Strontium in the structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) At 1.8 A Resolution (pdb 1nuv)

The binding sites of Strontium atom in the structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) At 1.8 A Resolution (pdb code 1nuv). This binding sites where shown with 5.0 Angstroms radius around Strontium atom. The 1nuv structure was solved by J.E.WEDEKIND, D.B.MCKAY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.1-1.8 Space group P61 a (A) 60.600 b (A) 60.600 c (A) 133.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21 Rfree (%) 21.9 Strontium Binding Sites: Strontium binding site 1 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: C23, B: G43, B: G44, B: A45, A: Hoh422, A: Hoh424, A: Hoh449, B: Hoh456, B: Hoh457, B: Hoh461, B: Hoh465, B: Hoh466, B: Hoh467, conact list: Atom Atom Distance (A) Sr N3 A:C23 4.47 Sr N4 A:C23 4.64 Sr C8 B:G43 4.99 Sr N7 B:G43 4.53 Sr OP2 B:G43 4.60 Sr C8 B:G44 4.98 Sr C5 B:G44 4.97 Sr N7 B:G44 4.03 Sr O6 B:G44 4.51 Sr N6 B:A45 4.21 Sr O A:Hoh422 4.67 Sr O A:Hoh424 4.22 Sr O A:Hoh449 4.27 Sr O B:Hoh456 2.82 Sr O B:Hoh457 4.07 Sr O B:Hoh461 4.25 Sr O B:Hoh465 2.33 Sr O B:Hoh466 2.18 Sr O B:Hoh467 2.20 interactive model: Strontium binding site 2 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: C23, C: A25, D: G44, D: A45, C: Hoh147, C: Hoh157, C: Hoh244, C: Hoh325, C: Hoh395, conact list: Atom Atom Distance (A) Sr C2 C:C23 4.42 Sr C1' C:C23 4.78 Sr O2 C:C23 3.36 Sr C2' C:C23 4.81 Sr O2' C:C23 3.77 Sr OP1 C:A25 2.87 Sr P C:A25 3.87 Sr OP2 C:A25 3.92 Sr O5' C:A25 4.81 Sr O6 D:G44 4.81 Sr N3 D:A45 4.38 Sr C2 D:A45 3.10 Sr C6 D:A45 4.10 Sr N1 D:A45 2.85 Sr N6 D:A45 4.55 Sr O C:Hoh147 2.67 Sr O C:Hoh157 2.28 Sr O C:Hoh244 4.75 Sr O C:Hoh325 2.83 Sr O C:Hoh395 3.00 interactive model: Strontium binding site 3 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: G42, D: G43, C: Hoh197, D: Hoh121, D: Hoh123, D: Hoh135, D: Hoh139, D: Hoh183, D: Hoh186, D: Hoh192, conact list: Atom Atom Distance (A) Sr N7 D:G42 4.97 Sr O6 D:G42 4.98 Sr O6 D:G43 4.96 Sr O C:Hoh197 4.30 Sr O D:Hoh121 2.61 Sr O D:Hoh123 2.33 Sr O D:Hoh135 4.56 Sr O D:Hoh139 4.93 Sr O D:Hoh183 4.39 Sr O D:Hoh186 4.12 Sr O D:Hoh192 2.54 interactive model: Strontium binding site 4 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: C23, E: A25, F: G44, F: A45, C: Hoh393, E: Hoh82, E: Hoh83, E: Hoh329, E: Hoh340, F: Hoh114, conact list: Atom Atom Distance (A) Sr C2 E:C23 4.44 Sr C1' E:C23 4.82 Sr O2 E:C23 3.39 Sr C2' E:C23 4.83 Sr O2' E:C23 3.79 Sr OP1 E:A25 2.85 Sr P E:A25 3.85 Sr OP2 E:A25 3.92 Sr O5' E:A25 4.82 Sr O6 F:G44 4.81 Sr N3 F:A45 4.48 Sr C2 F:A45 3.18 Sr C6 F:A45 4.04 Sr N1 F:A45 2.84 Sr N6 F:A45 4.42 Sr O C:Hoh393 4.75 Sr O E:Hoh82 2.43 Sr O E:Hoh83 3.06 Sr O E:Hoh329 2.94 Sr O E:Hoh340 4.79 Sr O F:Hoh114 2.49 interactive model: Strontium binding site 5 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: G42, F: G43, F: Hoh92, F: Hoh330, F: Hoh331, F: Hoh387, F: Hoh392, F: Hoh396, F: Hoh397, conact list: Atom Atom Distance (A) Sr N7 F:G42 4.92 Sr O6 F:G42 4.85 Sr O6 F:G43 4.88 Sr O F:Hoh92 4.60 Sr O F:Hoh330 2.32 Sr O F:Hoh331 2.21 Sr O F:Hoh387 4.47 Sr O F:Hoh392 2.42 Sr O F:Hoh396 4.98 Sr O F:Hoh397 4.21 interactive model: Strontium binding site 6 out of 6 in 1nuv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Strontium in the PDB 1nuv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: C23, H: G43, H: G44, H: A45, G: Hoh229, G: Hoh234, G: Hoh261, G: Hoh284, G: Hoh403, H: Hoh236, H: Hoh243, H: Hoh270, H: Hoh283, H: Hoh354, H: Hoh358, conact list: Atom Atom Distance (A) Sr N3 G:C23 4.47 Sr N4 G:C23 4.64 Sr C8 H:G43 4.92 Sr N7 H:G43 4.47 Sr OP2 H:G43 4.54 Sr N7 H:G44 4.08 Sr O6 H:G44 4.57 Sr N6 H:A45 4.19 Sr O G:Hoh229 4.74 Sr O G:Hoh234 4.15 Sr O G:Hoh261 4.39 Sr O G:Hoh284 2.41 Sr O G:Hoh403 4.89 Sr O H:Hoh236 2.13 Sr O H:Hoh243 2.25 Sr O H:Hoh270 2.29 Sr O H:Hoh283 2.68 Sr O H:Hoh354 4.30 Sr O H:Hoh358 4.23 interactive model: