Sodium in the structure of Mechanism Of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex With Hyaluronic Acid Disaccharide At 1.7 A Resolution (pdb 1c82)

The binding sites of Sodium atom in the structure of Mechanism Of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex With Hyaluronic Acid Disaccharide At 1.7 A Resolution (pdb code 1c82). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1c82 structure was solved by K.PONNURAJ, M.J.JEDRZEJAS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.7 Space group P212121 a (A) 83.550 b (A) 104.190 c (A) 99.880 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.5 Rfree (%) 25.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1c82 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1c82. 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: Lys584, A: Asp629, A: Ser630, A: Cac905, A: Cac907, conact list: Atom Atom Distance (A) Na NZ A:Lys584 4.19 Na O A:Asp629 4.34 Na N A:Asp629 4.95 Na CB A:Asp629 3.64 Na OD2 A:Asp629 5.00 Na C A:Asp629 3.85 Na CG A:Asp629 4.87 Na CA A:Asp629 4.35 Na N A:Ser630 3.49 Na CB A:Ser630 3.79 Na OG A:Ser630 4.81 Na CA A:Ser630 3.75 Na O1 A:Cac905 4.14 Na O2 A:Cac905 2.10 Na AS A:Cac905 3.46 Na C2 A:Cac905 3.69 Na C1 A:Cac905 4.56 Na O1 A:Cac907 4.99 Na AS A:Cac907 4.48 Na C2 A:Cac907 4.27 Na C1 A:Cac907 3.52 interactive model: Sodium binding site 2 out of 2 in 1c82 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1c82. 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: Ala628, A: Cac907, conact list: Atom Atom Distance (A) Na N A:Ala628 4.85 Na CB A:Ala628 3.66 Na CA A:Ala628 4.14 Na O1 A:Cac907 3.75 Na O2 A:Cac907 2.01 Na AS A:Cac907 3.38 Na C2 A:Cac907 4.48 Na C1 A:Cac907 4.25 interactive model: