Sodium in the structure of Structure of Human Dna Polymerase Iota Complexed With N2-Ethylguanine (pdb 3epg)

The binding sites of Sodium atom in the structure of Structure of Human Dna Polymerase Iota Complexed With N2-Ethylguanine (pdb code 3epg). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3epg structure was solved by M.G.PENCE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.5 Space group P6522 a (A) 98.535 b (A) 98.535 c (A) 202.354 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.4 Rfree (%) 28.3 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3epg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3epg. 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: A: Ile236, A: Lys237, A: Glu238, A: Ile239, A: Pro240, A: Gly241, A: Ile242, A: Gly243, B: Dc11, B: Dc12, conact list: Atom Atom Distance (A) Na O A:Ile236 4.88 Na O A:Lys237 2.56 Na CD A:Lys237 4.97 Na C A:Lys237 3.56 Na CA A:Lys237 4.49 Na O A:Glu238 4.28 Na N A:Glu238 4.30 Na C A:Glu238 3.96 Na CA A:Glu238 4.30 Na O A:Ile239 2.47 Na N A:Ile239 3.92 Na C A:Ile239 3.21 Na CA A:Ile239 4.19 Na N A:Pro240 3.75 Na CD A:Pro240 4.93 Na C A:Pro240 4.44 Na CA A:Pro240 3.80 Na N A:Gly241 4.09 Na O A:Ile242 2.71 Na N A:Ile242 4.13 Na CB A:Ile242 4.97 Na C A:Ile242 3.80 Na CA A:Ile242 4.47 Na N A:Gly243 4.83 Na O3' B:Dc11 5.00 Na OP1 B:Dc12 2.60 Na P B:Dc12 3.90 Na OP2 B:Dc12 4.35 Na O5' B:Dc12 4.80 interactive model: Sodium binding site 2 out of 4 in 3epg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3epg. 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: A: Glu115, A: Phe116, A: Hoh453, conact list: Atom Atom Distance (A) Na O A:Glu115 4.79 Na OE1 A:Glu115 4.57 Na CB A:Glu115 4.67 Na OE2 A:Glu115 3.61 Na CD A:Glu115 4.02 Na C A:Glu115 4.91 Na CG A:Glu115 4.50 Na CE2 A:Phe116 4.51 Na CD1 A:Phe116 4.59 Na CD2 A:Phe116 4.79 Na CZ A:Phe116 4.26 Na CE1 A:Phe116 4.29 Na CG A:Phe116 4.84 Na O A:Hoh453 4.70 interactive model: Sodium binding site 3 out of 4 in 3epg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3epg. 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: A: Leu123, A: Lys207, A: Pro240, A: Gly241, B: Dc12, A: Hoh461, A: Hoh470, conact list: Atom Atom Distance (A) Na CD2 A:Leu123 4.61 Na NZ A:Lys207 4.91 Na O A:Pro240 4.07 Na CB A:Pro240 3.75 Na C A:Pro240 4.09 Na CA A:Pro240 4.41 Na N A:Gly241 4.49 Na CA A:Gly241 4.96 Na C5' B:Dc12 4.15 Na C4' B:Dc12 4.30 Na O A:Hoh461 3.77 Na O A:Hoh470 3.64 interactive model: Sodium binding site 4 out of 4 in 3epg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3epg. 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: Dc845, conact list: Atom Atom Distance (A) Na OP1 C:Dc845 4.58 Na C3' C:Dc845 4.66 Na P C:Dc845 4.98 Na O3' C:Dc845 4.47 Na C5' C:Dc845 3.69 Na C4' C:Dc845 4.90 Na O5' C:Dc845 4.16 interactive model: