Sodium in the structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex With Aps (pdb 1g8g)

The binding sites of Sodium atom in the structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex With Aps (pdb code 1g8g). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1g8g structure was solved by T.C.ULLRICH, M.BLAESSE, R.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-2.6 Space group H32 a (A) 185.922 b (A) 185.922 c (A) 223.674 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.6 Rfree (%) 22.7 Sodium Binding Sites: Sodium binding site 1 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1g8g. 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: Asp107, A: Asp108, A: Hoh971, A: Hoh1135, conact list: Atom Atom Distance (A) Na O A:Asp107 4.46 Na CB A:Asp108 4.69 Na O A:Hoh971 4.56 Na O A:Hoh1135 2.29 interactive model: Sodium binding site 2 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1g8g. 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: Arg134, A: Gly306, A: Asp309, A: Hoh762, A: Hoh1173, A: Hoh1174, A: Hoh1190, conact list: Atom Atom Distance (A) Na NH2 A:Arg134 4.91 Na NH1 A:Arg134 4.85 Na N A:Gly306 4.35 Na CA A:Gly306 4.33 Na CB A:Asp309 4.59 Na OD2 A:Asp309 2.68 Na OD1 A:Asp309 2.88 Na CG A:Asp309 3.12 Na O A:Hoh762 4.88 Na O A:Hoh1173 2.46 Na O A:Hoh1174 4.33 Na O A:Hoh1190 2.18 interactive model: Sodium binding site 3 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1g8g. 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: Asp322, A: Hoh740, A: Hoh1161, conact list: Atom Atom Distance (A) Na O A:Asp322 4.85 Na CB A:Asp322 4.40 Na OD2 A:Asp322 2.73 Na OD1 A:Asp322 2.35 Na CG A:Asp322 2.88 Na O A:Hoh740 2.30 Na O A:Hoh1161 4.54 interactive model: Sodium binding site 4 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1g8g. 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: Thr126, A: Glu130, A: Hoh693, A: Hoh1002, A: Hoh1101, A: Hoh1131, conact list: Atom Atom Distance (A) Na CG2 A:Thr126 4.33 Na OE1 A:Glu130 2.13 Na OE2 A:Glu130 2.65 Na CD A:Glu130 2.72 Na CG A:Glu130 4.23 Na O A:Hoh693 4.66 Na O A:Hoh1002 2.78 Na O A:Hoh1101 2.57 Na O A:Hoh1131 4.74 interactive model: Sodium binding site 5 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1g8g. 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: Arg190, A: His285, A: Glu324, A: Hoh985, A: Hoh1116, conact list: Atom Atom Distance (A) Na NH1 A:Arg190 4.14 Na NE2 A:His285 4.00 Na CD2 A:His285 4.83 Na CE1 A:His285 4.95 Na OE1 A:Glu324 4.19 Na OE2 A:Glu324 2.26 Na CD A:Glu324 3.38 Na CG A:Glu324 4.25 Na O A:Hoh985 2.57 Na O A:Hoh1116 4.85 interactive model: Sodium binding site 6 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1g8g. 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: Asp505, A: Hoh930, A: Hoh987, conact list: Atom Atom Distance (A) Na O A:Asp505 4.73 Na CB A:Asp505 4.29 Na OD2 A:Asp505 2.50 Na OD1 A:Asp505 2.50 Na CG A:Asp505 2.81 Na O A:Hoh930 1.94 Na O A:Hoh987 2.46 interactive model: Sodium binding site 7 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1g8g. 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: Asp107, B: Asp108, B: Glu109, B: Hoh821, B: Hoh851, conact list: Atom Atom Distance (A) Na O B:Asp107 4.49 Na CB B:Asp108 4.99 Na OE1 B:Glu109 4.64 Na O B:Hoh821 2.75 Na O B:Hoh851 2.35 interactive model: Sodium binding site 8 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1g8g. 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: Arg134, B: Gly306, B: Asp309, B: Glu312, B: Hoh809, B: Hoh897, B: Hoh902, B: Hoh1010, B: Hoh1111, B: Hoh1141, conact list: Atom Atom Distance (A) Na NH2 B:Arg134 4.76 Na NH1 B:Arg134 4.63 Na N B:Gly306 4.80 Na CA B:Gly306 4.92 Na CB B:Asp309 4.32 Na OD2 B:Asp309 2.72 Na OD1 B:Asp309 2.94 Na CG B:Asp309 3.04 Na CA B:Asp309 4.91 Na OE2 B:Glu312 4.53 Na O B:Hoh809 1.98 Na O B:Hoh897 3.27 Na O B:Hoh902 4.94 Na O B:Hoh1010 4.39 Na O B:Hoh1111 4.83 Na O B:Hoh1141 2.01 interactive model: Sodium binding site 9 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 1g8g. 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: Arg190, B: His285, B: Glu324, B: Hoh868, B: Hoh1041, B: Hoh1385, conact list: Atom Atom Distance (A) Na NH1 B:Arg190 4.45 Na NE2 B:His285 4.39 Na OE1 B:Glu324 2.40 Na OE2 B:Glu324 4.56 Na CD B:Glu324 3.45 Na CG B:Glu324 3.86 Na O B:Hoh868 2.16 Na O B:Hoh1041 5.00 Na O B:Hoh1385 2.59 interactive model: Sodium binding site 10 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 1g8g. 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: His319, B: Asp322, B: Hoh892, B: Hoh899, B: Hoh965, B: Hoh1106, conact list: Atom Atom Distance (A) Na O B:His319 3.89 Na CB B:Asp322 4.50 Na OD1 B:Asp322 3.30 Na CG B:Asp322 4.14 Na O B:Hoh892 2.14 Na O B:Hoh899 2.29 Na O B:Hoh965 3.21 Na O B:Hoh1106 3.72 interactive model: Sodium binding site 11 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 1g8g. 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: Pro2, B: Ala3, B: Asp322, B: Hoh706, B: Hoh759, B: Hoh1089, conact list: Atom Atom Distance (A) Na N B:Pro2 5.00 Na CB B:Pro2 3.58 Na C B:Pro2 3.92 Na CG B:Pro2 4.58 Na CA B:Pro2 3.63 Na O B:Ala3 4.93 Na N B:Ala3 3.17 Na CB B:Ala3 3.93 Na CA B:Ala3 4.15 Na OD2 B:Asp322 2.64 Na OD1 B:Asp322 4.04 Na CG B:Asp322 3.69 Na O B:Hoh706 2.47 Na O B:Hoh759 4.46 Na O B:Hoh1089 3.08 interactive model: Sodium binding site 12 out of 12 in 1g8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 1g8g. 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: Asp505, B: Hoh882, B: Hoh991, B: Hoh1075, B: Hoh1264, conact list: Atom Atom Distance (A) Na CB B:Asp505 4.50 Na OD2 B:Asp505 3.13 Na OD1 B:Asp505 2.22 Na CG B:Asp505 3.04 Na O B:Hoh882 2.11 Na O B:Hoh991 4.29 Na O B:Hoh1075 4.95 Na O B:Hoh1264 2.67 interactive model: