Magnesium in PDB 3o3p: Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose

All present enzymatic activity of Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose:
2.4.1.217;

The structure of Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose, PDB code: 3o3p 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)	54.19 / 2.53
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.370, 108.370, 311.960, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 23.1

The structure of Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose (pdb code 3o3p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose, PDB code: 3o3p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg338 b:32.8 occ:1.00 O A:HOH390 2.1 31.9 1.0 O B:HOH373 2.2 23.2 1.0 O A:HOH391 2.2 19.9 1.0 O B:HOH365 2.2 27.7 1.0 O A:ASP302 2.2 34.2 1.0 O A:GLN299 2.4 31.3 1.0 C A:ASP302 3.4 39.1 1.0 C A:GLN299 3.4 31.9 1.0 CB A:ASP302 3.7 44.2 1.0 CA A:ASP302 3.9 36.0 1.0 N A:ASP302 4.1 32.1 1.0 N A:GLN299 4.1 37.0 1.0 O B:ASN194 4.2 32.4 1.0 CA A:GLN299 4.2 36.4 1.0 OD1 B:ASN194 4.3 33.8 1.0 N A:LEU300 4.3 27.4 1.0 CB A:GLN299 4.4 42.5 1.0 O B:HOH367 4.4 30.4 1.0 CA A:LEU300 4.4 24.9 1.0 N A:TYR303 4.5 27.7 1.0 C A:LEU300 4.6 29.7 1.0 CG A:ASP302 4.6 64.6 1.0 OD2 A:ASP302 4.6 70.8 1.0 O A:LEU300 4.6 29.4 1.0 O A:PHE297 4.6 47.5 1.0 O B:HOH374 4.7 36.8 1.0 OH A:TYR269 4.7 29.8 1.0 CA A:TYR303 4.9 27.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of R. Xylanophilus Mpgs in Complex with Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg339 b:65.8 occ:1.00 OD1 A:ASN256 2.3 98.5 1.0 OD2 A:ASP137 2.3 47.7 1.0 O2B A:GDD340 2.3 74.0 1.0 O2A A:GDD340 2.7 53.8 1.0 CG A:ASN256 3.1 95.2 1.0 CG A:ASP137 3.1 37.6 1.0 OD1 A:ASP137 3.2 33.3 1.0 ND2 A:ASN256 3.3 90.9 1.0 PB A:GDD340 3.6 69.8 1.0 PA A:GDD340 4.0 52.3 1.0 O3B A:GDD340 4.0 72.0 1.0 CG A:ARG257 4.0 94.7 1.0 O3A A:GDD340 4.1 0.5 1.0 NH2 A:ARG254 4.3 78.5 1.0 C5' A:GDD340 4.3 44.1 1.0 N A:ARG257 4.4 92.7 1.0 CB A:ASN256 4.5 95.4 1.0 CB A:ASP137 4.5 25.1 1.0 O A:ARG257 4.6 77.9 1.0 OD2 A:ASP135 4.7 52.2 1.0 O5' A:GDD340 4.7 46.6 1.0 CB A:ARG257 4.8 93.9 1.0 O1B A:GDD340 4.9 93.0 1.0 CD A:ARG257 4.9 97.5 1.0

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