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Magnesium 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:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5ojz

Go back to Magnesium Binding Sites List in 5ojz
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg301

b:14.0
occ:1.00
 F1 A:BEF303 2.0 14.0 1.0
OD2 A:ASP8 2.0 13.3 1.0
O A:HOH517 2.0 16.8 1.0
O A:ASN10 2.1 13.9 1.0
OD1 A:ASP170 2.1 14.1 1.0
O A:HOH432 2.1 16.5 1.0
CG A:ASP8 3.0 12.4 1.0
CG A:ASP170 3.1 13.1 1.0
BE A:BEF303 3.2 13.4 1.0
C A:ASN10 3.3 12.9 1.0
OD1 A:ASP8 3.4 13.0 1.0
OD2 A:ASP170 3.4 16.2 1.0
OE1 A:GLU169 3.9 16.8 1.0
CA A:ASN10 4.0 13.9 1.0
CB A:ASN10 4.0 15.7 1.0
N A:ASN10 4.1 13.0 1.0
O A:HOH588 4.2 27.4 1.0
F2 A:BEF303 4.2 13.5 1.0
F3 A:BEF303 4.3 14.1 1.0
N A:GLY11 4.3 12.9 1.0
CB A:ASP170 4.4 14.7 1.0
CB A:ASP8 4.4 12.5 1.0
ND2 A:ASN10 4.5 25.2 1.0
N A:ASP170 4.6 13.0 1.0
CA A:GLY11 4.6 13.7 1.0
CD A:GLU169 4.6 15.3 1.0
CG A:ASN10 4.7 20.2 1.0
OE2 A:GLU169 4.8 16.4 1.0
C A:LEU9 4.9 12.2 0.5
C A:LEU9 4.9 12.6 0.5
CB A:SER171 4.9 20.2 1.0
CA A:ASP170 4.9 13.6 1.0
N A:SER171 4.9 14.6 1.0
OG A:SER171 4.9 22.2 1.0

Magnesium binding site 2 out of 2 in 5ojz

Go back to Magnesium Binding Sites List in 5ojz
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg302

b:34.7
occ:1.00
 O A:HOH629 2.0 38.1 1.0
O A:HOH643 2.0 41.5 1.0
O A:HOH644 2.1 44.6 1.0
O A:HOH638 2.1 46.8 1.0
O A:HOH585 2.2 52.8 1.0
O A:HOH439 2.2 35.9 1.0
O A:HOH429 3.1 45.9 1.0
OD2 A:ASP51 4.3 30.0 1.0
O A:HOH526 4.4 30.1 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: Mon Dec 14 20:59:58 2020

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