Sodium in the structure of Hincii Bound to Cognate Dna (pdb 1tx3)

The binding sites of Sodium atom in the structure of Hincii Bound to Cognate Dna (pdb code 1tx3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1tx3 structure was solved by N.C.HORTON, L.F.DORNER, J.J.PERONA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.5 Space group I212121 a (A) 67.120 b (A) 177.670 c (A) 256.360 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 27.1 Sodium Binding Sites: Sodium binding site 1 out of 4 in 1tx3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1tx3. 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: F: Dc7, F: Dg8, A: Thr112, A: Asp127, A: Lys129, A: Ile142, A: Ile143, A: Tyr168, A: Gln207, F: Hoh196, A: Hoh849, A: Hoh920, A: Hoh921, A: Hoh943, conact list: Atom Atom Distance (A) Na OP1 F:Dc7 4.14 Na C3' F:Dc7 3.85 Na P F:Dc7 4.31 Na O3' F:Dc7 4.27 Na OP2 F:Dc7 4.55 Na C5' F:Dc7 4.56 Na C2' F:Dc7 4.61 Na C4' F:Dc7 4.83 Na O5' F:Dc7 3.70 Na OP1 F:Dg8 4.71 Na P F:Dg8 3.92 Na OP2 F:Dg8 2.59 Na O A:Thr112 4.42 Na CB A:Asp127 4.99 Na OD2 A:Asp127 2.82 Na OD1 A:Asp127 4.52 Na CG A:Asp127 3.93 Na CE A:Lys129 4.54 Na NZ A:Lys129 3.48 Na O A:Ile142 2.51 Na C A:Ile142 3.59 Na CA A:Ile142 4.73 Na N A:Ile143 4.22 Na CB A:Ile143 4.50 Na CG1 A:Ile143 4.79 Na CA A:Ile143 4.02 Na CE1 A:Tyr168 4.84 Na OE1 A:Gln207 4.60 Na O F:Hoh196 4.05 Na O A:Hoh849 4.58 Na O A:Hoh920 2.45 Na O A:Hoh921 2.12 Na O A:Hoh943 3.45 interactive model: Sodium binding site 2 out of 4 in 1tx3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1tx3. 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: E: Dc7, E: Dg8, B: Thr112, B: Asp127, B: Lys129, B: Asn141, B: Ile142, B: Ile143, B: Gln207, E: Hoh251, E: Hoh508, E: Hoh776, B: Hoh917, B: Hoh1043, B: Hoh1056, conact list: Atom Atom Distance (A) Na OP1 E:Dc7 4.82 Na C3' E:Dc7 3.69 Na P E:Dc7 4.70 Na O3' E:Dc7 4.00 Na OP2 E:Dc7 4.79 Na C5' E:Dc7 4.77 Na C2' E:Dc7 4.32 Na C4' E:Dc7 4.85 Na O5' E:Dc7 3.92 Na OP1 E:Dg8 4.32 Na P E:Dg8 3.51 Na OP2 E:Dg8 2.15 Na O5' E:Dg8 4.63 Na O B:Thr112 4.57 Na CB B:Asp127 4.73 Na OD2 B:Asp127 4.20 Na OD1 B:Asp127 2.47 Na CG B:Asp127 3.62 Na CE B:Lys129 4.17 Na NZ B:Lys129 4.10 Na O B:Asn141 4.64 Na O B:Ile142 2.55 Na C B:Ile142 3.58 Na CA B:Ile142 4.55 Na N B:Ile143 4.32 Na CB B:Ile143 4.70 Na CA B:Ile143 4.27 Na OE1 B:Gln207 4.85 Na O E:Hoh251 3.79 Na O E:Hoh508 2.08 Na O E:Hoh776 4.88 Na O B:Hoh917 3.84 Na O B:Hoh1043 4.50 Na O B:Hoh1056 2.34 interactive model: Sodium binding site 3 out of 4 in 1tx3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1tx3. 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: H: Dc7, H: Dg8, C: Thr112, C: Asp127, C: Lys129, C: Asn141, C: Ile142, C: Ile143, C: Tyr168, C: Hoh809, C: Hoh832, conact list: Atom Atom Distance (A) Na OP1 H:Dc7 4.84 Na C3' H:Dc7 3.71 Na P H:Dc7 4.74 Na O3' H:Dc7 4.14 Na OP2 H:Dc7 4.72 Na C5' H:Dc7 4.84 Na C2' H:Dc7 4.16 Na C4' H:Dc7 4.90 Na O5' H:Dc7 3.97 Na OP1 H:Dg8 4.65 Na P H:Dg8 3.76 Na OP2 H:Dg8 2.40 Na O5' H:Dg8 4.81 Na O C:Thr112 4.52 Na CB C:Asp127 4.89 Na OD2 C:Asp127 2.82 Na OD1 C:Asp127 4.04 Na CG C:Asp127 3.70 Na CE C:Lys129 4.67 Na NZ C:Lys129 3.57 Na O C:Asn141 4.58 Na O C:Ile142 2.42 Na C C:Ile142 3.58 Na CA C:Ile142 4.64 Na N C:Ile143 4.33 Na CB C:Ile143 4.61 Na CG2 C:Ile143 3.68 Na CA C:Ile143 4.22 Na CE1 C:Tyr168 4.85 Na O C:Hoh809 3.24 Na O C:Hoh832 2.67 interactive model: Sodium binding site 4 out of 4 in 1tx3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1tx3. 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: G: Dc7, G: Dg8, D: Thr112, D: Asp127, D: Lys129, D: Asn141, D: Ile142, D: Ile143, D: Gln207, G: Hoh511, D: Hoh812, D: Hoh813, D: Hoh861, conact list: Atom Atom Distance (A) Na OP1 G:Dc7 4.58 Na C3' G:Dc7 3.72 Na P G:Dc7 4.60 Na O3' G:Dc7 4.13 Na OP2 G:Dc7 4.59 Na C5' G:Dc7 4.80 Na C2' G:Dc7 4.26 Na C4' G:Dc7 4.88 Na O5' G:Dc7 3.95 Na OP1 G:Dg8 4.54 Na P G:Dg8 3.73 Na OP2 G:Dg8 2.41 Na O5' G:Dg8 4.85 Na O D:Thr112 4.38 Na CB D:Asp127 4.95 Na OD2 D:Asp127 4.35 Na OD1 D:Asp127 2.67 Na CG D:Asp127 3.81 Na CE D:Lys129 4.24 Na NZ D:Lys129 3.30 Na O D:Asn141 4.97 Na O D:Ile142 2.55 Na C D:Ile142 3.55 Na CA D:Ile142 4.47 Na N D:Ile143 4.33 Na CB D:Ile143 4.95 Na CG2 D:Ile143 4.22 Na CA D:Ile143 4.39 Na OE1 D:Gln207 4.79 Na O G:Hoh511 2.52 Na O D:Hoh812 4.21 Na O D:Hoh813 3.54 Na O D:Hoh861 2.43 interactive model: