Sodium in the structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak (pdb 3dio)

The binding sites of Sodium atom in the structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak (pdb code 3dio). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3dio structure was solved by A.A.SERGANOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.4 Space group P212121 a (A) 53.918 b (A) 78.004 c (A) 140.835 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 24.3 Sodium Binding Sites: Sodium binding site 1 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3dio. 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: X: C19, X: G20, X: C70, X: G71, X: Hoh308, X: Hoh381, X: Hoh393, X: Hoh421, X: Hoh484, X: Hoh485, X: Hoh486, X: Hoh509, conact list: Atom Atom Distance (A) Na C5 X:C19 4.65 Na OP2 X:C19 4.19 Na C6 X:G20 3.60 Na N1 X:G20 4.76 Na C5 X:G20 4.20 Na N7 X:G20 4.06 Na O6 X:G20 2.53 Na OP2 X:C70 4.79 Na C6 X:G71 3.54 Na N1 X:G71 4.63 Na C5 X:G71 4.18 Na N7 X:G71 4.13 Na O6 X:G71 2.49 Na O X:Hoh308 4.57 Na O X:Hoh381 2.23 Na O X:Hoh393 2.58 Na O X:Hoh421 4.23 Na O X:Hoh484 4.67 Na O X:Hoh485 4.65 Na O X:Hoh486 3.12 Na O X:Hoh509 3.89 interactive model: Sodium binding site 2 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3dio. 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: X: A23, X: U24, X: G25, X: A67, X: G68, X: G69, X: Na212, X: Hoh305, X: Hoh306, X: Hoh307, conact list: Atom Atom Distance (A) Na N6 X:A23 4.42 Na N3 X:U24 4.62 Na O4 X:U24 4.42 Na N3 X:G25 4.67 Na N2 X:G25 3.88 Na C2 X:G25 4.46 Na C8 X:A67 4.18 Na C5 X:A67 4.62 Na N7 X:A67 3.85 Na OP2 X:A67 4.57 Na C8 X:G68 3.76 Na C6 X:G68 4.59 Na C5 X:G68 4.09 Na N7 X:G68 2.96 Na OP2 X:G68 4.22 Na O6 X:G68 4.28 Na C6 X:G69 3.56 Na N1 X:G69 4.59 Na C5 X:G69 4.06 Na N7 X:G69 4.01 Na O6 X:G69 2.78 Na NA X:Na212 2.88 Na O X:Hoh305 2.39 Na O X:Hoh306 2.51 Na O X:Hoh307 2.43 interactive model: Sodium binding site 3 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3dio. 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: X: A10, X: G11, X: G12, X: C79, X: Hoh309, X: Hoh310, X: Hoh447, conact list: Atom Atom Distance (A) Na OP1 X:A10 4.17 Na C3' X:A10 4.76 Na P X:A10 4.67 Na O3' X:A10 4.34 Na OP2 X:A10 4.72 Na O5' X:A10 4.58 Na OP1 X:G11 3.96 Na N2 X:G11 3.86 Na P X:G11 3.65 Na OP2 X:G11 2.58 Na C6 X:G12 3.69 Na N1 X:G12 4.66 Na C5 X:G12 4.51 Na N7 X:G12 4.59 Na O6 X:G12 2.58 Na C4 X:C79 4.80 Na N4 X:C79 3.96 Na O X:Hoh309 2.34 Na O X:Hoh310 4.48 Na O X:Hoh447 2.99 interactive model: Sodium binding site 4 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3dio. 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: X: G8, X: C79, X: Iri264, X: Hoh313, X: Hoh398, X: Hoh411, X: Hoh512, conact list: Atom Atom Distance (A) Na OP1 X:G8 4.90 Na P X:G8 4.45 Na OP2 X:G8 3.25 Na O5' X:G8 4.92 Na OP1 X:C79 4.44 Na OP2 X:C79 4.73 Na N1 X:Iri264 4.74 Na N2 X:Iri264 3.21 Na IR X:Iri264 5.00 Na O X:Hoh313 3.45 Na O X:Hoh398 2.32 Na O X:Hoh411 4.71 Na O X:Hoh512 2.92 interactive model: Sodium binding site 5 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3dio. 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: X: G80, X: U113, X: G163, X: A164, X: Hoh314, X: Hoh315, X: Hoh316, X: Hoh480, X: Hoh481, conact list: Atom Atom Distance (A) Na N9 X:G80 4.82 Na C8 X:G80 3.53 Na C6 X:G80 4.36 Na C5 X:G80 3.85 Na N7 X:G80 2.72 Na C4 X:G80 4.98 Na O6 X:G80 4.08 Na N3 X:U113 4.96 Na C6 X:U113 4.76 Na C5 X:U113 3.87 Na C4 X:U113 3.98 Na O4 X:U113 3.78 Na C3' X:G163 3.81 Na O3' X:G163 3.88 Na OP2 X:G163 4.92 Na C2' X:G163 4.55 Na O5' X:G163 4.61 Na O2' X:G163 4.45 Na OP1 X:A164 2.46 Na C8 X:A164 4.55 Na P X:A164 3.62 Na N7 X:A164 4.53 Na OP2 X:A164 4.38 Na O5' X:A164 4.89 Na O X:Hoh314 2.32 Na O X:Hoh315 4.31 Na O X:Hoh316 2.45 Na O X:Hoh480 4.04 Na O X:Hoh481 2.64 interactive model: Sodium binding site 6 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3dio. 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: X: G83, X: G116, X: C132, X: A133, X: Na214, X: Hoh319, X: Hoh352, X: Hoh382, X: Hoh384, X: Hoh452, X: Hoh453, X: Hoh454, X: Hoh516, conact list: Atom Atom Distance (A) Na O2' X:G83 4.57 Na OP1 X:G116 4.28 Na P X:G116 4.85 Na OP2 X:G116 4.44 Na OP1 X:C132 4.16 Na OP1 X:A133 4.34 Na P X:A133 4.72 Na OP2 X:A133 4.10 Na NA X:Na214 3.86 Na O X:Hoh319 2.39 Na O X:Hoh352 2.54 Na O X:Hoh382 4.24 Na O X:Hoh384 4.32 Na O X:Hoh452 3.60 Na O X:Hoh453 4.77 Na O X:Hoh454 4.26 Na O X:Hoh516 2.68 interactive model: Sodium binding site 7 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3dio. 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: X: A91, X: G92, X: U93, X: G101, X: C102, X: Hoh437, conact list: Atom Atom Distance (A) Na C6 X:A91 4.93 Na N6 X:A91 4.11 Na C6 X:G92 3.65 Na N1 X:G92 4.82 Na C5 X:G92 4.23 Na N7 X:G92 4.08 Na O6 X:G92 2.57 Na N3 X:U93 4.40 Na C5 X:U93 5.00 Na C4 X:U93 3.90 Na O4 X:U93 2.93 Na O6 X:G101 4.17 Na N4 X:C102 4.02 Na O X:Hoh437 2.24 interactive model: Sodium binding site 8 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3dio. 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: X: G168, X: U169, X: Hoh400, X: Hoh401, conact list: Atom Atom Distance (A) Na N9 X:G168 4.51 Na C3' X:G168 4.38 Na C8 X:G168 3.89 Na C5 X:G168 4.90 Na N7 X:G168 4.16 Na O4' X:G168 4.86 Na OP2 X:G168 4.65 Na O5' X:G168 4.23 Na C6 X:U169 4.80 Na C5 X:U169 3.99 Na C4 X:U169 4.88 Na OP2 X:U169 3.80 Na O4 X:U169 4.84 Na O X:Hoh400 4.00 Na O X:Hoh401 4.00 interactive model: Sodium binding site 9 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3dio. 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: X: A29, X: G31, conact list: Atom Atom Distance (A) Na OP2 X:A29 4.06 Na O6 X:G31 4.66 interactive model: Sodium binding site 10 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3dio. 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: X: C13, X: Hoh551, conact list: Atom Atom Distance (A) Na O4' X:C13 4.22 Na C5' X:C13 3.78 Na C4' X:C13 4.15 Na O5' X:C13 4.87 Na O X:Hoh551 4.12 interactive model: Sodium binding site 11 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3dio. 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: X: G118, X: C130, X: Iri255, conact list: Atom Atom Distance (A) Na OP1 X:G118 4.88 Na OP1 X:C130 4.00 Na N4 X:Iri255 4.53 interactive model: Sodium binding site 12 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 3dio. 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: X: G68, X: G69, X: C70, X: Na202, X: Hoh305, X: Hoh307, X: Hoh308, X: Hoh394, X: Hoh421, X: Hoh485, conact list: Atom Atom Distance (A) Na OP1 X:G68 4.80 Na C8 X:G68 3.79 Na P X:G68 3.96 Na N7 X:G68 3.76 Na OP2 X:G68 2.85 Na O5' X:G68 3.93 Na C8 X:G69 3.97 Na C6 X:G69 3.80 Na C5 X:G69 3.68 Na N7 X:G69 2.87 Na C4 X:G69 4.97 Na OP2 X:G69 4.57 Na O6 X:G69 3.20 Na C5 X:C70 4.74 Na C4 X:C70 4.82 Na N4 X:C70 4.18 Na NA X:Na202 2.88 Na O X:Hoh305 3.40 Na O X:Hoh307 4.39 Na O X:Hoh308 4.64 Na O X:Hoh394 4.61 Na O X:Hoh421 4.42 Na O X:Hoh485 2.51 interactive model: Sodium binding site 13 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 3dio. 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: X: G69, X: C70, X: G124, X: A129, X: C130, X: C131, conact list: Atom Atom Distance (A) Na C3' X:G69 3.88 Na O3' X:G69 3.17 Na O4' X:G69 4.89 Na C5' X:G69 4.82 Na C2' X:G69 4.02 Na C4' X:G69 3.91 Na O2' X:G69 3.08 Na OP1 X:C70 4.24 Na P X:C70 4.34 Na C5' X:C70 4.64 Na O5' X:C70 4.89 Na N2 X:G124 4.04 Na N1 X:A129 4.98 Na C2 X:C130 4.30 Na N1 X:C130 4.74 Na C1' X:C130 4.12 Na O2 X:C130 3.20 Na C2' X:C130 3.75 Na O2' X:C130 3.07 Na C6 X:C131 4.99 Na N1 X:C131 4.59 Na C1' X:C131 3.82 Na O4' X:C131 3.22 Na C5' X:C131 4.80 Na C4' X:C131 4.23 interactive model: Sodium binding site 14 out of 14 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 3dio. 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: X: C15, X: G16, X: A81, X: A82, X: G83, X: G116, X: C132, X: Na206, X: Hoh319, X: Hoh351, X: Hoh352, X: Hoh384, X: Hoh454, X: Hoh516, conact list: Atom Atom Distance (A) Na C3' X:C15 4.30 Na O3' X:C15 3.28 Na C5' X:C15 4.74 Na C2' X:C15 4.90 Na C4' X:C15 4.26 Na O2' X:C15 4.27 Na OP1 X:G16 3.62 Na P X:G16 4.14 Na C5' X:G16 4.69 Na O5' X:G16 4.92 Na N6 X:A81 4.91 Na N3 X:A82 4.65 Na C1' X:A82 4.42 Na C2' X:A82 3.81 Na O2' X:A82 2.73 Na C1' X:G83 4.18 Na O4' X:G83 3.31 Na C5' X:G83 4.42 Na C4' X:G83 3.99 Na OP1 X:G116 4.54 Na OP1 X:C132 4.42 Na NA X:Na206 3.86 Na O X:Hoh319 3.01 Na O X:Hoh351 3.84 Na O X:Hoh352 2.62 Na O X:Hoh384 3.53 Na O X:Hoh454 3.02 Na O X:Hoh516 4.46 interactive model: