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Fluorine in PDB 2wf8: Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride

Enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride

All present enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride:
5.4.2.6;

Protein crystallography data

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride, PDB code: 2wf8 was solved by M.W.Bowler, N.J.Baxter, C.E.Webster, S.Pollard, T.Alizadeh, A.M.Hounslow, M.J.Cliff, W.Bermel, N.H.Williams, F.Hollfelder, G.M.Blackburn, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.300, 54.300, 104.200, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.1

Other elements in 2wf8:

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride (pdb code 2wf8). 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 Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride, PDB code: 2wf8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2wf8

Go back to Fluorine Binding Sites List in 2wf8
Fluorine binding site 1 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium 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 Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:11.0
occ:1.00
 F1 A:BEF1221 0.0 11.0 1.0
BE A:BEF1221 1.5 9.4 1.0
OD1 A:ASP8 2.5 9.7 1.0
F3 A:BEF1221 2.6 10.6 1.0
F2 A:BEF1221 2.6 10.9 1.0
O1 A:BG61224 2.6 12.3 0.5
NZ A:LYS145 2.8 11.0 1.0
N A:ALA115 2.8 11.6 1.0
C1 A:BG61224 3.2 13.6 0.5
CB A:ALA115 3.4 14.0 1.0
C2 A:G1P1223 3.5 4.7 0.2
O6 A:G1P1223 3.6 5.3 0.2
O A:HOH2219 3.6 10.9 1.0
CA A:SER114 3.7 10.9 1.0
CG A:ASP8 3.7 9.0 1.0
CA A:ALA115 3.7 12.7 1.0
CE A:LYS145 3.7 11.1 1.0
C A:SER114 3.7 12.0 1.0
CA A:GLY46 3.8 11.4 1.0
O2 A:BG61224 3.8 11.3 0.5
O3 A:G1P1223 3.8 14.6 0.2
OG A:SER114 3.9 10.6 1.0
O5 A:BG61224 4.1 16.7 0.5
C2 A:BG61224 4.2 13.5 0.5
MG A:MG1222 4.2 10.1 1.0
CD A:LYS145 4.2 11.5 1.0
OD2 A:ASP8 4.2 10.0 1.0
CB A:SER114 4.3 11.2 1.0
O A:GLY46 4.4 12.9 1.0
C A:GLY46 4.5 11.3 1.0
O A:ALA113 4.5 11.6 1.0
OE2 A:GLU169 4.5 12.7 1.0
N A:SER116 4.6 11.6 1.0
C A:ALA115 4.6 12.2 1.0
O2 A:G1P1223 4.7 11.0 0.2
N A:GLY46 4.7 10.7 1.0
C3 A:G1P1223 4.7 13.2 0.2
CB A:ASP8 4.8 8.9 1.0
OD2 A:ASP10 4.8 14.7 1.0
N A:SER114 4.9 11.0 1.0
N A:LEU9 4.9 8.9 1.0
O A:SER114 4.9 13.7 1.0
C3 A:G1P1223 5.0 5.5 0.2

Fluorine binding site 2 out of 3 in 2wf8

Go back to Fluorine Binding Sites List in 2wf8
Fluorine binding site 2 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium 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 Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:10.9
occ:1.00
 F2 A:BEF1221 0.0 10.9 1.0
BE A:BEF1221 1.6 9.4 1.0
OD1 A:ASP8 2.5 9.7 1.0
F3 A:BEF1221 2.6 10.6 1.0
F1 A:BEF1221 2.6 11.0 1.0
OG A:SER114 2.6 10.6 1.0
O1 A:BG61224 2.6 12.3 0.5
N A:ASP10 2.9 9.1 1.0
N A:LEU9 3.0 8.9 1.0
CB A:SER114 3.2 11.2 1.0
CG A:ASP8 3.4 9.0 1.0
CB A:LEU9 3.4 9.8 1.0
CA A:LEU9 3.4 8.9 1.0
CA A:SER114 3.5 10.9 1.0
OD2 A:ASP10 3.5 14.7 1.0
C A:LEU9 3.6 8.4 1.0
CG A:ASP10 3.7 10.8 1.0
CB A:ASP10 3.9 9.7 1.0
OD2 A:ASP8 3.9 10.0 1.0
CA A:ASP10 3.9 9.0 1.0
C1 A:BG61224 3.9 13.6 0.5
N A:ALA115 4.0 11.6 1.0
C A:ASP8 4.1 9.0 1.0
O6 A:G1P1223 4.2 5.3 0.2
MG A:MG1222 4.2 10.1 1.0
C A:SER114 4.3 12.0 1.0
C2 A:G1P1223 4.4 4.7 0.2
CA A:ASP8 4.4 9.0 1.0
O3 A:G1P1223 4.4 14.6 0.2
OD1 A:ASP10 4.5 11.8 1.0
CB A:ASP8 4.5 8.9 1.0
O2 A:BG61224 4.5 11.3 0.5
O A:ASP10 4.5 9.6 1.0
C2 A:BG61224 4.6 13.5 0.5
NZ A:LYS145 4.6 11.0 1.0
N A:SER114 4.7 11.0 1.0
N A:SER116 4.7 11.6 1.0
C A:ASP10 4.7 9.3 1.0
O A:LEU9 4.8 8.8 1.0
O5 A:BG61224 4.8 16.7 0.5
CG A:LEU9 4.8 12.8 1.0
O A:HOH2219 4.8 10.9 1.0
CB A:SER116 4.9 11.4 1.0

Fluorine binding site 3 out of 3 in 2wf8

Go back to Fluorine Binding Sites List in 2wf8
Fluorine binding site 3 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium 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 Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:10.6
occ:1.00
 F3 A:BEF1221 0.0 10.6 1.0
BE A:BEF1221 1.5 9.4 1.0
MG A:MG1222 2.0 10.1 1.0
F2 A:BEF1221 2.6 10.9 1.0
F1 A:BEF1221 2.6 11.0 1.0
O6 A:G1P1223 2.6 5.3 0.2
OD1 A:ASP8 2.7 9.7 1.0
O A:HOH2219 2.7 10.9 1.0
O2 A:BG61224 2.8 11.3 0.5
OD2 A:ASP8 2.9 10.0 1.0
O1 A:BG61224 3.1 12.3 0.5
O A:HOH2220 3.1 10.5 1.0
O A:ASP10 3.1 9.6 1.0
CG A:ASP8 3.1 9.0 1.0
CB A:ASP10 3.3 9.7 1.0
O3 A:G1P1223 3.3 14.6 0.2
N A:ASP10 3.4 9.1 1.0
C2 A:G1P1223 3.5 4.7 0.2
C1 A:BG61224 3.6 13.6 0.5
C2 A:BG61224 3.6 13.5 0.5
CA A:ASP10 3.7 9.0 1.0
C A:ASP10 3.8 9.3 1.0
OD2 A:ASP10 3.9 14.7 1.0
CG A:ASP10 4.0 10.8 1.0
OD1 A:ASP170 4.0 10.0 1.0
CA A:GLY46 4.2 11.4 1.0
N A:GLY46 4.3 10.7 1.0
O A:HOH2250 4.4 11.1 1.0
C A:LEU9 4.5 8.4 1.0
N A:LEU9 4.5 8.9 1.0
CB A:ASP8 4.6 8.9 1.0
NZ A:LYS145 4.7 11.0 1.0
C3 A:G1P1223 4.7 13.2 0.2
C3 A:G1P1223 4.9 5.5 0.2
OG A:SER114 4.9 10.6 1.0
O5 A:BG61224 4.9 16.7 0.5
CA A:LEU9 5.0 8.9 1.0
CG A:ASP170 5.0 10.5 1.0

Reference:

J.L.Griffin, M.W.Bowler, N.J.Baxter, K.N.Leigh, H.R.Dannatt, A.M.Hounslow, G.M.Blackburn, C.E.Webster, M.J.Cliff, J.P.Waltho. Near Attack Conformers Dominate Beta-Phosphoglucomutase Complexes Where Geometry and Charge Distribution Reflect Those of Substrate. Proc. Natl. Acad. Sci. V. 109 6910 2012U.S.A..
ISSN: ESSN 1091-6490
PubMed: 22505741
DOI: 10.1073/PNAS.1116855109
Page generated: Wed Jul 31 16:25:07 2024

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