Sodium in the structure of Structure Of A Complex Between The Pair of The Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). (pdb 2fcw)

The binding sites of Sodium atom in the structure of Structure Of A Complex Between The Pair of The Ldl Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (Rap). (pdb code 2fcw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2fcw structure was solved by N.BEGLOVA, C.FISHER, S.C.BLACKLOW, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.3 Space group C121 a (A) 118.523 b (A) 30.019 c (A) 58.143 alpha (°) 90.00 beta (°) 96.57 gamma (°) 90.00 Rfactor (%) 15.2 Rfree (%) 20.1 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2fcw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2fcw. 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: Glu265, A: Glu269, B: Gln104, A: Hoh14, A: Hoh55, A: Hoh61, A: Hoh73, B: Hoh5023, conact list: Atom Atom Distance (A) Na OE1 A:Glu265 4.56 Na OE2 A:Glu265 2.42 Na CD A:Glu265 3.49 Na CG A:Glu265 3.91 Na OE1 A:Glu269 3.48 Na OE2 A:Glu269 2.28 Na CD A:Glu269 3.22 Na CG A:Glu269 4.59 Na OE1 B:Gln104 4.65 Na O A:Hoh14 4.64 Na O A:Hoh55 4.32 Na O A:Hoh61 2.27 Na O A:Hoh73 2.36 Na O B:Hoh5023 2.41 interactive model: Sodium binding site 2 out of 4 in 2fcw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2fcw. 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: Ile224, A: Asp228, A: Hoh34, A: Hoh68, A: Hoh110, A: Hoh162, A: Hoh174, conact list: Atom Atom Distance (A) Na CG2 A:Ile224 3.90 Na CB A:Asp228 4.93 Na OD2 A:Asp228 2.64 Na OD1 A:Asp228 3.75 Na CG A:Asp228 3.55 Na O A:Hoh34 4.35 Na O A:Hoh68 3.03 Na O A:Hoh110 2.54 Na O A:Hoh162 3.92 Na O A:Hoh174 3.33 interactive model: Sodium binding site 3 out of 4 in 2fcw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2fcw. 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: Asp237, A: Leu240, A: Hoh40, A: Hoh91, A: Hoh121, A: Hoh130, conact list: Atom Atom Distance (A) Na OD1 A:Asp237 4.89 Na CD2 A:Leu240 3.60 Na O A:Hoh40 3.26 Na O A:Hoh91 3.06 Na O A:Hoh121 2.99 Na O A:Hoh130 3.65 interactive model: Sodium binding site 4 out of 4 in 2fcw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2fcw. 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: Lys86, B: Thr87, B: Cys88, B: Gly98, B: Lys99, B: Cys100, B: Hoh5003, B: Hoh5004, B: Hoh5012, B: Hoh5014, B: Hoh5022, conact list: Atom Atom Distance (A) Na O B:Lys86 2.31 Na N B:Lys86 3.91 Na C B:Lys86 3.53 Na CG B:Lys86 4.86 Na CA B:Lys86 4.35 Na N B:Thr87 4.50 Na C B:Thr87 4.93 Na CA B:Thr87 4.66 Na N B:Cys88 4.78 Na SG B:Cys88 4.03 Na O B:Gly98 2.24 Na C B:Gly98 3.38 Na CA B:Gly98 4.15 Na N B:Lys99 4.32 Na C B:Lys99 4.65 Na CA B:Lys99 4.43 Na N B:Cys100 4.63 Na SG B:Cys100 3.72 Na O B:Hoh5003 2.28 Na O B:Hoh5004 2.47 Na O B:Hoh5012 2.50 Na O B:Hoh5014 3.91 Na O B:Hoh5022 4.62 interactive model: