Sodium in the structure of Axh Domain of Human Spinocerebellar Ataxin-1 (pdb 1oa8)

The binding sites of Sodium atom in the structure of Axh Domain of Human Spinocerebellar Ataxin-1 (pdb code 1oa8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1oa8 structure was solved by M.D.ALLEN, Y.W.CHEN, M.BYCROFT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 70.7-1.7 Space group P212121 a (A) 48.783 b (A) 82.441 c (A) 137.781 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 25.2 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1oa8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1oa8. 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: Ala603, A: Glu604, A: Ile605, A: Ser606, A: Asn607, A: Leu609, A: Lys610, A: Lys689, A: Hoh2033, A: Hoh2096, conact list: Atom Atom Distance (A) Na O A:Ala603 2.37 Na C A:Ala603 3.42 Na CB A:Ala603 4.88 Na CA A:Ala603 4.44 Na O A:Glu604 3.89 Na N A:Glu604 4.16 Na C A:Glu604 4.10 Na CA A:Glu604 4.19 Na N A:Ile605 4.84 Na C A:Ile605 4.92 Na O A:Ser606 2.56 Na N A:Ser606 4.46 Na CB A:Ser606 4.43 Na C A:Ser606 3.71 Na CA A:Ser606 4.44 Na N A:Asn607 4.72 Na CA A:Asn607 4.86 Na O A:Leu609 2.60 Na N A:Leu609 4.69 Na C A:Leu609 3.80 Na CA A:Leu609 4.84 Na N A:Lys610 4.57 Na CB A:Lys610 4.86 Na CA A:Lys610 4.46 Na CE A:Lys689 4.21 Na CD A:Lys689 4.47 Na NZ A:Lys689 3.45 Na O A:Hoh2033 4.47 Na O A:Hoh2096 2.11 interactive model: Sodium binding site 2 out of 3 in 1oa8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1oa8. 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: Gly655, B: Gln656, C: Ala603, C: Glu604, C: Ser606, C: Asn607, C: Leu609, C: Lys610, C: Lys689, B: Hoh2048, B: Hoh2049, B: Hoh2056, B: Hoh2057, conact list: Atom Atom Distance (A) Na O B:Gly655 4.54 Na NE2 B:Gln656 4.74 Na CG B:Gln656 5.00 Na O C:Ala603 2.08 Na C C:Ala603 3.27 Na CB C:Ala603 4.63 Na CA C:Ala603 4.06 Na O C:Glu604 4.52 Na N C:Glu604 4.30 Na C C:Glu604 4.59 Na CA C:Glu604 4.52 Na O C:Ser606 2.27 Na N C:Ser606 4.36 Na CB C:Ser606 4.72 Na OG C:Ser606 4.53 Na C C:Ser606 3.51 Na CA C:Ser606 4.38 Na O C:Asn607 4.94 Na N C:Asn607 4.47 Na C C:Asn607 4.70 Na CA C:Asn607 4.50 Na O C:Leu609 2.26 Na N C:Leu609 4.34 Na C C:Leu609 3.50 Na CA C:Leu609 4.51 Na N C:Lys610 4.35 Na CB C:Lys610 4.77 Na CA C:Lys610 4.31 Na CB C:Lys689 4.85 Na O B:Hoh2048 3.86 Na O B:Hoh2049 2.38 Na O B:Hoh2056 2.66 Na O B:Hoh2057 4.58 interactive model: Sodium binding site 3 out of 3 in 1oa8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1oa8. 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: D: Ala603, D: Glu604, D: Ser606, D: Asn607, D: Leu609, D: Lys610, D: Lys689, D: Hoh2115, conact list: Atom Atom Distance (A) Na O D:Ala603 2.26 Na C D:Ala603 3.42 Na CB D:Ala603 4.81 Na CA D:Ala603 4.21 Na O D:Glu604 4.43 Na N D:Glu604 4.43 Na C D:Glu604 4.53 Na CA D:Glu604 4.60 Na O D:Ser606 2.33 Na N D:Ser606 4.22 Na CB D:Ser606 4.72 Na OG D:Ser606 4.50 Na C D:Ser606 3.52 Na CA D:Ser606 4.32 Na O D:Asn607 4.81 Na N D:Asn607 4.51 Na C D:Asn607 4.64 Na CA D:Asn607 4.69 Na O D:Leu609 2.24 Na N D:Leu609 4.17 Na CB D:Leu609 4.86 Na C D:Leu609 3.50 Na CA D:Leu609 4.38 Na N D:Lys610 4.40 Na CB D:Lys610 4.98 Na CA D:Lys610 4.40 Na CE D:Lys689 3.40 Na CD D:Lys689 4.85 Na NZ D:Lys689 3.70 Na O D:Hoh2115 2.34 interactive model: