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 / R_free (%)*	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

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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

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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 Sep 30 01:01:06 2024

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