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Fluorine in PDB 5ojz: D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.

Enzymatic activity of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.

All present enzymatic activity of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.:
5.4.2.6;

Protein crystallography data

The structure of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution., PDB code: 5ojz was solved by A.J.Robertson, C.Bisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.30 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.760, 53.800, 81.550, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17

Other elements in 5ojz:

The structure of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution. (pdb code 5ojz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution., PDB code: 5ojz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5ojz

Go back to Fluorine Binding Sites List in 5ojz
Fluorine binding site 1 out of 3 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:14.0
occ:1.00
 F1 A:BEF303 0.0 14.0 1.0
BE A:BEF303 1.6 13.4 1.0
MG A:MG301 2.0 14.0 1.0
F2 A:BEF303 2.6 13.5 1.0
OD1 A:ASP8 2.7 13.0 1.0
F3 A:BEF303 2.7 14.1 1.0
OD2 A:ASP8 2.8 13.3 1.0
O A:HOH432 2.8 16.5 1.0
O A:HOH517 2.9 16.8 1.0
O A:ASN10 3.0 13.9 1.0
CG A:ASP8 3.1 12.4 1.0
CB A:ASN10 3.3 15.7 1.0
O A:HOH588 3.4 27.4 1.0
N A:ASN10 3.5 13.0 1.0
O A:HOH593 3.6 37.2 1.0
CA A:ASN10 3.7 13.9 1.0
C A:ASN10 3.7 12.9 1.0
OD1 A:ASP170 4.0 14.1 1.0
ND2 A:ASN10 4.3 25.2 1.0
CG A:ASN10 4.4 20.2 1.0
C A:LEU9 4.5 12.2 0.5
C A:LEU9 4.5 12.6 0.5
N A:LEU9 4.5 12.3 0.5
N A:LEU9 4.5 11.9 0.5
CB A:ASP8 4.6 12.5 1.0
NZ A:LYS145 4.6 14.4 1.0
CG A:ASP170 5.0 13.1 1.0
OE1 A:GLU169 5.0 16.8 1.0
CA A:LEU9 5.0 13.5 0.5

Fluorine binding site 2 out of 3 in 5ojz

Go back to Fluorine Binding Sites List in 5ojz
Fluorine binding site 2 out of 3 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:13.5
occ:1.00
 F2 A:BEF303 0.0 13.5 1.0
BE A:BEF303 1.6 13.4 1.0
OD1 A:ASP8 2.6 13.0 1.0
F1 A:BEF303 2.6 14.0 1.0
OG A:SER114 2.6 13.2 1.0
F3 A:BEF303 2.6 14.1 1.0
N A:ASN10 2.8 13.0 1.0
N A:LEU9 3.0 12.3 0.5
N A:LEU9 3.0 11.9 0.5
O A:HOH593 3.2 37.2 1.0
CB A:LEU9 3.3 13.4 0.5
CA A:LEU9 3.4 13.5 0.5
CB A:SER114 3.4 12.1 1.0
CB A:LEU9 3.4 11.7 0.5
CA A:LEU9 3.4 12.7 0.5
CG A:ASP8 3.5 12.4 1.0
C A:LEU9 3.5 12.6 0.5
C A:LEU9 3.5 12.2 0.5
CA A:SER114 3.8 12.5 1.0
CB A:ASN10 3.8 15.7 1.0
CA A:ASN10 3.9 13.9 1.0
OD2 A:ASP8 4.0 13.3 1.0
N A:ALA115 4.0 12.4 1.0
C A:ASP8 4.2 12.3 1.0
MG A:MG301 4.2 14.0 1.0
CG A:LEU9 4.4 15.2 0.5
C A:SER114 4.4 12.6 1.0
O A:ASN10 4.4 13.9 1.0
CA A:ASP8 4.5 12.0 1.0
N A:SER116 4.6 12.2 1.0
CB A:ASP8 4.6 12.5 1.0
C A:ASN10 4.6 12.9 1.0
CG A:LEU9 4.7 13.3 0.5
CD2 A:LEU9 4.7 17.4 0.5
O A:LEU9 4.7 12.4 0.5
O A:LEU9 4.7 12.0 0.5
NZ A:LYS145 4.7 14.4 1.0
CD2 A:LEU9 4.8 14.0 0.5
CB A:SER116 4.9 14.5 1.0
O A:HOH588 4.9 27.4 1.0

Fluorine binding site 3 out of 3 in 5ojz

Go back to Fluorine Binding Sites List in 5ojz
Fluorine binding site 3 out of 3 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited By A Beryllium Triflouride Phosphoenzyme Analogue to 1.3A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:14.1
occ:1.00
 F3 A:BEF303 0.0 14.1 1.0
BE A:BEF303 1.6 13.4 1.0
OD1 A:ASP8 2.6 13.0 1.0
F2 A:BEF303 2.6 13.5 1.0
F1 A:BEF303 2.7 14.0 1.0
O A:HOH588 2.8 27.4 1.0
N A:ALA115 2.8 12.4 1.0
NZ A:LYS145 2.8 14.4 1.0
CB A:ALA115 3.4 14.9 1.0
O A:HOH593 3.5 37.2 1.0
CA A:SER114 3.6 12.5 1.0
CA A:ALA115 3.7 13.2 1.0
C A:SER114 3.7 12.6 1.0
CG A:ASP8 3.7 12.4 1.0
OG A:SER114 3.8 13.2 1.0
CE A:LYS145 3.8 14.0 1.0
O A:HOH432 4.0 16.5 1.0
CB A:SER114 4.2 12.1 1.0
OD2 A:ASP8 4.3 13.3 1.0
CD A:LYS145 4.3 15.9 1.0
MG A:MG301 4.3 14.0 1.0
N A:SER116 4.5 12.2 1.0
O A:ALA113 4.6 13.3 1.0
C A:ALA115 4.6 13.9 1.0
OE2 A:GLU169 4.6 16.4 1.0
N A:SER114 4.9 12.5 1.0
O A:SER114 4.9 13.9 1.0
CB A:ASP8 4.9 12.5 1.0
N A:LEU9 4.9 12.3 0.5
N A:LEU9 4.9 11.9 0.5

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 12:29:51 2020

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