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

The binding sites of Iridium 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 Iridium 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 Iridium Binding Sites: Iridium binding site 1 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G1, X: G2, X: G172, X: U173, X: Iri250, X: Hoh320, X: Hoh321, X: Hoh555, X: Hoh558, conact list: Atom Atom Distance (A) Ir O6 X:G1 4.13 Ir O6 X:G2 4.95 Ir O6 X:G172 4.06 Ir C4 X:U173 4.91 Ir O4 X:U173 3.85 Ir N1 X:Iri250 2.03 Ir N6 X:Iri250 2.03 Ir N3 X:Iri250 2.03 Ir N2 X:Iri250 2.03 Ir IR X:Iri250 0.00 Ir N5 X:Iri250 2.03 Ir N4 X:Iri250 2.03 Ir O X:Hoh320 3.92 Ir O X:Hoh321 3.91 Ir O X:Hoh555 4.15 Ir O X:Hoh558 4.04 interactive model: Iridium binding site 2 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: U109, X: G110, X: Iri251, X: Hoh366, conact list: Atom Atom Distance (A) Ir OP1 X:U109 3.92 Ir P X:U109 4.78 Ir OP2 X:U109 4.81 Ir OP2 X:G110 3.90 Ir N1 X:Iri251 2.02 Ir N6 X:Iri251 2.02 Ir N3 X:Iri251 2.02 Ir N2 X:Iri251 2.02 Ir IR X:Iri251 0.00 Ir N5 X:Iri251 2.03 Ir N4 X:Iri251 2.02 Ir O X:Hoh366 4.68 interactive model: Iridium binding site 3 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G123, X: G124, X: G125, X: Iri252, X: Hoh489, conact list: Atom Atom Distance (A) Ir C6 X:G123 4.92 Ir C5 X:G123 4.88 Ir N7 X:G123 4.16 Ir O6 X:G123 4.28 Ir O6 X:G124 4.81 Ir C6 X:G125 4.58 Ir N1 X:G125 4.87 Ir O6 X:G125 3.76 Ir N1 X:Iri252 2.03 Ir N6 X:Iri252 2.02 Ir N3 X:Iri252 2.03 Ir N2 X:Iri252 2.02 Ir IR X:Iri252 0.00 Ir N5 X:Iri252 2.02 Ir N4 X:Iri252 2.03 Ir O X:Hoh489 4.38 interactive model: Iridium binding site 4 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G56, X: G57, X: Iri253, conact list: Atom Atom Distance (A) Ir C6 X:G56 4.70 Ir C5 X:G56 4.90 Ir N7 X:G56 4.35 Ir O6 X:G56 3.85 Ir C6 X:G57 4.53 Ir O6 X:G57 3.54 Ir N1 X:Iri253 2.02 Ir N6 X:Iri253 2.03 Ir N6 X:Iri253 4.08 Ir N3 X:Iri253 2.02 Ir N3 X:Iri253 2.13 Ir N2 X:Iri253 2.03 Ir N2 X:Iri253 3.90 Ir IR X:Iri253 0.00 Ir IR X:Iri253 3.93 Ir N5 X:Iri253 2.02 Ir N5 X:Iri253 4.74 Ir N4 X:Iri253 2.02 Ir N4 X:Iri253 4.89 interactive model: Iridium binding site 5 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G54, X: G55, X: Iri253, conact list: Atom Atom Distance (A) Ir OP2 X:G54 4.60 Ir N7 X:G55 4.30 Ir O6 X:G55 4.38 Ir N1 X:Iri253 3.03 Ir N1 X:Iri253 2.03 Ir N6 X:Iri253 4.78 Ir N6 X:Iri253 2.02 Ir N3 X:Iri253 2.02 Ir N2 X:Iri253 2.02 Ir IR X:Iri253 3.93 Ir IR X:Iri253 0.00 Ir N5 X:Iri253 4.04 Ir N5 X:Iri253 2.03 Ir N4 X:Iri253 2.82 Ir N4 X:Iri253 2.03 interactive model: Iridium binding site 6 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G83, X: G84, X: U109, X: Iri254, X: Hoh368, X: Hoh515, X: Hoh549, X: Hoh554, X: Hoh556, conact list: Atom Atom Distance (A) Ir N7 X:G83 4.27 Ir O6 X:G83 4.65 Ir N7 X:G84 4.63 Ir O6 X:G84 4.62 Ir C4 X:U109 4.94 Ir O4 X:U109 3.79 Ir N1 X:Iri254 2.03 Ir N6 X:Iri254 2.03 Ir N3 X:Iri254 2.02 Ir N2 X:Iri254 2.03 Ir IR X:Iri254 0.00 Ir N5 X:Iri254 2.03 Ir N4 X:Iri254 2.02 Ir O X:Hoh368 4.45 Ir O X:Hoh515 3.80 Ir O X:Hoh549 4.43 Ir O X:Hoh554 4.43 Ir O X:Hoh556 3.53 interactive model: Iridium binding site 7 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: C13, X: C15, X: G116, X: G117, X: C131, X: Iri255, X: Hoh312, X: Hoh383, conact list: Atom Atom Distance (A) Ir C2 X:C13 4.96 Ir O2 X:C13 4.17 Ir OP1 X:C15 4.19 Ir O3' X:G116 4.83 Ir OP1 X:G117 3.92 Ir OP1 X:C131 4.32 Ir N1 X:Iri255 2.03 Ir N6 X:Iri255 2.03 Ir N3 X:Iri255 2.03 Ir N2 X:Iri255 2.03 Ir IR X:Iri255 0.00 Ir N5 X:Iri255 2.03 Ir N4 X:Iri255 2.03 Ir O X:Hoh312 3.99 Ir O X:Hoh383 4.19 interactive model: Iridium binding site 8 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G146, X: G147, X: Iri256, X: Hoh470, X: Hoh471, X: Hoh472, conact list: Atom Atom Distance (A) Ir OP2 X:G146 4.26 Ir OP2 X:G147 4.53 Ir N1 X:Iri256 2.03 Ir N6 X:Iri256 2.03 Ir N3 X:Iri256 2.02 Ir N2 X:Iri256 2.02 Ir IR X:Iri256 0.00 Ir N5 X:Iri256 2.02 Ir N4 X:Iri256 2.02 Ir O X:Hoh470 4.32 Ir O X:Hoh471 3.79 Ir O X:Hoh472 4.47 interactive model: Iridium binding site 9 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G149, X: G150, X: Iri257, X: Hoh517, conact list: Atom Atom Distance (A) Ir C6 X:G149 4.91 Ir C5 X:G149 4.93 Ir N7 X:G149 4.21 Ir O6 X:G149 4.18 Ir O6 X:G150 4.17 Ir N1 X:Iri257 2.03 Ir N6 X:Iri257 2.03 Ir N3 X:Iri257 2.03 Ir N2 X:Iri257 2.03 Ir IR X:Iri257 0.00 Ir N5 X:Iri257 2.03 Ir N4 X:Iri257 2.02 Ir O X:Hoh517 4.67 interactive model: Iridium binding site 10 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: U113, X: G114, X: G115, X: Iri258, X: Hoh387, conact list: Atom Atom Distance (A) Ir O3' X:U113 4.31 Ir O2' X:U113 4.60 Ir OP1 X:G114 3.99 Ir P X:G114 4.81 Ir C8 X:G115 4.97 Ir N7 X:G115 4.10 Ir OP2 X:G115 4.45 Ir O6 X:G115 4.67 Ir N1 X:Iri258 2.03 Ir N6 X:Iri258 2.03 Ir N3 X:Iri258 2.03 Ir N2 X:Iri258 2.03 Ir IR X:Iri258 0.00 Ir N5 X:Iri258 2.03 Ir N4 X:Iri258 2.03 Ir O X:Hoh387 3.99 interactive model: Iridium binding site 11 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G124, X: G125, X: A127, X: Iri259, X: Hoh322, X: Hoh323, conact list: Atom Atom Distance (A) Ir P X:G124 4.95 Ir OP2 X:G124 4.01 Ir C8 X:G125 4.90 Ir N7 X:G125 4.22 Ir OP2 X:G125 4.71 Ir OP1 X:A127 4.21 Ir OP2 X:A127 4.80 Ir N1 X:Iri259 2.03 Ir N6 X:Iri259 2.03 Ir N3 X:Iri259 2.02 Ir N2 X:Iri259 2.02 Ir IR X:Iri259 0.00 Ir N5 X:Iri259 2.02 Ir N4 X:Iri259 2.02 Ir O X:Hoh322 3.41 Ir O X:Hoh323 3.85 interactive model: Iridium binding site 12 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: C139, X: U140, X: C157, X: G158, X: Iri260, X: Iri265, X: Hoh324, X: Hoh390, X: Hoh408, X: Hoh409, X: Hoh505, conact list: Atom Atom Distance (A) Ir OP1 X:C139 4.66 Ir OP2 X:U140 4.19 Ir OP1 X:C157 4.50 Ir P X:C157 4.90 Ir OP2 X:C157 4.46 Ir P X:G158 4.73 Ir OP2 X:G158 3.47 Ir N1 X:Iri260 2.03 Ir N6 X:Iri260 2.03 Ir N6 X:Iri260 4.01 Ir N3 X:Iri260 2.03 Ir N3 X:Iri260 3.64 Ir N2 X:Iri260 2.03 Ir IR X:Iri260 0.00 Ir IR X:Iri260 3.89 Ir N5 X:Iri260 2.03 Ir N5 X:Iri260 4.74 Ir N4 X:Iri260 2.03 Ir N4 X:Iri260 2.25 Ir N6 X:Iri265 4.83 Ir O X:Hoh324 4.46 Ir O X:Hoh390 3.92 Ir O X:Hoh408 3.97 Ir O X:Hoh409 4.72 Ir O X:Hoh505 3.50 interactive model: Iridium binding site 13 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: C139, X: U140, X: C157, X: Iri260, X: Hoh390, conact list: Atom Atom Distance (A) Ir OP1 X:C139 3.96 Ir OP1 X:U140 4.81 Ir OP2 X:U140 4.98 Ir OP1 X:C157 4.35 Ir N1 X:Iri260 4.67 Ir N1 X:Iri260 2.03 Ir N6 X:Iri260 2.87 Ir N6 X:Iri260 2.03 Ir N3 X:Iri260 4.09 Ir N3 X:Iri260 2.02 Ir N2 X:Iri260 2.85 Ir N2 X:Iri260 2.02 Ir IR X:Iri260 3.89 Ir IR X:Iri260 0.00 Ir N5 X:Iri260 2.03 Ir N4 X:Iri260 2.02 Ir O X:Hoh390 3.32 interactive model: Iridium binding site 14 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: A26, X: G27, X: Iri261, X: Hoh344, conact list: Atom Atom Distance (A) Ir O3' X:A26 4.68 Ir O2' X:A26 4.83 Ir P X:G27 4.74 Ir O4' X:G27 5.00 Ir OP2 X:G27 4.30 Ir O5' X:G27 4.16 Ir N1 X:Iri261 2.02 Ir N6 X:Iri261 2.02 Ir N3 X:Iri261 2.03 Ir N2 X:Iri261 2.02 Ir IR X:Iri261 0.00 Ir N5 X:Iri261 2.03 Ir N4 X:Iri261 2.02 Ir O X:Hoh344 3.41 interactive model: Iridium binding site 15 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: U40, X: U52, X: C53, X: Iri262, conact list: Atom Atom Distance (A) Ir C4 X:U40 4.82 Ir O4 X:U40 3.79 Ir O2' X:U52 3.61 Ir OP2 X:C53 4.20 Ir N1 X:Iri262 2.02 Ir N6 X:Iri262 2.03 Ir N3 X:Iri262 2.02 Ir N2 X:Iri262 2.02 Ir IR X:Iri262 0.00 Ir N5 X:Iri262 2.02 Ir N4 X:Iri262 2.03 interactive model: Iridium binding site 16 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: A91, X: G92, X: C98, X: Iri263, X: Hoh438, conact list: Atom Atom Distance (A) Ir OP1 X:A91 4.71 Ir P X:A91 4.97 Ir OP2 X:A91 4.45 Ir OP2 X:G92 3.99 Ir OP1 X:C98 4.86 Ir OP2 X:C98 4.54 Ir N1 X:Iri263 2.03 Ir N6 X:Iri263 2.02 Ir N3 X:Iri263 2.02 Ir N2 X:Iri263 2.03 Ir IR X:Iri263 0.00 Ir N5 X:Iri263 2.03 Ir N4 X:Iri263 2.02 Ir O X:Hoh438 4.81 interactive model: Iridium binding site 17 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G8, X: G9, X: G80, X: Na204, X: Iri264, X: Hoh301, X: Hoh397, X: Hoh398, conact list: Atom Atom Distance (A) Ir N7 X:G8 4.97 Ir O6 X:G8 4.54 Ir C6 X:G9 4.86 Ir N7 X:G9 4.42 Ir O6 X:G9 3.97 Ir OP1 X:G80 4.65 Ir NA X:Na204 5.00 Ir N1 X:Iri264 2.02 Ir N6 X:Iri264 2.03 Ir N3 X:Iri264 2.02 Ir N2 X:Iri264 2.02 Ir IR X:Iri264 0.00 Ir N5 X:Iri264 2.02 Ir N4 X:Iri264 2.03 Ir O X:Hoh301 3.76 Ir O X:Hoh397 4.06 Ir O X:Hoh398 3.71 interactive model: Iridium binding site 18 out of 18 in 3dio Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Iridium in the PDB 3dio. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: U140, X: G141, X: U142, X: U159, X: G160, X: Iri265, X: Hoh325, X: Hoh547, X: Hoh548, conact list: Atom Atom Distance (A) Ir O4 X:U140 4.50 Ir O6 X:G141 4.66 Ir O4 X:U142 3.85 Ir O4 X:U159 4.56 Ir C6 X:G160 4.47 Ir C5 X:G160 4.75 Ir N7 X:G160 4.27 Ir O6 X:G160 3.57 Ir N1 X:Iri265 2.03 Ir N6 X:Iri265 2.02 Ir N3 X:Iri265 2.02 Ir N2 X:Iri265 2.02 Ir IR X:Iri265 0.00 Ir N5 X:Iri265 2.02 Ir N4 X:Iri265 2.02 Ir O X:Hoh325 4.81 Ir O X:Hoh547 4.11 Ir O X:Hoh548 4.55 interactive model: