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

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

All present enzymatic activity 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 Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvl 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) 45.08 / 2.81
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.456, 113.456, 195.982, 90.00, 90.00, 90.00
R / Rfree (%) 17.27 / 23.396

Other elements in 2wvl:

The structure 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) 5 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 2wvl

Go back to Magnesium Binding Sites List in 2wvl
Magnesium binding site 1 out of 2 in the 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 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:86.8
occ:1.00
 O2B A:GDD400 1.9 0.4 1.0
O1A A:GDD400 1.9 73.0 1.0
OD2 A:ASP169 2.0 78.3 1.0
CG A:ASP169 2.9 73.3 1.0
OD1 A:ASP169 3.2 74.5 1.0
PA A:GDD400 3.2 90.6 1.0
PB A:GDD400 3.3 64.6 1.0
OD1 A:ASN313 3.5 88.6 1.0
O3A A:GDD400 3.6 83.2 1.0
O5' A:GDD400 3.7 90.9 1.0
CB A:HIS311 4.0 79.1 1.0
O1B A:GDD400 4.2 52.2 1.0
C11 A:GDD400 4.3 57.7 1.0
CB A:ASP169 4.3 70.2 1.0
CD2 A:HIS311 4.3 0.5 1.0
O3B A:GDD400 4.3 73.8 1.0
O A:GLU312 4.4 99.8 1.0
CG A:HIS311 4.5 0.1 1.0
OD1 A:ASP167 4.5 77.0 1.0
O2A A:GDD400 4.5 71.9 1.0
CG A:ASN313 4.7 0.8 1.0
O51 A:GDD400 4.8 1.0 1.0

Magnesium binding site 2 out of 2 in 2wvl

Go back to Magnesium Binding Sites List in 2wvl
Magnesium binding site 2 out of 2 in the 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 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:0.3
occ:1.00
 O2B B:GDD400 1.9 69.1 1.0
OD2 B:ASP169 1.9 80.8 1.0
O1A B:GDD400 2.0 0.9 1.0
CG B:ASP169 2.8 0.2 1.0
PA B:GDD400 3.1 68.4 1.0
OD1 B:ASP169 3.1 98.8 1.0
O5' B:GDD400 3.1 0.1 1.0
PB B:GDD400 3.2 74.6 1.0
OD1 B:ASN313 3.5 92.0 1.0
O3A B:GDD400 3.5 72.9 1.0
C11 B:GDD400 3.6 62.8 1.0
O1B B:GDD400 3.9 73.9 1.0
O51 B:GDD400 4.0 0.2 1.0
OD1 B:ASP167 4.1 77.9 1.0
CB B:ASP169 4.2 48.2 1.0
O2A B:GDD400 4.5 85.3 1.0
C5' B:GDD400 4.5 51.8 1.0
O3B B:GDD400 4.5 51.7 1.0
ND1 B:HIS311 4.6 0.7 1.0
CG B:ASN313 4.7 0.6 1.0
CB B:HIS311 4.7 91.8 1.0
C21 B:GDD400 4.8 86.7 1.0
CG B:HIS311 4.8 0.4 1.0
C3' B:GDD400 4.8 94.7 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 06:17:43 2024

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