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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 / Rfree (%) 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

Go back to 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

Go back to 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: Mon Dec 14 07:45:34 2020

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