Magnesium in PDB 3o69: Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++

The structure of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++, PDB code: 3o69 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)	22.81 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.379, 69.260, 98.554, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 28

The structure of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ (pdb code 3o69). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++, PDB code: 3o69:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the E100A 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 E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:46.0 occ:1.00 OE2 A:GLU104 1.9 43.2 1.0 O A:HOH297 2.3 31.9 1.0 O A:HOH213 2.3 26.6 1.0 O A:ALA85 2.6 25.2 1.0 CD A:GLU104 3.0 42.5 1.0 OE1 A:GLU104 3.5 39.8 1.0 C A:ALA85 3.7 25.0 1.0 O A:HOH201 4.1 41.8 1.0 NE2 A:GLN65 4.2 21.5 1.0 NH2 A:ARG67 4.3 19.3 1.0 CG A:GLU104 4.3 43.0 1.0 O A:HOH271 4.3 40.4 1.0 CA A:GLY86 4.4 25.6 1.0 OE1 A:GLN65 4.4 24.1 1.0 N A:GLY86 4.5 25.8 1.0 O A:HOH252 4.5 34.9 1.0 O A:HOH287 4.6 25.2 1.0 O A:HOH246 4.7 17.9 1.0 CA A:ALA85 4.7 24.0 1.0 CD1 A:ILE153 4.7 36.2 1.0 N A:ALA85 4.7 23.2 1.0 CD A:GLN65 4.8 22.1 1.0 O A:HOH293 4.9 38.0 1.0

Magnesium binding site 2 out of 4 in the Structure of the E100A 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 E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:35.6 occ:1.00 O B:HOH308 1.8 51.4 1.0 O B:HOH236 1.9 29.8 1.0 O B:HOH305 1.9 19.8 1.0 O B:HOH405 2.3 15.0 1.0 O B:HOH307 2.4 28.6 1.0 O B:HOH241 4.1 32.9 1.0 OE1 B:GLU103 4.1 15.8 1.0 OD2 B:ASP89 4.2 27.1 1.0 O B:HOH207 4.2 26.4 1.0 O B:HOH233 4.2 19.3 1.0 O B:HOH304 4.3 28.0 1.0 OE2 B:GLU103 4.4 15.7 1.0 NZ B:LYS99 4.4 27.4 1.0 O B:HOH237 4.5 17.1 1.0 CD B:GLU103 4.7 17.8 1.0 CE B:LYS99 4.7 26.4 1.0 O B:HOH262 4.8 35.8 1.0 O B:HOH214 4.8 42.2 1.0 CD B:LYS99 4.9 24.1 1.0 CG2 B:VAL148 5.0 18.1 1.0

Magnesium binding site 3 out of 4 in the Structure of the E100A 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 E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:14.7 occ:1.00 O B:HOH199 2.0 16.7 1.0 OE2 B:GLU104 2.1 15.5 1.0 O B:HOH365 2.1 13.6 1.0 O B:ALA85 2.2 14.5 1.0 O B:HOH315 2.2 12.4 1.0 O B:HOH218 2.2 14.5 1.0 CD B:GLU104 3.1 14.8 1.0 C B:ALA85 3.3 14.4 1.0 OE1 B:GLU104 3.5 15.0 1.0 O B:HOH328 4.0 20.1 1.0 O B:HOH344 4.1 20.6 1.0 CA B:GLY86 4.1 14.9 1.0 N B:GLY86 4.2 14.7 1.0 O B:HOH248 4.2 18.3 1.0 O B:HOH212 4.3 17.8 1.0 O B:HOH211 4.3 12.4 1.0 OE2 B:GLU151 4.3 20.5 1.0 CA B:ALA85 4.3 13.9 1.0 N B:ALA85 4.3 13.4 1.0 NH2 B:ARG67 4.4 13.8 1.0 CG B:GLU104 4.4 14.1 1.0 NE2 B:GLN65 4.5 13.9 1.0 CD1 B:ILE153 4.6 17.0 1.0 OE1 B:GLN65 4.6 14.5 1.0 CB B:ALA85 4.9 13.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the E100A 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 4 of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg250 b:27.6 occ:1.00 O B:HOH345 2.0 29.6 1.0 O B:HOH230 2.0 26.6 1.0 O B:HOH319 2.0 30.2 1.0 O B:HOH318 2.0 20.1 1.0 O B:HOH316 2.1 21.9 1.0 O B:HOH317 2.2 16.5 1.0 OD1 B:ASP150 3.9 20.7 1.0 OD2 B:ASP150 4.1 23.3 1.0 OE1 B:GLU149 4.2 24.7 1.0 O B:HOH265 4.3 39.2 1.0 CG B:ASP150 4.3 20.4 1.0 NH1 A:ARG39 4.6 20.3 1.0 O B:HOH255 4.7 29.4 1.0 NH2 A:ARG39 4.7 19.1 1.0 CZ A:ARG39 4.8 20.5 1.0 O A:HOH285 4.9 24.0 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