Sodium in the structure of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli At 1.8 Angstroms Resolution. (pdb 1ag9)

The binding sites of Sodium atom in the structure of Flavodoxins That Are Required For Enzyme Activation: the Structure of Oxidized Flavodoxin From Escherichia Coli At 1.8 Angstroms Resolution. (pdb code 1ag9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1ag9 structure was solved by D.M.HOOVER, M.L.LUDWIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.8 Space group P212121 a (A) 126.400 b (A) 41.100 c (A) 68.150 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 25 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1ag9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1ag9. 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: Glu61, B: Glu61, B: Asp67, A: Ca200, A: Cl405, B: Cl404, A: Hoh406, A: Hoh407, A: Hoh474, A: Hoh512, B: Hoh1036, B: Hoh1052, B: Hoh1054, B: Hoh1073, B: Hoh1116, B: Hoh1129, B: Hoh1151, conact list: Atom Atom Distance (A) Na OE1 A:Glu61 2.46 Na OE2 A:Glu61 2.53 Na CD A:Glu61 2.82 Na CG A:Glu61 4.32 Na OE1 B:Glu61 4.38 Na CB B:Asp67 4.54 Na OD2 B:Asp67 2.61 Na OD1 B:Asp67 2.90 Na CG B:Asp67 3.09 Na CA A:Ca200 4.04 Na CL A:Cl405 4.86 Na CL B:Cl404 4.94 Na O A:Hoh406 4.96 Na O A:Hoh407 4.40 Na O A:Hoh474 2.39 Na O A:Hoh512 2.60 Na O B:Hoh1036 4.21 Na O B:Hoh1052 4.63 Na O B:Hoh1054 4.62 Na O B:Hoh1073 4.25 Na O B:Hoh1116 2.36 Na O B:Hoh1129 2.33 Na O B:Hoh1151 4.70 interactive model: Sodium binding site 2 out of 4 in 1ag9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1ag9. 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: Glu61, A: Asp67, B: Glu61, A: Cl405, B: Ca1000, B: Cl404, A: Hoh470, A: Hoh474, A: Hoh484, A: Hoh538, B: Hoh1002, B: Hoh1003, B: Hoh1052, B: Hoh1074, B: Hoh1116, B: Hoh1136, B: Hoh1151, conact list: Atom Atom Distance (A) Na OE1 A:Glu61 4.43 Na CB A:Asp67 4.61 Na OD2 A:Asp67 2.80 Na OD1 A:Asp67 2.88 Na CG A:Asp67 3.17 Na OE1 B:Glu61 2.53 Na OE2 B:Glu61 2.44 Na CD B:Glu61 2.81 Na CG B:Glu61 4.31 Na CL A:Cl405 4.93 Na CA B:Ca1000 4.16 Na CL B:Cl404 4.95 Na O A:Hoh470 4.22 Na O A:Hoh474 4.68 Na O A:Hoh484 2.44 Na O A:Hoh538 4.25 Na O B:Hoh1002 4.89 Na O B:Hoh1003 4.46 Na O B:Hoh1052 2.39 Na O B:Hoh1074 2.44 Na O B:Hoh1116 4.52 Na O B:Hoh1136 4.86 Na O B:Hoh1151 2.39 interactive model: Sodium binding site 3 out of 4 in 1ag9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1ag9. 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: Lys38, B: Ser39, B: Ser40, B: Asp43, B: Hoh1012, B: Hoh1070, B: Hoh1075, B: Hoh1076, B: Hoh1085, B: Hoh1158, conact list: Atom Atom Distance (A) Na O B:Lys38 4.14 Na CA B:Ser39 4.69 Na N B:Ser40 4.56 Na CB B:Ser40 4.80 Na OG B:Ser40 4.09 Na CB B:Asp43 4.39 Na OD2 B:Asp43 2.42 Na OD1 B:Asp43 2.67 Na CG B:Asp43 2.89 Na O B:Hoh1012 4.11 Na O B:Hoh1070 2.53 Na O B:Hoh1075 2.43 Na O B:Hoh1076 2.51 Na O B:Hoh1085 2.33 Na O B:Hoh1158 2.41 interactive model: Sodium binding site 4 out of 4 in 1ag9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1ag9. 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: Ala2, B: Ala46, B: Tyr47, B: Hoh1014, B: Hoh1015, B: Hoh1071, B: Hoh1079, B: Hoh1091, B: Hoh1144, B: Hoh1145, B: Hoh1152, B: Hoh1167, conact list: Atom Atom Distance (A) Na O B:Ala2 4.33 Na O B:Ala46 2.41 Na C B:Ala46 3.63 Na CB B:Ala46 4.57 Na CA B:Ala46 4.49 Na N B:Tyr47 4.56 Na CD2 B:Tyr47 4.74 Na CA B:Tyr47 4.61 Na O B:Hoh1014 4.85 Na O B:Hoh1015 4.70 Na O B:Hoh1071 2.51 Na O B:Hoh1079 4.67 Na O B:Hoh1091 2.56 Na O B:Hoh1144 4.84 Na O B:Hoh1145 4.67 Na O B:Hoh1152 2.41 Na O B:Hoh1167 2.43 interactive model: