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 |
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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:
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