Sodium in the structure of Crystal Structure Of the 1ST Pdz Domain of Human DLG3 (pdb 2i1n)

The binding sites of Sodium atom in the structure of Crystal Structure Of the 1ST Pdz Domain of Human DLG3 (pdb code 2i1n). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2i1n structure was solved by A.P.TURNBULL, C.PHILLIPS, G.BUNKOCZI, J.DEBRECZENI, E.UGOCHUKWU, A.C.W.PIKE, F.GORREC, C.UMEANO, J.ELKINS, G.BERRIDGE, P.SAVITSKY, O.GILEADI, F.VON DELFT, J.WEIGELT, A.EDWARDS, C.ARROWSMITH, M.SUNDSTROM, D.DOYLE, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.2-1.9 Space group C2221 a (A) 81.817 b (A) 80.545 c (A) 67.693 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 21.8 Sodium Binding Sites: Sodium binding site 1 out of 5 in 2i1n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2i1n. 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: Ile149, A: Glu193, A: Val194, A: Val195, A: Arg198, conact list: Atom Atom Distance (A) Na CD1 A:Ile149 4.72 Na O A:Glu193 4.89 Na N A:Val194 4.97 Na CB A:Val194 3.86 Na C A:Val194 3.97 Na CG1 A:Val194 4.22 Na CA A:Val194 3.67 Na N A:Val195 3.28 Na CB A:Val195 4.27 Na CG2 A:Val195 3.76 Na CG1 A:Val195 4.11 Na CA A:Val195 4.34 Na CB A:Arg198 4.31 Na CG A:Arg198 4.48 interactive model: Sodium binding site 2 out of 5 in 2i1n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2i1n. 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: Tyr129, B: Glu130, B: Glu131, B: Val213, B: Hoh321, B: Hoh364, conact list: Atom Atom Distance (A) Na O B:Tyr129 4.63 Na CB B:Tyr129 4.20 Na C B:Tyr129 4.49 Na O B:Glu130 4.88 Na N B:Glu130 4.44 Na C B:Glu130 4.42 Na CA B:Glu130 4.62 Na N B:Glu131 4.35 Na CB B:Glu131 4.77 Na CG2 B:Val213 4.97 Na CG1 B:Val213 4.22 Na O B:Hoh321 4.64 Na O B:Hoh364 4.92 interactive model: Sodium binding site 3 out of 5 in 2i1n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2i1n. 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: Glu188, B: Asp190, B: Hoh312, B: Hoh315, conact list: Atom Atom Distance (A) Na O B:Glu188 4.92 Na CB B:Asp190 4.13 Na OD2 B:Asp190 4.63 Na CG B:Asp190 4.89 Na O B:Hoh312 3.60 Na O B:Hoh315 3.36 interactive model: Sodium binding site 4 out of 5 in 2i1n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2i1n. 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: Ile165, B: Ile166, B: Pro167, B: Ala172, B: Hoh391, conact list: Atom Atom Distance (A) Na O B:Ile165 3.78 Na CB B:Ile165 4.89 Na CG2 B:Ile165 4.49 Na C B:Ile165 4.66 Na C B:Ile166 4.95 Na N B:Pro167 4.74 Na CD B:Pro167 4.88 Na CG B:Pro167 4.71 Na CA B:Pro167 4.96 Na CB B:Ala172 4.40 Na O B:Hoh391 3.91 interactive model: Sodium binding site 5 out of 5 in 2i1n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2i1n. 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: His153, A: Asn180, B: His153, B: Val154, B: Phe161, B: Asn180, A: Hoh313, A: Hoh344, B: Hoh343, B: Hoh367, conact list: Atom Atom Distance (A) Na O A:His153 4.94 Na NE2 A:His153 3.90 Na ND1 A:His153 4.66 Na CD2 A:His153 4.61 Na CE1 A:His153 3.95 Na OD1 A:Asn180 4.71 Na NE2 B:His153 4.70 Na CD2 B:His153 4.53 Na CG2 B:Val154 4.09 Na CD1 B:Phe161 4.12 Na CZ B:Phe161 4.89 Na CE1 B:Phe161 4.21 Na CG B:Phe161 4.75 Na O B:Asn180 4.45 Na CB B:Asn180 4.21 Na ND2 B:Asn180 4.98 Na OD1 B:Asn180 4.08 Na CG B:Asn180 4.23 Na CA B:Asn180 4.72 Na O A:Hoh313 4.65 Na O A:Hoh344 4.35 Na O B:Hoh343 4.73 Na O B:Hoh367 4.19 interactive model: