Magnesium in PDB 3o6z: Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++

The structure of Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++, PDB code: 3o6z was solved by L.M.Amzel, S.B.Gabelli, A.N.Boto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.47 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.916, 69.333, 99.612, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 30.3

The structure of Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ (pdb code 3o6z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++, PDB code: 3o6z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:53.1 occ:1.00 O A:HOH417 1.9 31.1 1.0 OE2 A:GLU104 2.0 48.5 1.0 O A:HOH311 2.2 41.3 1.0 O A:HOH324 2.3 41.8 1.0 O A:ALA85 2.4 30.8 1.0 CD A:GLU104 2.8 48.3 1.0 OE1 A:GLU104 3.2 45.1 1.0 C A:ALA85 3.5 30.6 1.0 NE2 A:GLN65 4.1 30.6 1.0 CG A:GLU104 4.1 49.5 1.0 O A:HOH214 4.2 26.2 1.0 N A:ALA85 4.2 28.6 1.0 CA A:GLY86 4.3 32.9 1.0 CA A:ALA85 4.4 29.2 1.0 OE1 A:GLU100 4.4 49.1 1.0 N A:GLY86 4.4 31.7 1.0 OE1 A:GLN65 4.5 34.0 1.0 NH2 A:ARG67 4.7 25.0 1.0 CD A:GLN65 4.8 29.8 1.0 O A:HOH266 4.8 40.8 1.0 CB A:ALA85 4.8 27.7 1.0 O A:HOH246 4.9 41.6 1.0 CD A:GLU100 5.0 46.1 1.0

Magnesium binding site 2 out of 3 in the Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:25.8 occ:1.00 O B:HOH414 1.9 22.0 1.0 OE2 B:GLU104 1.9 21.7 1.0 OE1 B:GLU100 2.0 25.9 1.0 O B:HOH415 2.2 24.4 1.0 OE2 B:GLU151 2.3 23.0 1.0 O B:HOH229 2.3 20.8 1.0 CD B:GLU104 3.0 20.3 1.0 CD B:GLU100 3.0 24.4 1.0 MG B:MG202 3.1 30.2 1.0 CD B:GLU151 3.2 22.9 1.0 OE2 B:GLU100 3.4 27.6 1.0 OE1 B:GLU151 3.5 24.9 1.0 CG B:GLU104 3.5 18.4 1.0 O B:HOH347 3.8 26.7 1.0 O B:HOH290 3.9 47.7 1.0 O B:ALA85 4.0 19.6 1.0 OE1 B:GLU104 4.1 19.4 1.0 O B:HOH328 4.1 42.4 1.0 O B:HOH268 4.3 31.1 1.0 CG B:GLU100 4.3 23.8 1.0 OE1 B:GLU103 4.4 24.6 1.0 CG B:GLU151 4.6 23.6 1.0 CB B:GLU100 4.7 22.0 1.0 CA B:GLY86 4.8 22.0 1.0 O B:HOH199 4.9 39.2 1.0 O B:HOH240 4.9 21.8 1.0 CD1 B:ILE153 5.0 21.9 1.0 C B:ALA85 5.0 19.3 1.0

Magnesium binding site 3 out of 3 in the Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the D152A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:30.2 occ:1.00 O B:HOH414 2.1 22.0 1.0 O B:HOH240 2.2 21.8 1.0 O B:ALA85 2.3 19.6 1.0 OE2 B:GLU104 2.3 21.7 1.0 O B:HOH214 2.4 32.7 1.0 O B:HOH347 2.5 26.7 1.0 MG B:MG201 3.1 25.8 1.0 CD B:GLU104 3.2 20.3 1.0 OE1 B:GLU104 3.3 19.4 1.0 C B:ALA85 3.5 19.3 1.0 OE2 B:GLU151 3.7 23.0 1.0 OE1 B:GLU100 4.0 25.9 1.0 CA B:GLY86 4.2 22.0 1.0 N B:GLY86 4.3 20.4 1.0 O B:HOH216 4.4 19.8 1.0 NE2 B:GLN65 4.4 22.2 1.0 N B:ALA85 4.4 18.4 1.0 CA B:ALA85 4.5 19.2 1.0 NH2 B:ARG67 4.5 21.3 1.0 O B:HOH268 4.5 31.1 1.0 CG B:GLU104 4.6 18.4 1.0 OE1 B:GLN65 4.7 24.9 1.0 O B:HOH415 4.7 24.4 1.0 CD1 B:ILE153 4.8 21.9 1.0 CD B:GLU151 4.9 22.9 1.0 CD B:GLU100 4.9 24.4 1.0 CB B:ALA85 4.9 18.4 1.0

A.N.Boto, W.Xu, J.Jakoncic, A.Pannuri, T.Romeo, M.J.Bessman, S.B.Gabelli, L.M.Amzel. Structural Studies of the Nudix Gdp-Mannose Hydrolase From E. Coli Reveals A New Motif For Mannose Recognition. Proteins V. 79 2455 2011.
ISSN: ISSN 0887-3585
PubMed: 21638333
DOI: 10.1002/PROT.23069