Magnesium in PDB 1rya: Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg

The structure of Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg, PDB code: 1rya was solved by S.B.Gabelli, M.A.Bianchet, P.M.Legler, A.S.Mildvan, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.25 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.069, 81.363, 98.974, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.1

The structure of Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg (pdb code 1rya). 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 the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg, PDB code: 1rya:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg


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 the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:8.8 occ:1.00 O2A A:GDP770 2.0 9.3 1.0 O3B A:GDP770 2.0 9.6 1.0 OE2 A:GLU70 2.1 9.2 1.0 O A:GLY50 2.1 8.6 1.0 O A:HOH1002 2.1 9.2 1.0 OE1 A:GLN123 2.2 9.9 1.0 CD A:GLU70 3.1 9.4 1.0 CD A:GLN123 3.2 9.7 1.0 C A:GLY50 3.2 7.7 1.0 PB A:GDP770 3.3 8.9 1.0 PA A:GDP770 3.3 9.1 1.0 OE1 A:GLU70 3.5 9.3 1.0 O3A A:GDP770 3.5 12.4 1.0 NE2 A:GLN123 3.5 11.1 1.0 CA A:GLY51 3.9 7.5 1.0 N A:GLY50 4.0 7.9 1.0 N A:GLY51 4.0 7.3 1.0 O A:HOH1078 4.0 18.3 1.0 O A:HOH1003 4.0 9.5 1.0 CA A:GLY50 4.2 7.8 1.0 O1B A:GDP770 4.3 10.0 1.0 O2B A:GDP770 4.3 12.5 1.0 NH1 A:ARG37 4.3 9.6 1.0 CG A:GLU70 4.4 9.9 1.0 O5' A:GDP770 4.4 11.5 1.0 O1A A:GDP770 4.4 9.7 1.0 C5' A:GDP770 4.5 11.2 1.0 CG A:GLN123 4.5 9.3 1.0 O3 A:TRS870 4.6 18.1 1.0 O A:HOH1005 4.7 16.0 1.0 O A:HOH1004 4.7 9.0 1.0 CB A:GLN123 4.9 9.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg


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 the E. Coli Gdp-Mannose Mannosyl Hydrolase in Complex with Gdp and Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:8.5 occ:1.00 O3B B:GDP771 2.0 9.4 1.0 O B:GLY50 2.0 9.3 1.0 OE2 B:GLU70 2.1 8.9 1.0 O2A B:GDP771 2.1 9.5 1.0 O B:HOH1004 2.1 9.2 1.0 OE1 B:GLN123 2.1 9.8 1.0 CD B:GLU70 3.1 9.5 1.0 CD B:GLN123 3.1 9.4 1.0 C B:GLY50 3.2 8.4 1.0 PA B:GDP771 3.3 9.0 1.0 PB B:GDP771 3.3 8.8 1.0 OE1 B:GLU70 3.5 9.3 1.0 NE2 B:GLN123 3.5 11.0 1.0 O3A B:GDP771 3.5 13.1 1.0 CA B:GLY51 3.9 7.8 1.0 N B:GLY50 4.0 8.1 1.0 N B:GLY51 4.0 7.9 1.0 O B:HOH1067 4.0 15.8 1.0 O B:HOH1007 4.1 9.8 1.0 CA B:GLY50 4.2 8.5 1.0 O2B B:GDP771 4.3 12.3 1.0 O1B B:GDP771 4.3 10.8 1.0 NH2 B:ARG37 4.3 10.0 1.0 O5' B:GDP771 4.3 13.1 1.0 C5' B:GDP771 4.4 11.1 1.0 CG B:GLU70 4.4 10.1 1.0 O1A B:GDP771 4.4 10.8 1.0 CG B:GLN123 4.5 10.1 1.0 O B:HOH1009 4.6 14.1 1.0 O B:HOH1005 4.7 9.1 1.0 O3 B:TRS871 4.7 15.9 1.0 CB B:GLN123 4.9 10.2 1.0

S.B.Gabelli, M.A.Bianchet, H.F.Azurmendi, Z.Xia, V.Sarawat, A.S.Mildvan, L.M.Amzel. Structure and Mechanism of Gdp-Mannose Glycosyl Hydrolase, A Nudix Enzyme That Cleaves at Carbon Instead of Phosphorus. Structure V. 12 927 2004.
ISSN: ISSN 0969-2126
PubMed: 15274914
DOI: 10.1016/J.STR.2004.03.028