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Fluorine in PDB 5o6r: Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride

Enzymatic activity of Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride

All present enzymatic activity of Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride:
5.4.2.6;

Protein crystallography data

The structure of Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride, PDB code: 5o6r was solved by M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.300, 54.900, 107.560, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 14.9

Other elements in 5o6r:

The structure of Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride (pdb code 5o6r). 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 D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride, PDB code: 5o6r:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5o6r

Go back to Fluorine Binding Sites List in 5o6r
Fluorine binding site 1 out of 4 in the Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with 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 D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:6.5
occ:0.80
 F1 A:ALF303 0.0 6.5 0.8
AL A:ALF303 1.8 6.7 0.8
F4 A:ALF303 2.5 8.7 0.8
F3 A:ALF303 2.5 7.0 0.8
O A:HOH407 2.5 10.1 1.0
OD1 A:ASP8 2.6 6.8 1.0
NZ A:LYS145 2.7 7.9 1.0
N A:ALA115 2.8 7.0 1.0
CA A:SER114 3.0 6.8 1.0
OG A:SER114 3.2 7.6 1.0
C A:SER114 3.4 6.9 1.0
CE A:LYS145 3.5 7.6 1.0
CB A:SER114 3.5 6.7 1.0
F2 A:ALF303 3.6 6.3 0.8
O A:ALA113 3.9 8.2 1.0
CG A:ASP8 3.9 6.8 1.0
CA A:ALA115 3.9 7.4 1.0
CB A:ALA115 4.0 8.7 1.0
CA A:GLY46 4.2 8.5 1.0
N A:SER114 4.2 6.5 1.0
O6 A:XGP302 4.2 11.3 1.0
CD A:LYS145 4.3 7.8 1.0
C A:ALA113 4.5 6.7 1.0
N A:LEU9 4.5 6.9 1.0
N A:SER116 4.6 6.5 1.0
O A:SER114 4.6 8.2 1.0
OD2 A:ASP8 4.7 6.9 1.0
N A:GLY46 4.8 8.0 1.0
C A:ALA115 4.8 7.1 1.0
CB A:ASP8 4.8 6.4 1.0
OE2 A:GLU169 4.8 10.4 1.0
CA A:ASP8 4.8 6.5 1.0
C6 A:XGP302 4.8 10.2 1.0
O A:HOH443 4.9 9.5 1.0

Fluorine binding site 2 out of 4 in 5o6r

Go back to Fluorine Binding Sites List in 5o6r
Fluorine binding site 2 out of 4 in the Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with 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 D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:6.3
occ:0.80
 F2 A:ALF303 0.0 6.3 0.8
AL A:ALF303 1.8 6.7 0.8
MG A:MG301 2.0 8.2 1.0
F3 A:ALF303 2.6 7.0 0.8
O A:HOH407 2.6 10.1 1.0
F4 A:ALF303 2.6 8.7 0.8
OD1 A:ASP8 2.7 6.8 1.0
OD2 A:ASP8 2.7 6.9 1.0
O A:HOH576 2.8 9.5 1.0
O A:ASN10 2.9 8.2 1.0
O A:HOH656 2.9 11.1 1.0
O A:HOH443 2.9 9.5 1.0
CG A:ASP8 3.0 6.8 1.0
N A:ASN10 3.3 6.2 1.0
CB A:ASN10 3.4 7.1 1.0
CA A:ASN10 3.6 6.9 1.0
C A:ASN10 3.6 6.7 1.0
F1 A:ALF303 3.6 6.5 0.8
OD1 A:ASP170 4.0 8.4 1.0
O6 A:XGP302 4.3 11.3 1.0
C A:LEU9 4.3 6.6 1.0
N A:LEU9 4.4 6.9 1.0
CG A:ASN10 4.4 7.1 1.0
ND2 A:ASN10 4.5 8.7 1.0
N A:GLY46 4.5 8.0 1.0
CB A:ASP8 4.5 6.4 1.0
N A:GLY11 4.9 7.1 1.0
O A:HOH505 4.9 25.2 1.0
C6 A:XGP302 4.9 10.2 1.0
CA A:LEU9 4.9 6.9 0.5
CA A:LEU9 4.9 7.1 0.5
NZ A:LYS145 5.0 7.9 1.0

Fluorine binding site 3 out of 4 in 5o6r

Go back to Fluorine Binding Sites List in 5o6r
Fluorine binding site 3 out of 4 in the Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with 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 D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:7.0
occ:0.80
 F3 A:ALF303 0.0 7.0 0.8
AL A:ALF303 1.8 6.7 0.8
F1 A:ALF303 2.5 6.5 0.8
F2 A:ALF303 2.6 6.3 0.8
OD1 A:ASP8 2.6 6.8 1.0
O A:HOH407 2.7 10.1 1.0
OG A:SER114 2.8 7.6 1.0
N A:ASN10 2.9 6.2 1.0
N A:LEU9 3.2 6.9 1.0
CB A:LEU9 3.2 7.8 0.5
CB A:LEU9 3.5 8.2 0.5
O6 A:XGP302 3.5 11.3 1.0
CA A:LEU9 3.5 6.9 0.5
CA A:LEU9 3.6 7.1 0.5
CG A:ASP8 3.6 6.8 1.0
CB A:SER114 3.6 6.7 1.0
F4 A:ALF303 3.6 8.7 0.8
C A:LEU9 3.7 6.6 1.0
ND2 A:ASN10 3.7 8.7 1.0
CB A:ASN10 3.8 7.1 1.0
CA A:ASN10 3.9 6.9 1.0
OD2 A:ASP8 4.1 6.9 1.0
CA A:SER114 4.1 6.8 1.0
CG A:LEU9 4.1 8.5 0.5
CG A:ASN10 4.1 7.1 1.0
C A:ASP8 4.3 6.6 1.0
MG A:MG301 4.3 8.2 1.0
O A:HOH656 4.4 11.1 1.0
O A:ASN10 4.5 8.2 1.0
N A:ALA115 4.5 7.0 1.0
CG A:LEU9 4.5 9.8 0.5
CD2 A:LEU9 4.6 8.5 0.5
C6 A:XGP302 4.6 10.2 1.0
CA A:ASP8 4.6 6.5 1.0
CB A:ASP8 4.7 6.4 1.0
C A:ASN10 4.7 6.7 1.0
NZ A:LYS145 4.8 7.9 1.0
O A:LEU9 4.9 7.2 1.0
C A:SER114 4.9 6.9 1.0

Fluorine binding site 4 out of 4 in 5o6r

Go back to Fluorine Binding Sites List in 5o6r
Fluorine binding site 4 out of 4 in the Structure of Beta-Phosphoglucomutase D10N Mutant in Complex with 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 D10N Mutant in Complex with Glucose-1-Phosphate and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:8.7
occ:0.80
 F4 A:ALF303 0.0 8.7 0.8
AL A:ALF303 1.8 6.7 0.8
F1 A:ALF303 2.5 6.5 0.8
O A:HOH407 2.5 10.1 1.0
O A:HOH443 2.5 9.5 1.0
F2 A:ALF303 2.6 6.3 0.8
OD1 A:ASP8 2.6 6.8 1.0
NZ A:LYS145 2.9 7.9 1.0
CA A:GLY46 3.2 8.5 1.0
CG A:ASP8 3.3 6.8 1.0
N A:GLY46 3.4 8.0 1.0
MG A:MG301 3.5 8.2 1.0
OE2 A:GLU169 3.5 10.4 1.0
OD2 A:ASP8 3.5 6.9 1.0
CD A:LYS145 3.6 7.8 1.0
F3 A:ALF303 3.6 7.0 0.8
CE A:LYS145 3.7 7.6 1.0
O A:HOH656 4.0 11.1 1.0
OE1 A:GLU169 4.2 10.4 1.0
CD A:GLU169 4.3 9.1 1.0
C A:LYS45 4.3 9.1 1.0
O A:HOH576 4.4 9.5 1.0
OG A:SER171 4.5 12.5 1.0
C A:GLY46 4.6 7.7 1.0
CB A:ASP8 4.6 6.4 1.0
O A:LYS45 4.9 9.6 1.0
CG A:LYS145 4.9 7.7 1.0

Reference:

L.A.Johnson, A.J.Robertson, N.J.Baxter, C.R.Trevitt, C.Bisson, Y.Jin, H.P.Wood, A.M.Hounslow, M.J.Cliff, G.M.Blackburn, M.W.Bowler, J.P.Waltho. Van Der Waals Contact Between Nucleophile and Transferring Phosphorus Is Insufficient to Achieve Enzyme Transition-State Architecture Acs Catalysis 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B01612
Page generated: Sun Dec 13 12:29:26 2020

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