Sodium in the structure of Crystal Structure of The Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex With the Large Ribosomal Subunit (pdb 3pip)

The binding sites of Sodium atom in the structure of Crystal Structure of The Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex With the Large Ribosomal Subunit (pdb code 3pip). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3pip structure was solved by M.J.BELOUSOFF, T.SHAPIRA, A.BASHAN, E.ZIMMERMAN, H.KINASHI, H.ROZENBERG, A.YONATH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.5 Space group I222 a (A) 169.723 b (A) 408.562 c (A) 693.334 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 25.7 Rfree (%) 30.1 Sodium Binding Sites: Sodium binding site 1 out of 5 in 3pip Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pip. 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: X: U2057, X: A2060, X: G2217, X: A2220, X: G2221, X: U2222, conact list: Atom Atom Distance (A) Na O4 X:U2057 4.39 Na N6 X:A2060 4.68 Na C8 X:G2217 4.26 Na N7 X:G2217 4.28 Na C8 X:A2220 4.51 Na C6 X:A2220 4.00 Na C5 X:A2220 3.98 Na N6 X:A2220 3.39 Na N7 X:A2220 3.51 Na C6 X:G2221 4.62 Na C5 X:G2221 4.94 Na N7 X:G2221 4.46 Na O6 X:G2221 3.72 Na C4 X:U2222 4.99 Na O4 X:U2222 4.20 interactive model: Sodium binding site 2 out of 5 in 3pip Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pip. 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: X: G1670, X: A1984, X: G1985, X: G1986, X: G1987, conact list: Atom Atom Distance (A) Na N2 X:G1670 4.15 Na N6 X:A1984 4.97 Na N7 X:A1984 4.78 Na C8 X:G1985 4.59 Na C6 X:G1985 3.89 Na C5 X:G1985 4.00 Na N7 X:G1985 3.42 Na O6 X:G1985 3.15 Na C6 X:G1986 4.48 Na C5 X:G1986 4.93 Na N7 X:G1986 4.56 Na O6 X:G1986 3.44 Na O6 X:G1987 4.55 interactive model: Sodium binding site 3 out of 5 in 3pip Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3pip. 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: X: A1693, X: A1694, X: G1975, X: U1976, conact list: Atom Atom Distance (A) Na N3 X:A1693 3.41 Na C2 X:A1693 3.23 Na N1 X:A1693 4.34 Na C4 X:A1693 4.70 Na N9 X:A1694 4.20 Na N3 X:A1694 3.88 Na C2 X:A1694 4.83 Na C1' X:A1694 3.50 Na O4' X:A1694 3.61 Na C4 X:A1694 4.33 Na C2' X:A1694 4.63 Na C4' X:A1694 4.86 Na O2' X:A1694 4.53 Na C3' X:G1975 4.61 Na O3' X:G1975 3.99 Na C5' X:G1975 4.93 Na C4' X:G1975 4.71 Na OP1 X:U1976 4.66 Na C6 X:U1976 4.85 Na P X:U1976 4.22 Na O4' X:U1976 3.88 Na C5' X:U1976 3.12 Na C4' X:U1976 4.08 Na O5' X:U1976 3.13 interactive model: Sodium binding site 4 out of 5 in 3pip Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3pip. 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: X: A168, X: C169, X: C180, X: G812, X: A813, X: A815, conact list: Atom Atom Distance (A) Na C2 X:A168 4.74 Na C6 X:A168 4.74 Na N1 X:A168 4.05 Na N6 X:A168 4.65 Na N3 X:C169 3.90 Na C2 X:C169 4.67 Na O2 X:C169 4.44 Na C4 X:C169 4.76 Na N4 X:C169 4.59 Na O2' X:C180 4.92 Na C3' X:G812 4.79 Na O3' X:G812 4.30 Na C2' X:G812 4.16 Na O2' X:G812 3.88 Na OP1 X:A813 2.05 Na C8 X:A813 4.64 Na P X:A813 3.49 Na N7 X:A813 4.74 Na OP2 X:A813 4.17 Na O5' X:A813 4.50 Na O2' X:A815 4.83 interactive model: Sodium binding site 5 out of 5 in 3pip Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3pip. 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: X: U187, X: G188, X: A189, conact list: Atom Atom Distance (A) Na C5 X:U187 4.52 Na C4 X:U187 4.51 Na O4 X:U187 4.15 Na N7 X:G188 4.62 Na O6 X:G188 4.22 Na N6 X:A189 3.94 interactive model: