Sodium in the structure of Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase With Adenosine & Vyp(Isp)Ha Substrate (pdb 1jg3)

The binding sites of Sodium atom in the structure of Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase With Adenosine & Vyp(Isp)Ha Substrate (pdb code 1jg3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1jg3 structure was solved by S.C.GRIFFITH, M.R.SAWAYA, D.BOUTZ, N.THAPAR, J.KATZ, S.CLARKE, T.O.YEATES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 500.0-2.1 Space group P61 a (A) 91.573 b (A) 91.573 c (A) 124.547 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.4 Rfree (%) 23.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1jg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1jg3. 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: Thr73, A: Val74, A: Ser75, A: Thr165, A: Val219, C: Pro3, C: Ias4, A: Adn500, A: Hoh1185, A: Hoh1307, conact list: Atom Atom Distance (A) Na O A:Thr73 2.57 Na N A:Thr73 3.88 Na CB A:Thr73 3.97 Na OG1 A:Thr73 2.84 Na C A:Thr73 3.36 Na CA A:Thr73 3.95 Na N A:Val74 4.30 Na C A:Val74 4.60 Na CA A:Val74 4.60 Na N A:Ser75 4.44 Na OG A:Ser75 4.24 Na O A:Thr165 4.20 Na CB A:Val219 4.60 Na CG2 A:Val219 4.11 Na O C:Pro3 4.91 Na O C:Ias4 3.12 Na C C:Ias4 3.04 Na CA C:Ias4 4.45 Na OXT C:Ias4 2.37 Na C5' A:Adn500 3.77 Na O5' A:Adn500 3.13 Na O A:Hoh1185 2.60 Na O A:Hoh1307 2.60 interactive model: Sodium binding site 2 out of 2 in 1jg3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1jg3. 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: Thr73, B: Val74, B: Ser75, B: Thr165, B: Val219, D: Pro3, D: Ias4, B: Adn550, B: Hoh1275, B: Hoh1309, B: Hoh1336, conact list: Atom Atom Distance (A) Na O B:Thr73 2.41 Na N B:Thr73 3.81 Na CB B:Thr73 3.88 Na CG2 B:Thr73 5.00 Na OG1 B:Thr73 2.78 Na C B:Thr73 3.26 Na CA B:Thr73 3.85 Na N B:Val74 4.23 Na C B:Val74 4.54 Na CA B:Val74 4.53 Na N B:Ser75 4.38 Na OG B:Ser75 4.22 Na CA B:Ser75 4.99 Na O B:Thr165 4.30 Na CB B:Val219 4.86 Na CG2 B:Val219 4.07 Na CG1 B:Val219 4.35 Na O D:Pro3 4.86 Na O D:Ias4 3.18 Na C D:Ias4 3.07 Na CA D:Ias4 4.46 Na OXT D:Ias4 2.38 Na C5' B:Adn550 3.96 Na O5' B:Adn550 3.00 Na O B:Hoh1275 4.56 Na O B:Hoh1309 2.53 Na O B:Hoh1336 2.59 interactive model: