Magnesium in PDB 2wvm: H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

Enzymatic activity of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

All present enzymatic activity of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II):
2.4.1.217;

Protein crystallography data

The structure of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvm was solved by S.Goncalves, N.Borges, A.M.Esteves, B.Victor, C.M.Soares, H.Santos, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	98.19 / 2.98
*Space group*	P 4₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	112.766, 112.766, 199.690, 90.00, 90.00, 90.00
*R / R_free (%)*	17.355 / 23.163

Other elements in 2wvm:

The structure of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) (pdb code 2wvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2wvm

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Magnesium Binding Sites List in 2wvm

Magnesium binding site 1 out of 2 in the H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:69.0 occ:1.00	O2B	A:GDD400	1.9	56.7	1.0
	OD2	A:ASP169	1.9	63.5	1.0
	O1A	A:GDD400	2.0	68.5	1.0
	CG	A:ASP169	2.9	56.5	1.0
	OD1	A:ASP169	3.1	56.0	1.0
	PA	A:GDD400	3.2	49.9	1.0
	PB	A:GDD400	3.3	46.6	1.0
	O5'	A:GDD400	3.6	63.6	1.0
	O3A	A:GDD400	3.7	39.6	1.0
	CB	A:ASP169	4.2	53.4	1.0
	O3B	A:GDD400	4.3	28.6	1.0
	OD1	A:ASN313	4.3	66.1	1.0
	OD1	A:ASP167	4.3	63.1	1.0
	C11	A:GDD400	4.3	46.7	1.0
	O	A:GLU312	4.3	60.1	1.0
	O1B	A:GDD400	4.3	41.6	1.0
	CB	A:HIS311	4.5	49.1	1.0
	O2A	A:GDD400	4.6	37.8	1.0
	ND1	A:HIS311	4.7	81.9	1.0
	CG	A:HIS311	4.8	51.0	1.0
	O51	A:GDD400	4.9	59.4	1.0
	C5'	A:GDD400	5.0	33.5	1.0

Magnesium binding site 2 out of 2 in 2wvm

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Magnesium Binding Sites List in 2wvm

Magnesium binding site 2 out of 2 in the H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg401 b:73.4 occ:1.00	O2B	B:GDD400	1.9	0.7	1.0
	OD2	B:ASP169	1.9	70.4	1.0
	O1A	B:GDD400	2.0	0.8	1.0
	CG	B:ASP169	2.7	64.0	1.0
	OD1	B:ASP169	2.9	47.6	1.0
	PA	B:GDD400	3.2	50.1	1.0
	PB	B:GDD400	3.3	44.1	1.0
	O5'	B:GDD400	3.5	58.4	1.0
	O3A	B:GDD400	3.7	56.0	1.0
	C11	B:GDD400	4.1	35.2	1.0
	OD1	B:ASP167	4.1	66.6	1.0
	O1B	B:GDD400	4.1	44.7	1.0
	ND1	B:HIS311	4.2	79.7	1.0
	CB	B:ASP169	4.2	54.0	1.0
	O3B	B:GDD400	4.5	52.1	1.0
	O	B:GLU312	4.6	52.5	1.0
	CB	B:HIS311	4.6	52.3	1.0
	O2A	B:GDD400	4.6	41.0	1.0
	O51	B:GDD400	4.7	82.2	1.0
	CG	B:HIS311	4.7	50.7	1.0
	C5'	B:GDD400	4.9	48.2	1.0

Reference:

S.Goncalves, N.Borges, A.M.Esteves, B.Victor, C.M.Soares, H.Santos, P.M.Matias. Structural Analysis of Thermus Thermophilus HB27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence For A Second Catalytic Metal Ion and New Insight Into the Retaining Mechanism of Glycosyltransferases. J.Biol.Chem. V. 285 17857 2010.
ISSN: ISSN 0021-9258
PubMed: 20356840
DOI: 10.1074/JBC.M109.095976

Page generated: Wed Aug 14 06:18:19 2024

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