Sodium in the structure of Crystal Structure of GP41 Derived Protein Complexed With Fab 8066 (pdb 3ma9)

The binding sites of Sodium atom in the structure of Crystal Structure of GP41 Derived Protein Complexed With Fab 8066 (pdb code 3ma9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ma9 structure was solved by M.LI, E.GUSTCHINA, J.LOUIS, A.GUSTCHINA, A.WLODAWER, M.CLORE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.4-2.0 Space group P212121 a (A) 41.527 b (A) 124.698 c (A) 133.657 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 24.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3ma9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ma9. 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: Trp30, A: Gln34, H: Trp47, H: Ser50, H: Asn58, H: Tyr98, L: Trp90, L: Val95, L: Asp96, conact list: Atom Atom Distance (A) Na CD1 A:Trp30 4.07 Na CZ2 A:Trp30 3.89 Na CE2 A:Trp30 3.76 Na NE1 A:Trp30 2.99 Na NE2 A:Gln34 4.30 Na CZ2 H:Trp47 3.95 Na CE2 H:Trp47 4.76 Na NE1 H:Trp47 4.90 Na CH2 H:Trp47 4.74 Na N H:Ser50 4.69 Na CB H:Ser50 3.13 Na OG H:Ser50 2.88 Na CA H:Ser50 4.46 Na CB H:Asn58 4.99 Na ND2 H:Asn58 3.53 Na OD1 H:Asn58 2.73 Na CG H:Asn58 3.51 Na CZ H:Tyr98 4.75 Na OH H:Tyr98 3.70 Na CE3 L:Trp90 4.12 Na CZ3 L:Trp90 3.45 Na CH2 L:Trp90 4.15 Na O L:Val95 2.73 Na CB L:Val95 3.83 Na CG2 L:Val95 3.88 Na C L:Val95 3.83 Na CA L:Val95 4.42 Na N L:Asp96 4.93 interactive model: Sodium binding site 2 out of 2 in 3ma9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ma9. 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: L: Gly24, L: Asp25, L: Asn26, L: Asn68, L: Hoh233, L: Hoh375, conact list: Atom Atom Distance (A) Na O L:Gly24 2.95 Na N L:Gly24 4.60 Na C L:Gly24 3.50 Na CA L:Gly24 3.75 Na O L:Asp25 3.77 Na N L:Asp25 4.45 Na C L:Asp25 4.43 Na ND2 L:Asn26 4.65 Na OD1 L:Asn26 3.10 Na CG L:Asn26 4.18 Na CB L:Asn68 3.77 Na ND2 L:Asn68 3.24 Na CG L:Asn68 4.01 Na O L:Hoh233 3.66 Na O L:Hoh375 3.95 interactive model: