Sodium in the structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Cs+ Soak (pdb 3dim)

The binding sites of Sodium atom in the structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Cs+ Soak (pdb code 3dim). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3dim structure was solved by A.A.SERGANOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.9 Space group P212121 a (A) 54.249 b (A) 79.043 c (A) 141.978 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 24.8 Sodium Binding Sites: Sodium binding site 1 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3dim. 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: C19, A: G20, A: C70, A: G71, A: Hoh313, conact list: Atom Atom Distance (A) Na OP2 A:C19 4.19 Na C6 A:G20 3.88 Na C5 A:G20 4.33 Na N7 A:G20 4.03 Na O6 A:G20 2.88 Na OP2 A:C70 4.85 Na C6 A:G71 3.65 Na N1 A:G71 4.69 Na C5 A:G71 4.43 Na N7 A:G71 4.44 Na O6 A:G71 2.47 Na O A:Hoh313 2.92 interactive model: Sodium binding site 2 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3dim. 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: G83, A: G116, A: C132, A: A133, conact list: Atom Atom Distance (A) Na O2' A:G83 4.63 Na OP1 A:G116 4.23 Na P A:G116 4.78 Na OP2 A:G116 4.24 Na OP1 A:C132 4.73 Na OP1 A:A133 4.72 Na OP2 A:A133 4.33 interactive model: Sodium binding site 3 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3dim. 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: G124, A: G125, A: Na212, A: Hoh306, A: Hoh307, A: Hoh308, A: Hoh318, conact list: Atom Atom Distance (A) Na C8 A:G124 4.82 Na P A:G124 4.43 Na N7 A:G124 4.57 Na OP2 A:G124 3.12 Na O5' A:G124 4.78 Na C8 A:G125 4.47 Na C6 A:G125 3.95 Na C5 A:G125 3.99 Na N7 A:G125 3.32 Na O6 A:G125 3.22 Na NA A:Na212 3.24 Na O A:Hoh306 4.45 Na O A:Hoh307 2.98 Na O A:Hoh308 2.67 Na O A:Hoh318 4.53 interactive model: Sodium binding site 4 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3dim. 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: A10, A: G11, A: G12, A: C79, conact list: Atom Atom Distance (A) Na OP1 A:A10 4.82 Na C3' A:A10 4.91 Na O3' A:A10 4.66 Na O5' A:A10 4.54 Na OP1 A:G11 4.48 Na N2 A:G11 3.92 Na P A:G11 3.85 Na OP2 A:G11 2.47 Na O5' A:G11 4.89 Na C6 A:G12 3.75 Na N1 A:G12 4.82 Na C5 A:G12 4.42 Na N7 A:G12 4.39 Na O6 A:G12 2.68 Na C4 A:C79 4.87 Na N4 A:C79 4.11 interactive model: Sodium binding site 5 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3dim. 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: G9, A: G80, conact list: Atom Atom Distance (A) Na C6 A:G9 4.27 Na C5 A:G9 4.51 Na N7 A:G9 3.99 Na O6 A:G9 3.40 Na OP1 A:G80 3.67 interactive model: Sodium binding site 6 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3dim. 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: G118, conact list: Atom Atom Distance (A) Na OP1 A:G118 3.84 Na P A:G118 4.41 Na OP2 A:G118 4.00 interactive model: Sodium binding site 7 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3dim. 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: G146, A: G147, A: Na214, conact list: Atom Atom Distance (A) Na C8 A:G146 4.36 Na C6 A:G146 4.70 Na C5 A:G146 4.36 Na N7 A:G146 3.71 Na OP2 A:G146 4.69 Na O6 A:G146 4.51 Na C8 A:G147 3.81 Na C6 A:G147 4.55 Na C5 A:G147 4.08 Na N7 A:G147 2.97 Na O6 A:G147 4.21 Na NA A:Na214 3.19 interactive model: Sodium binding site 8 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3dim. 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: G1, A: G2, A: C3, A: G171, A: G172, A: U173, A: Ccc174, A: Hoh320, conact list: Atom Atom Distance (A) Na C6 A:G1 5.00 Na O6 A:G1 4.20 Na O6 A:G2 3.89 Na N4 A:C3 4.25 Na O6 A:G171 4.62 Na C6 A:G172 3.78 Na N1 A:G172 4.85 Na C5 A:G172 4.51 Na N7 A:G172 4.48 Na O6 A:G172 2.65 Na N3 A:U173 4.10 Na C4 A:U173 3.86 Na O4 A:U173 3.00 Na N4 A:Ccc174 4.87 Na O A:Hoh320 3.25 interactive model: Sodium binding site 9 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3dim. 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: G84, A: G85, A: A108, A: U109, conact list: Atom Atom Distance (A) Na N7 A:G84 4.47 Na O6 A:G84 4.30 Na C6 A:G85 4.97 Na O6 A:G85 3.86 Na C6 A:A108 4.73 Na N6 A:A108 3.83 Na N3 A:U109 3.94 Na C5 A:U109 4.80 Na C4 A:U109 3.52 Na O4 A:U109 2.44 interactive model: Sodium binding site 10 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3dim. 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: C3, A: C166, A: Na211, conact list: Atom Atom Distance (A) Na OP2 A:C3 4.27 Na OP1 A:C166 4.89 Na OP2 A:C166 4.39 Na NA A:Na211 4.87 interactive model: Sodium binding site 11 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3dim. 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: C167, A: Na210, conact list: Atom Atom Distance (A) Na OP2 A:C167 4.56 Na NA A:Na210 4.87 interactive model: Sodium binding site 12 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 3dim. 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: G124, A: G125, A: A127, A: Na203, A: Hoh307, A: Hoh308, A: Hoh318, conact list: Atom Atom Distance (A) Na OP1 A:G124 4.67 Na P A:G124 4.82 Na OP2 A:G124 4.24 Na C8 A:G125 4.82 Na N7 A:G125 4.37 Na OP2 A:G125 3.65 Na OP2 A:A127 4.87 Na NA A:Na203 3.24 Na O A:Hoh307 4.85 Na O A:Hoh308 4.44 Na O A:Hoh318 4.27 interactive model: Sodium binding site 13 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 3dim. 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: A29, A: G30, conact list: Atom Atom Distance (A) Na OP1 A:A29 4.42 Na OP2 A:G30 4.18 interactive model: Sodium binding site 14 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 3dim. 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: C145, A: G146, A: G147, A: Na207, conact list: Atom Atom Distance (A) Na C5 A:C145 4.84 Na C4 A:C145 4.89 Na N4 A:C145 4.26 Na O6 A:G146 4.58 Na O6 A:G147 4.16 Na NA A:Na207 3.19 interactive model: Sodium binding site 15 out of 15 in 3dim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Sodium in the PDB 3dim. 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: G8, A: G9, A: C79, conact list: Atom Atom Distance (A) Na P A:G8 4.89 Na OP2 A:G8 3.90 Na OP2 A:G9 4.80 Na OP1 A:C79 4.19 Na P A:C79 4.74 Na OP2 A:C79 4.26 interactive model: