Sodium in the structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (pdb 2fld)

The binding sites of Sodium atom in the structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (pdb code 2fld). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2fld structure was solved by J.ASHWORTH, C.M.DUARTE, J.J.HAVRANEK, D.SUSSMAN, R.J.MONNAT, B.L.STODDARD, D.BAKER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.5-2.0 Space group P1 a (A) 41.961 b (A) 42.981 c (A) 71.545 alpha (°) 72.29 beta (°) 72.30 gamma (°) 70.51 Rfactor (%) 22.9 Rfree (%) 27.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2fld Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2fld. 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: Da514, C: Dg515, D: Dc564, D: Dg565, A: Gly21, A: Asp22, B: Gly221, B: Asp222, A: Ca601, B: Ca602, C: Hoh8, D: Hoh39, conact list: Atom Atom Distance (A) Na OP1 C:Da514 4.80 Na C3' C:Da514 4.12 Na O3' C:Da514 3.08 Na C4' C:Da514 4.47 Na OP1 C:Dg515 4.40 Na P C:Dg515 3.25 Na OP2 C:Dg515 2.24 Na O5' C:Dg515 4.24 Na OP1 D:Dc564 4.37 Na C3' D:Dc564 3.81 Na O3' D:Dc564 2.74 Na C4' D:Dc564 4.22 Na OP1 D:Dg565 4.35 Na P D:Dg565 3.12 Na OP2 D:Dg565 2.35 Na O5' D:Dg565 4.01 Na O A:Gly21 3.77 Na C A:Gly21 4.26 Na N A:Asp22 4.53 Na CB A:Asp22 4.59 Na OD2 A:Asp22 4.40 Na OD1 A:Asp22 2.44 Na CG A:Asp22 3.65 Na CA A:Asp22 4.33 Na O B:Gly221 3.73 Na C B:Gly221 4.11 Na N B:Asp222 4.32 Na CB B:Asp222 4.40 Na OD2 B:Asp222 4.30 Na OD1 B:Asp222 2.27 Na CG B:Asp222 3.50 Na CA B:Asp222 4.14 Na CA A:Ca601 3.76 Na CA B:Ca602 3.62 Na O C:Hoh8 4.95 Na O D:Hoh39 4.86 interactive model: