Magnesium in PDB 6ouw: 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound:
2.2.1.7;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound, PDB code: 6ouw was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.39 / 2.40
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	129.750, 85.540, 60.572, 90.00, 114.77, 90.00
*R / R_free (%)*	15.8 / 19.6

Other elements in 6ouw:

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound (pdb code 6ouw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound, PDB code: 6ouw:

Magnesium binding site 1 out of 1 in 6ouw

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Magnesium Binding Sites List in 6ouw

Magnesium binding site 1 out of 1 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxps) From Deinococcus Radiodurans with Enamine Intermediate Bound within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg702 b:48.0 occ:1.00	O21	A:HTL701	2.0	48.5	1.0
	OD1	A:ASN183	2.0	46.7	1.0
	O	A:HOH845	2.0	46.6	1.0
	O	A:HOH835	2.1	51.4	1.0
	O13	A:HTL701	2.1	48.3	1.0
	OD1	A:ASP154	2.1	46.8	1.0
	CG	A:ASN183	2.9	43.3	1.0
	CG	A:ASP154	3.0	47.1	1.0
	P2	A:HTL701	3.2	52.5	1.0
	ND2	A:ASN183	3.2	42.2	1.0
	P1	A:HTL701	3.2	53.0	1.0
	OD2	A:ASP154	3.3	45.8	1.0
	O11	A:HTL701	3.3	53.9	1.0
	N	A:ASP154	4.1	43.9	1.0
	O22	A:HTL701	4.1	52.0	1.0
	O5G	A:HTL701	4.1	63.1	1.0
	N	A:GLY155	4.2	41.0	1.0
	N	A:ASN183	4.2	45.6	1.0
	O	A:HOH804	4.2	43.8	1.0
	O23	A:HTL701	4.2	48.7	1.0
	CB	A:ASN183	4.3	43.9	1.0
	O	A:ASN181	4.3	45.8	1.0
	CB	A:ASP154	4.3	47.0	1.0
	O12	A:HTL701	4.4	50.4	1.0
	CA	A:ASN183	4.6	48.5	1.0
	CA	A:ASP154	4.7	45.7	1.0
	C	A:ASN183	4.8	54.9	1.0
	CA	A:GLY153	4.8	38.1	1.0
	C	A:GLY153	4.8	42.5	1.0
	N	A:GLU184	4.9	57.8	1.0
	C	A:ASP154	4.9	42.5	1.0

Reference:

P.Y.Chen, A.A.Decolli, C.L.Freel Meyers, C.L.Drennan. X-Ray Crystallography-Based Structural Elucidation of Enzyme-Bound Intermediates Along the 1-Deoxy-D-Xylulose 5-Phosphate Synthase Reaction Coordinate. J.Biol.Chem. V. 294 12405 2019.
ISSN: ESSN 1083-351X
PubMed: 31239351
DOI: 10.1074/JBC.RA119.009321

Page generated: Tue Oct 1 13:41:24 2024

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