Sodium 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:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:51.8 occ:1.00 OG1 A:THR19 2.6 38.8 1.0 CB A:THR19 3.4 40.1 1.0 CG2 A:THR19 3.8 40.0 1.0 OD1 A:ASP15 4.3 49.4 1.0 OD2 A:ASP43 4.5 38.0 1.0 NE2 A:HIS21 4.7 39.6 1.0 CA A:THR19 4.8 39.0 1.0 N A:THR19 5.0 40.9 1.0

Sodium binding site 2 out of 2 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 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 Gdp-Mannose and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ C:Na230 b:51.5 occ:1.00 O C:HOH217 2.4 36.8 1.0 OE2 C:GLU82 2.7 42.5 1.0 NH2 C:ARG67 3.0 35.8 1.0 O C:SER83 3.1 39.8 1.0 CD C:GLU82 3.3 41.2 1.0 CB C:ALA85 3.6 39.3 1.0 O2B C:GDD3846 3.6 50.8 1.0 N C:ALA85 3.7 41.2 1.0 NE2 C:GLN65 3.7 41.3 1.0 CE C:LYS176 3.8 36.7 1.0 NZ C:LYS176 3.8 34.8 1.0 MG C:MG202 3.9 40.6 1.0 OE1 C:GLU82 3.9 45.1 1.0 O51 C:GDD3846 4.0 51.8 1.0 CG C:GLU82 4.0 39.0 1.0 CB C:GLU82 4.1 38.6 1.0 CA C:ALA85 4.1 39.8 1.0 O C:ALA85 4.2 40.3 1.0 C C:SER83 4.2 40.1 1.0 CZ C:ARG67 4.3 35.8 1.0 C C:CYS84 4.3 41.5 1.0 C11 C:GDD3846 4.4 51.7 1.0 C C:ALA85 4.5 40.0 1.0 OE1 C:GLU104 4.6 46.6 1.0 CA C:CYS84 4.6 42.0 1.0 NE C:ARG67 4.8 33.9 1.0 N C:CYS84 4.8 42.3 1.0 CD C:GLN65 4.9 40.6 1.0 PB C:GDD3846 4.9 54.2 1.0 OE2 C:GLU104 5.0 45.1 1.0 O C:HOH215 5.0 32.6 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