Sodium in the structure of Crystal Structure of the Non-Neutralizing Hiv Antibody 13H11 Fab Fragment With A GP41 Mper-Derived Peptide Bearing Ala Substitutions in A Helical Conformation (pdb 3mnz)

The binding sites of Sodium atom in the structure of Crystal Structure of the Non-Neutralizing Hiv Antibody 13H11 Fab Fragment With A GP41 Mper-Derived Peptide Bearing Ala Substitutions in A Helical Conformation (pdb code 3mnz). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3mnz structure was solved by N.I.NICELY, S.M.DENNISON, G.KELSOE, H.-X.LIAO, S.M.ALAM, B.F.HAYNES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.0-1.8 Space group P21212 a (A) 66.890 b (A) 121.692 c (A) 58.097 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3mnz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3mnz. 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: Pro9, B: Glu10, B: Leu11, B: Thr108, B: Leu109, B: Thr110, B: Hoh259, B: Hoh311, B: Hoh363, B: Hoh364, B: Hoh365, B: Hoh378, B: Hoh542, conact list: Atom Atom Distance (A) Na CB B:Pro9 3.91 Na C B:Pro9 4.31 Na CA B:Pro9 4.34 Na O B:Glu10 2.90 Na N B:Glu10 3.68 Na C B:Glu10 3.79 Na CA B:Glu10 4.36 Na N B:Leu11 4.75 Na CD2 B:Leu11 3.82 Na CG B:Leu11 4.76 Na O B:Thr108 3.38 Na CB B:Thr108 3.76 Na OG1 B:Thr108 2.99 Na C B:Thr108 3.56 Na CA B:Thr108 4.33 Na O B:Leu109 4.62 Na N B:Leu109 3.79 Na C B:Leu109 3.83 Na CA B:Leu109 3.85 Na N B:Thr110 3.51 Na CB B:Thr110 3.90 Na OG1 B:Thr110 3.23 Na CA B:Thr110 4.32 Na O B:Hoh259 4.83 Na O B:Hoh311 4.63 Na O B:Hoh363 2.91 Na O B:Hoh364 4.99 Na O B:Hoh365 4.98 Na O B:Hoh378 4.47 Na O B:Hoh542 4.74 interactive model: