Sodium in the structure of Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Guanine Complex (pdb 1orn)

The binding sites of Sodium atom in the structure of Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Guanine Complex (pdb code 1orn). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1orn structure was solved by J.C.FROMME, G.L.VERDINE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.6-1.7 Space group P21212 a (A) 67.826 b (A) 106.828 c (A) 41.708 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.5 Rfree (%) 24.8 Sodium Binding Sites: Sodium binding site 1 out of 1 in 1orn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1orn. 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: C: Dt20, C: Dc21, A: Leu112, A: Met113, A: Lys114, A: Leu115, A: Pro116, A: Gly117, A: Val118, A: Gly119, C: Hoh210, C: Hoh217, A: Hoh345, conact list: Atom Atom Distance (A) Na O3' C:Dt20 4.52 Na OP1 C:Dc21 2.56 Na P C:Dc21 3.58 Na OP2 C:Dc21 3.73 Na O5' C:Dc21 4.81 Na O A:Leu112 4.86 Na O A:Met113 2.38 Na CB A:Met113 4.87 Na C A:Met113 3.40 Na CA A:Met113 4.15 Na O A:Lys114 4.41 Na N A:Lys114 4.31 Na C A:Lys114 4.07 Na CA A:Lys114 4.44 Na O A:Leu115 2.39 Na N A:Leu115 4.01 Na C A:Leu115 3.46 Na CA A:Leu115 4.38 Na N A:Pro116 4.26 Na C A:Pro116 4.59 Na CA A:Pro116 4.28 Na N A:Gly117 4.33 Na C A:Gly117 4.87 Na O A:Val118 2.47 Na N A:Val118 3.81 Na CB A:Val118 4.31 Na C A:Val118 3.49 Na CA A:Val118 4.05 Na N A:Gly119 4.57 Na CA A:Gly119 4.90 Na O C:Hoh210 2.57 Na O C:Hoh217 4.68 Na O A:Hoh345 2.33 interactive model: