Magnesium in PDB 3o61: Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++

The structure of Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++, PDB code: 3o61 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)	32.40 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.276, 55.824, 158.121, 90.00, 91.71, 90.00
R / Rfree (%)	22.4 / 29

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

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and Mg++ (pdb code 3o61). 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 Gdp-Mannose and Mg++, PDB code: 3o61:
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 Gdp-Mannose and 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:44.3 occ:1.00 O A:HOH206 2.0 43.8 1.0 O2B A:GDD3846 2.0 53.7 1.0 O A:ALA85 2.3 43.8 1.0 OE2 A:GLU104 2.3 57.3 1.0 O1A A:GDD3846 2.4 52.6 1.0 OE1 A:GLU104 2.9 58.6 1.0 CD A:GLU104 3.0 57.5 1.0 PB A:GDD3846 3.4 53.9 1.0 C A:ALA85 3.4 42.1 1.0 PA A:GDD3846 3.6 56.9 1.0 NE2 A:GLN65 3.7 49.5 1.0 O3A A:GDD3846 3.8 55.3 1.0 NH2 A:ARG67 4.2 44.4 1.0 N A:ALA85 4.3 42.7 1.0 CA A:ALA85 4.3 41.5 1.0 N A:GLY86 4.4 41.5 1.0 O1B A:GDD3846 4.4 53.7 1.0 CG A:GLU104 4.4 55.3 1.0 O3B A:GDD3846 4.5 50.7 1.0 CA A:GLY86 4.5 43.4 1.0 OE1 A:GLN65 4.5 56.1 1.0 CD A:GLN65 4.6 51.3 1.0 O2A A:GDD3846 4.6 54.5 1.0 C11 A:GDD3846 4.6 53.8 1.0 CB A:ALA85 4.7 39.5 1.0 O5' A:GDD3846 4.8 57.7 1.0 CD1 A:ILE153 4.9 68.0 1.0 CD1 A:ILE63 4.9 49.1 1.0

Magnesium binding site 2 out of 4 in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:42.9 occ:1.00 OE2 B:GLU104 1.9 45.4 1.0 O1A B:GDD3846 2.1 55.9 1.0 O2B B:GDD3846 2.1 50.9 1.0 O B:ALA85 2.3 45.4 1.0 O B:HOH219 2.3 44.3 1.0 O B:HOH218 2.5 38.1 1.0 CD B:GLU104 2.9 50.1 1.0 PB B:GDD3846 3.2 54.9 1.0 OE1 B:GLU104 3.3 49.7 1.0 PA B:GDD3846 3.4 55.1 1.0 C B:ALA85 3.5 45.0 1.0 O3A B:GDD3846 3.6 56.2 1.0 O5' B:GDD3846 4.0 57.8 1.0 O3B B:GDD3846 4.1 53.7 1.0 CG B:GLU104 4.2 51.3 1.0 CA B:GLY86 4.3 45.1 1.0 N B:GLY86 4.3 45.6 1.0 N B:ALA85 4.4 45.4 1.0 CA B:ALA85 4.4 44.7 1.0 O1B B:GDD3846 4.5 51.9 1.0 OE1 B:GLN65 4.6 47.5 1.0 NE2 B:GLN65 4.6 43.8 1.0 NH2 B:ARG67 4.6 38.5 1.0 C11 B:GDD3846 4.6 52.2 1.0 O2A B:GDD3846 4.7 56.1 1.0 OE2 B:GLU151 4.8 65.4 1.0 CD1 B:ILE153 4.9 52.8 1.0 CB B:ALA85 4.9 43.4 1.0

Magnesium binding site 3 out of 4 in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:40.6 occ:1.00 O2B C:GDD3846 1.7 50.8 1.0 O C:ALA85 2.0 40.3 1.0 OE2 C:GLU104 2.1 45.1 1.0 O1A C:GDD3846 2.2 50.9 1.0 O C:HOH217 2.2 36.8 1.0 O C:HOH215 2.4 32.6 1.0 CD C:GLU104 3.0 46.9 1.0 PB C:GDD3846 3.0 54.2 1.0 C C:ALA85 3.1 40.0 1.0 OE1 C:GLU104 3.3 46.6 1.0 PA C:GDD3846 3.4 53.9 1.0 O3A C:GDD3846 3.5 52.0 1.0 NA C:NA230 3.9 51.5 1.0 O3B C:GDD3846 3.9 54.6 1.0 CA C:GLY86 3.9 39.7 1.0 N C:GLY86 3.9 39.7 1.0 N C:ALA85 4.0 41.2 1.0 CA C:ALA85 4.1 39.8 1.0 O1B C:GDD3846 4.2 52.6 1.0 O5' C:GDD3846 4.2 54.9 1.0 CG C:GLU104 4.3 46.9 1.0 C11 C:GDD3846 4.3 51.7 1.0 NH2 C:ARG67 4.3 35.8 1.0 NE2 C:GLN65 4.6 41.3 1.0 CB C:ALA85 4.6 39.3 1.0 O2A C:GDD3846 4.6 55.0 1.0 OE1 C:GLN65 4.8 42.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Gdp-Mannose and 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:39.8 occ:1.00 O1A D:GDD3846 2.1 54.9 1.0 OE2 D:GLU104 2.1 52.0 1.0 O D:ALA85 2.1 41.2 1.0 O2B D:GDD3846 2.2 52.5 1.0 O D:HOH223 2.3 34.2 1.0 CD D:GLU104 2.9 48.7 1.0 OE1 D:GLU104 3.0 48.1 1.0 PA D:GDD3846 3.3 58.0 1.0 PB D:GDD3846 3.3 56.8 1.0 C D:ALA85 3.3 40.5 1.0 O3A D:GDD3846 3.5 59.1 1.0 OE2 D:GLU151 4.0 73.1 1.0 CA D:GLY86 4.0 40.6 1.0 O5' D:GDD3846 4.1 58.5 1.0 N D:GLY86 4.1 39.8 1.0 O3B D:GDD3846 4.3 54.0 1.0 CG D:GLU104 4.4 49.0 1.0 CA D:ALA85 4.4 40.0 1.0 N D:ALA85 4.4 41.4 1.0 NE2 D:GLN65 4.5 43.0 1.0 O1B D:GDD3846 4.5 55.3 1.0 O2A D:GDD3846 4.6 57.9 1.0 NH2 D:ARG67 4.6 39.6 1.0 O D:HOH197 4.7 38.5 1.0 C11 D:GDD3846 4.7 55.0 1.0 CB D:ALA85 4.9 39.1 1.0 CD D:GLU151 4.9 74.0 1.0 CD1 D:ILE153 4.9 53.0 1.0 OE1 D:GLN65 5.0 49.5 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