Sodium in the structure of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability (pdb 1iyn)

The binding sites of Sodium atom in the structure of Crystal Structure of Chloroplastic Ascorbate Peroxidase From Tobacco Plants and Structural Insights For Its Instability (pdb code 1iyn). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1iyn structure was solved by K.WADA, T.TADA, Y.NAKAMURA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.6 Space group P212121 a (A) 37.188 b (A) 76.790 c (A) 98.776 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 22.2 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1iyn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1iyn. 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: Thr164, A: Leu165, A: Thr196, A: Gln198, A: Trp199, A: Leu200, A: Lys201, A: Phe202, A: Asp203, A: Hoh312, A: Hoh328, conact list: Atom Atom Distance (A) Na O A:Thr164 2.41 Na CB A:Thr164 3.66 Na CG2 A:Thr164 4.21 Na OG1 A:Thr164 2.62 Na C A:Thr164 3.34 Na CA A:Thr164 3.78 Na N A:Leu165 4.49 Na CD2 A:Leu165 5.00 Na CA A:Leu165 4.96 Na CB A:Thr196 3.64 Na CG2 A:Thr196 4.02 Na OG1 A:Thr196 2.75 Na O A:Gln198 2.53 Na N A:Gln198 4.80 Na CB A:Gln198 4.67 Na C A:Gln198 3.48 Na CA A:Gln198 4.54 Na N A:Trp199 4.10 Na C A:Trp199 4.38 Na CA A:Trp199 3.92 Na O A:Trp199 4.97 Na N A:Leu200 4.66 Na O A:Lys201 2.47 Na N A:Lys201 4.05 Na CB A:Lys201 4.30 Na C A:Lys201 3.61 Na CA A:Lys201 4.21 Na N A:Phe202 4.70 Na CA A:Phe202 4.91 Na N A:Asp203 4.80 Na OD2 A:Asp203 3.96 Na OD1 A:Asp203 4.98 Na CG A:Asp203 4.68 Na O A:Hoh312 2.86 Na O A:Hoh328 4.73 interactive model: Sodium binding site 2 out of 2 in 1iyn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1iyn. 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: Asp35, A: Thr38, A: Gly50, A: Gly51, A: Ala52, A: Asn53, A: Gly54, A: Ser55, A: Leu56, A: Glu61, A: Pro125, A: Hoh306, A: Hoh317, conact list: Atom Atom Distance (A) Na O A:Asp35 3.38 Na CB A:Asp35 4.46 Na OD2 A:Asp35 2.53 Na C A:Asp35 4.11 Na OD1 A:Asp35 4.00 Na CG A:Asp35 3.44 Na CA A:Asp35 4.26 Na OG1 A:Thr38 4.15 Na C A:Gly50 4.72 Na O A:Gly51 2.42 Na N A:Gly51 4.06 Na C A:Gly51 3.61 Na CA A:Gly51 4.39 Na N A:Ala52 4.61 Na C A:Ala52 4.79 Na CA A:Ala52 4.78 Na N A:Asn53 3.84 Na CB A:Asn53 4.47 Na ND2 A:Asn53 3.75 Na C A:Asn53 4.52 Na OD1 A:Asn53 2.45 Na CG A:Asn53 3.30 Na CA A:Asn53 4.47 Na N A:Gly54 4.25 Na C A:Gly54 4.73 Na CA A:Gly54 4.95 Na N A:Ser55 3.69 Na CB A:Ser55 3.62 Na OG A:Ser55 2.57 Na C A:Ser55 4.64 Na CA A:Ser55 4.16 Na N A:Leu56 4.23 Na OE1 A:Glu61 4.47 Na OE2 A:Glu61 4.29 Na CD A:Glu61 4.84 Na CD A:Pro125 4.79 Na O A:Hoh306 2.45 Na O A:Hoh317 4.58 interactive model: