Sodium in the structure of Xylanase XYN10A From Streptomyces Lividans in Complex With Xylobio-Isofagomine Lactam (pdb 1od8)

The binding sites of Sodium atom in the structure of Xylanase XYN10A From Streptomyces Lividans in Complex With Xylobio-Isofagomine Lactam (pdb code 1od8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1od8 structure was solved by T.M.GLOSTER, S.ROBERTS, G.J.DAVIES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-1.1 Space group P212121 a (A) 65.814 b (A) 45.878 c (A) 85.737 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 10.3 Rfree (%) 12.6 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1od8. 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: Thr294, A: Ala295, A: Leu297, A: Asp298, A: Hoh2009, A: Hoh2303, A: Hoh2308, A: Hoh2606, A: Hoh2609, A: Hoh2611, A: Hoh2612, conact list: Atom Atom Distance (A) Na O A:Thr294 2.95 Na CB A:Thr294 4.12 Na CG2 A:Thr294 3.34 Na OG1 A:Thr294 4.67 Na C A:Thr294 3.74 Na CA A:Thr294 3.78 Na N A:Ala295 4.99 Na O A:Leu297 4.95 Na N A:Leu297 4.95 Na CB A:Leu297 3.75 Na CD2 A:Leu297 3.89 Na C A:Leu297 4.15 Na CG A:Leu297 4.03 Na CA A:Leu297 4.47 Na N A:Asp298 3.46 Na CB A:Asp298 3.70 Na CB A:Asp298 3.77 Na OD2 A:Asp298 1.86 Na OD1 A:Asp298 3.29 Na CG A:Asp298 4.88 Na CG A:Asp298 2.72 Na CA A:Asp298 3.88 Na O A:Hoh2009 4.51 Na O A:Hoh2303 2.41 Na O A:Hoh2308 4.44 Na O A:Hoh2606 3.31 Na O A:Hoh2609 3.06 Na O A:Hoh2611 4.38 Na O A:Hoh2612 4.94 interactive model: Sodium binding site 2 out of 4 in 1od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1od8. 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: Asp298, A: Asn301, A: Gly302, A: Gly303, A: Hoh2611, A: Hoh2617, conact list: Atom Atom Distance (A) Na O A:Asp298 3.81 Na CB A:Asp298 4.97 Na OD2 A:Asp298 4.07 Na C A:Asp298 4.69 Na OD1 A:Asp298 3.17 Na CG A:Asp298 3.91 Na O A:Asn301 4.53 Na C A:Asn301 4.64 Na O A:Gly302 1.92 Na N A:Gly302 4.43 Na C A:Gly302 2.81 Na CA A:Gly302 4.16 Na N A:Gly303 3.05 Na O A:Hoh2611 3.96 Na O A:Hoh2617 4.23 interactive model: Sodium binding site 3 out of 4 in 1od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1od8. 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: Glu2, A: Ser3, A: Thr4, A: Ala7, A: Hoh2014, conact list: Atom Atom Distance (A) Na O A:Glu2 4.65 Na N A:Glu2 4.51 Na OE1 A:Glu2 2.10 Na CB A:Glu2 3.00 Na OE2 A:Glu2 4.14 Na CD A:Glu2 3.06 Na C A:Glu2 3.44 Na CG A:Glu2 3.53 Na CA A:Glu2 3.11 Na N A:Ser3 2.84 Na CB A:Ser3 4.07 Na OG A:Ser3 3.55 Na C A:Ser3 4.62 Na CA A:Ser3 3.95 Na N A:Thr4 4.30 Na OG1 A:Thr4 4.70 Na CB A:Ala7 4.02 Na O A:Hoh2014 2.78 interactive model: Sodium binding site 4 out of 4 in 1od8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1od8. 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: Ser3, A: Thr4, A: Arg36, A: Hoh2014, A: Hoh2040, A: Hoh2042, A: Hoh2102, conact list: Atom Atom Distance (A) Na OG A:Ser3 4.69 Na CB A:Thr4 4.79 Na CG2 A:Thr4 3.73 Na OG1 A:Thr4 4.55 Na O A:Arg36 4.62 Na CG A:Arg36 4.26 Na O A:Hoh2014 3.33 Na O A:Hoh2040 4.47 Na O A:Hoh2042 4.11 Na O A:Hoh2102 2.71 interactive model: