 1.0
C5 A:GRX1219 4.7 8.0 1.0
N A:GLY46 4.7 8.2 1.0
C A:ALA115 4.8 10.7 1.0
N A:SER116 4.8 9.8 1.0
O5 A:GRX1219 4.8 8.5 1.0
CB A:ASP8 4.9 8.0 1.0
N A:SER114 4.9 8.5 1.0
O A:SER114 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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