Sodium in PDB 3l8g: Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate

The structure of Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate, PDB code: 3l8g was solved by H.Nguyen, E.Peisach, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.34 / 2.18
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.669, 51.572, 52.185, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25.5

The structure of Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate (pdb code 3l8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate, PDB code: 3l8g:

Sodium binding site 1 out of 1 in the Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli Complexed with D-Glycero-D-Manno-Heptose 1 ,7-Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na190 b:47.9 occ:1.00 OH A:TYR22 2.8 50.1 1.0 OP3 A:GMB3523 3.0 47.8 1.0 O1 A:GMB3523 3.0 53.3 1.0 OG A:SER56 3.1 33.5 1.0 P1 A:GMB3523 3.4 57.3 1.0 CZ A:TYR22 3.6 45.6 1.0 CE1 A:TYR22 3.7 41.5 1.0 OP1 A:GMB3523 3.7 42.1 1.0 C1 A:GMB3523 3.8 46.2 1.0 CB A:SER56 4.2 31.0 1.0 C2 A:GMB3523 4.4 46.7 1.0 O A:HOH249 4.7 32.1 1.0 OP2 A:GMB3523 4.9 51.3 1.0 CE2 A:TYR22 4.9 44.1 1.0 O A:HOH197 4.9 32.0 1.0 CD1 A:TYR22 4.9 41.9 1.0 CD2 A:HIS95 5.0 29.1 1.0

H.H.Nguyen, L.Wang, H.Huang, E.Peisach, D.Dunaway-Mariano, K.N.Allen. Structural Determinants of Substrate Recognition in the Had Superfamily Member D-Glycero-D-Manno-Heptose-1,7-Bisphosphate Phosphatase (Gmhb) . Biochemistry V. 49 1082 2010.
ISSN: ISSN 0006-2960
PubMed: 20050614
DOI: 10.1021/BI902019Q