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Magnesium in PDB 3f1y: Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus

Enzymatic activity of Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus

All present enzymatic activity of Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus:
2.4.1.217;

Protein crystallography data

The structure of Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus, PDB code: 3f1y was solved by S.Macedo-Ribeiro, P.J.B.Pereira, N.Empadinhas, M.S.Da Costa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.39 / 2.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.881, 108.881, 311.651, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.8

Other elements in 3f1y:

The structure of Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus (pdb code 3f1y). 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 Rubrobacter Xylanophilus, PDB code: 3f1y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3f1y

Go back to Magnesium Binding Sites List in 3f1y
Magnesium binding site 1 out of 2 in the Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus


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 Rubrobacter Xylanophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg336

b:47.7
occ:1.00
O A:ASP302 2.3 53.9 1.0
O C:HOH439 2.4 40.2 1.0
O A:HOH437 2.4 37.6 1.0
O A:HOH440 2.5 40.2 1.0
O A:GLN299 2.5 55.2 1.0
O A:HOH438 2.6 44.5 1.0
C A:ASP302 3.3 54.4 1.0
C A:GLN299 3.4 55.3 1.0
CB A:ASP302 3.5 57.4 1.0
CA A:ASP302 3.9 55.6 1.0
N A:GLN299 4.0 57.5 1.0
CA A:GLN299 4.1 57.4 1.0
N A:ASP302 4.2 54.2 1.0
CB A:GLN299 4.3 59.4 1.0
OD1 C:ASN194 4.3 41.2 1.0
N A:LEU300 4.3 46.8 1.0
O C:ASN194 4.4 39.2 1.0
CA A:LEU300 4.5 44.9 1.0
N A:TYR303 4.5 47.4 1.0
O A:LEU300 4.6 44.1 1.0
C A:LEU300 4.6 45.0 1.0
O C:HOH446 4.6 44.0 1.0
O C:HOH344 4.7 41.2 1.0
O A:PHE297 4.7 44.6 1.0
OH A:TYR269 4.7 41.0 1.0
CG A:ASP302 4.7 60.0 1.0
CD2 A:LEU304 4.8 47.4 1.0
OD2 A:ASP302 4.8 61.0 1.0
CA A:TYR303 4.8 46.7 1.0

Magnesium binding site 2 out of 2 in 3f1y

Go back to Magnesium Binding Sites List in 3f1y
Magnesium binding site 2 out of 2 in the Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus


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 Rubrobacter Xylanophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg336

b:51.1
occ:1.00
O C:HOH432 2.4 43.1 1.0
O C:HOH431 2.4 35.2 1.0
O C:ASP302 2.4 51.9 1.0
O A:HOH430 2.5 43.2 1.0
O C:HOH381 2.6 41.7 1.0
O C:GLN299 2.6 57.1 1.0
C C:GLN299 3.4 57.3 1.0
C C:ASP302 3.5 52.4 1.0
CB C:ASP302 3.9 55.3 1.0
N C:GLN299 4.0 58.8 1.0
CA C:GLN299 4.1 59.1 1.0
CA C:ASP302 4.1 53.7 1.0
CB C:GLN299 4.2 60.7 1.0
N C:ASP302 4.2 52.9 1.0
N C:LEU300 4.3 50.7 1.0
O C:PHE297 4.4 48.8 1.0
OD1 A:ASN194 4.4 47.4 1.0
O A:ASN194 4.5 42.5 1.0
O A:HOH502 4.5 44.5 1.0
CA C:LEU300 4.5 48.9 1.0
O C:HOH366 4.6 61.7 1.0
N C:TYR303 4.6 48.7 1.0
O A:HOH401 4.7 41.8 1.0
C C:LEU300 4.7 49.0 1.0
OH C:TYR269 4.8 43.2 1.0
O C:LEU300 4.9 47.9 1.0

Reference:

N.Empadinhas, P.J.B.Pereira, L.Albuquerque, J.Costa, B.Sa-Moura, A.T.Marques, S.Macedo-Ribeiro, M.S.Da Costa. Functional and Structural Characterization of A Novel Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus Reveals Its Dual Substrate Specificity Mol.Microbiol. V. 79 76 2011.
ISSN: ISSN 0950-382X
PubMed: 21166895
DOI: 10.1111/J.1365-2958.2010.07432.X
Page generated: Mon Dec 14 08:07:34 2020

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