Sodium in the structure of Crystal Structure of The Uncharacterized Lipoprotein Yceb From E. Coli At the Resolution 2.0A. Northeast Structural Genomics Consortium Target ER542 (pdb 3l6i)

The binding sites of Sodium atom in the structure of Crystal Structure of The Uncharacterized Lipoprotein Yceb From E. Coli At the Resolution 2.0A. Northeast Structural Genomics Consortium Target ER542 (pdb code 3l6i). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3l6i structure was solved by A.P.KUZIN, H.NEELY, J.SEETHARAMAN, C.X.CHEN, H.JANJUA, K.CUNNINGHAM, L-.C.MA, R.XIAO, J.LIU, M.C.BARAN, T.B.ACTON, B.ROST, G.T.MONTELIONE, L.TONG, J.F.HUNT, NORTHEAST STRUCTURALGENOMICS CONSORTIUM (NESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-2.0 Space group C222 a (A) 109.050 b (A) 174.550 c (A) 43.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 24.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3l6i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3l6i. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gln133, A: Ala134, A: Asn137, A: Hoh218, A: Hoh253, conact list: Atom Atom Distance (A) Na O A:Gln133 4.11 Na OE1 A:Gln133 3.45 Na CB A:Gln133 4.86 Na CD A:Gln133 4.15 Na C A:Gln133 4.26 Na CG A:Gln133 3.98 Na O A:Ala134 4.86 Na N A:Ala134 4.05 Na C A:Ala134 4.74 Na CB A:Ala134 4.14 Na CA A:Ala134 3.61 Na CB A:Asn137 4.13 Na ND2 A:Asn137 3.30 Na CG A:Asn137 4.20 Na O A:Hoh218 3.43 Na O A:Hoh253 4.66 interactive model: Sodium binding site 2 out of 2 in 3l6i Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3l6i. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Gln133, B: Ala134, B: Asn137, B: Hoh213, conact list: Atom Atom Distance (A) Na O B:Gln133 4.22 Na NE2 B:Gln133 3.40 Na CB B:Gln133 4.86 Na CD B:Gln133 4.14 Na C B:Gln133 4.31 Na CG B:Gln133 3.84 Na O B:Ala134 4.98 Na N B:Ala134 4.08 Na C B:Ala134 4.87 Na CB B:Ala134 4.14 Na CA B:Ala134 3.70 Na CB B:Asn137 4.45 Na ND2 B:Asn137 3.53 Na CG B:Asn137 4.47 Na O B:Hoh213 3.35 interactive model: