Sodium 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:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the E100A E.Coli Gdp-Mannose Hydrolase (Yffh) in Complex with Mg++, PDB code: 3o69:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na210 b:16.3 occ:1.00 O A:HOH196 3.2 31.1 1.0 O B:HOH298 3.2 22.6 1.0 N A:GLU40 3.3 18.4 1.0 NH2 B:ARG44 3.4 13.6 0.5 CE2 B:PHE18 3.8 19.3 1.0 CD A:ARG39 3.9 20.5 1.0 CA A:ARG39 3.9 20.0 1.0 CB A:GLU40 3.9 17.9 1.0 NH1 B:ARG44 4.1 10.5 0.5 C A:ARG39 4.1 19.3 1.0 CA A:GLU40 4.2 17.7 1.0 CZ B:ARG44 4.2 13.6 0.5 O A:GLU40 4.3 16.4 1.0 CB A:ARG39 4.4 19.9 1.0 CD2 B:PHE18 4.5 19.1 1.0 O A:HOH203 4.5 22.0 1.0 O A:LYS38 4.6 21.9 1.0 O B:HOH345 4.6 29.6 1.0 C A:GLU40 4.7 17.1 1.0 O A:HOH197 4.7 20.0 1.0 CG A:ARG39 4.8 19.9 1.0 CZ B:PHE18 4.8 18.5 1.0 NE A:ARG39 4.9 21.1 1.0 NH2 B:ARG44 5.0 12.8 0.5 O A:HOH254 5.0 19.6 1.0

Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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 A:Na219 b:26.4 occ:1.00 OG1 A:THR2 2.1 41.0 1.0 O B:ASP152 2.6 18.8 1.0 O B:HOH413 2.7 25.3 1.0 N B:PHE66 2.8 15.2 1.0 CB A:THR2 3.4 40.6 1.0 CB B:PHE66 3.6 15.0 1.0 CA B:GLN65 3.6 15.2 1.0 C B:ASP152 3.7 18.9 1.0 C B:GLN65 3.7 15.2 1.0 CG2 A:THR2 3.7 41.5 1.0 CB B:GLN65 3.7 15.4 1.0 CA B:PHE66 3.8 14.8 1.0 CB B:ASP152 3.8 20.3 1.0 CD1 A:LEU27 4.0 24.7 1.0 CA B:ASP152 4.1 19.9 1.0 N B:ASP152 4.3 19.3 1.0 O B:HOH372 4.3 36.5 1.0 CA A:THR2 4.4 40.7 1.0 OE1 B:GLN79 4.5 16.2 1.0 OD2 B:ASP152 4.5 24.6 1.0 NE2 B:GLN79 4.5 18.0 1.0 CG B:ASP152 4.5 23.7 1.0 O B:HOH347 4.5 29.2 1.0 O B:PHE66 4.6 14.8 1.0 C B:PHE66 4.7 14.6 1.0 O B:HOH217 4.8 23.5 1.0 CD2 A:LEU27 4.8 25.6 1.0 N B:ILE153 4.8 18.2 1.0 O B:GLN65 4.9 16.1 1.0 CG A:LEU27 4.9 26.2 1.0 N A:THR2 4.9 41.0 1.0 CG B:GLN65 4.9 14.4 1.0 CD B:GLN79 4.9 18.4 1.0 N B:GLN65 5.0 15.0 1.0

Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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:Na215 b:10.7 occ:1.00 O B:HOH252 2.7 44.1 1.0 O B:HOH248 3.1 18.3 1.0 O B:HOH245 3.2 17.4 1.0 NH1 B:ARG44 3.2 11.3 0.5 O B:HOH251 3.4 17.2 1.0 O B:HOH344 3.7 20.6 1.0 NH2 B:ARG44 3.7 12.8 0.5 CA A:GLY123 3.8 14.6 1.0 CZ B:ARG44 3.9 13.1 0.5 CD2 B:LEU87 3.9 15.1 1.0 CG B:LEU87 4.1 15.9 1.0 O B:HOH218 4.2 14.5 1.0 O B:HOH247 4.3 16.1 1.0 OE2 B:GLU127 4.6 14.6 1.0 CD1 B:LEU87 4.6 15.3 1.0 N A:GLY123 4.6 15.1 1.0 O B:HOH292 4.7 17.1 1.0 C A:GLY123 4.7 14.8 1.0 O B:HOH212 4.7 17.8 1.0 O A:HOH230 4.8 13.4 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