Sodium in the structure of Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant (pdb 3f72)

The binding sites of Sodium atom in the structure of Crystal Structure of the Staphylococcus Aureus PI258 Cadc Metal Binding Site 2 Mutant (pdb code 3f72). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3f72 structure was solved by A.KANDEGEDARA, S.THIYAGARAJAN, K.C.KONDAPALLI, T.L.STEMMLER, B.P.ROSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.3-2.3 Space group P43 a (A) 89.471 b (A) 89.471 c (A) 148.536 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.7 Rfree (%) 28.8 Sodium Binding Sites: Sodium binding site 1 out of 5 in 3f72 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3f72. 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: Ala63, A: Asn64, A: Gly67, A: Val68, conact list: Atom Atom Distance (A) Na O A:Ala63 4.26 Na C A:Ala63 4.77 Na O A:Asn64 4.00 Na N A:Asn64 4.62 Na CB A:Asn64 4.15 Na ND2 A:Asn64 4.67 Na C A:Asn64 4.39 Na OD1 A:Asn64 2.46 Na CG A:Asn64 3.54 Na CA A:Asn64 3.70 Na N A:Gly67 4.76 Na C A:Gly67 4.69 Na CA A:Gly67 4.07 Na N A:Val68 4.98 interactive model: Sodium binding site 2 out of 5 in 3f72 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3f72. 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: Arg44, A: His75, A: Hoh145, conact list: Atom Atom Distance (A) Na CZ A:Arg44 4.25 Na NH2 A:Arg44 3.92 Na NH1 A:Arg44 3.64 Na NE2 A:His75 3.98 Na ND1 A:His75 4.85 Na CE1 A:His75 3.62 Na O A:Hoh145 4.45 interactive model: Sodium binding site 3 out of 5 in 3f72 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3f72. 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: His114, B: Gly101, B: Glu102, B: Ala103, A: Hoh141, B: Hoh138, conact list: Atom Atom Distance (A) Na ND1 A:His114 4.52 Na O B:Gly101 4.85 Na C B:Gly101 3.83 Na CA B:Gly101 3.73 Na N B:Glu102 3.32 Na CB B:Glu102 4.16 Na C B:Glu102 4.30 Na CA B:Glu102 4.08 Na N B:Ala103 3.52 Na CB B:Ala103 3.89 Na CA B:Ala103 4.34 Na O A:Hoh141 4.98 Na O B:Hoh138 2.33 interactive model: Sodium binding site 4 out of 5 in 3f72 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3f72. 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: Arg44, B: His75, B: His76, B: Thr79, conact list: Atom Atom Distance (A) Na CD B:Arg44 4.88 Na CZ B:Arg44 4.20 Na NE B:Arg44 3.79 Na NH2 B:Arg44 3.63 Na O B:His75 4.30 Na NE2 B:His75 3.83 Na CD2 B:His75 3.41 Na C B:His75 4.54 Na CE1 B:His75 4.96 Na CG B:His75 4.46 Na NE2 B:His76 4.94 Na N B:His76 4.49 Na CB B:His76 4.64 Na ND1 B:His76 3.29 Na CE1 B:His76 3.85 Na CG B:His76 4.25 Na CA B:His76 4.14 Na CB B:Thr79 4.39 Na CG2 B:Thr79 4.74 Na OG1 B:Thr79 3.58 interactive model: Sodium binding site 5 out of 5 in 3f72 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3f72. 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: F: Arg44, F: His75, F: His76, F: Thr79, conact list: Atom Atom Distance (A) Na CZ F:Arg44 4.29 Na NE F:Arg44 4.13 Na NH2 F:Arg44 3.48 Na O F:His75 4.98 Na ND1 F:His75 3.56 Na C F:His75 4.98 Na CE1 F:His75 3.98 Na CG F:His75 4.82 Na NE2 F:His76 3.76 Na N F:His76 4.80 Na CD2 F:His76 3.37 Na CE1 F:His76 4.84 Na CG F:His76 4.37 Na CA F:His76 4.65 Na CB F:Thr79 4.63 Na CG2 F:Thr79 4.71 Na OG1 F:Thr79 4.27 interactive model: