Sodium in the structure of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase (pdb 3ddk)

The binding sites of Sodium atom in the structure of Coxsackievirus B3 3DPOL Rna Dependent Rna Polymerase (pdb code 3ddk). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ddk structure was solved by G.CAMPAGNOLA, M.H.WEYGANDT, K.E.SCOGGIN, O.B.PEERSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 52.6-2.2 Space group P43212 a (A) 74.360 b (A) 74.360 c (A) 288.050 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 23.4 Sodium Binding Sites: Sodium binding site 1 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ddk. 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: Glu2, A: Glu4, A: Asn65, A: Asn67, A: Arg284, A: Hoh546, conact list: Atom Atom Distance (A) Na CB A:Glu2 4.65 Na CG A:Glu2 4.47 Na OE1 A:Glu4 4.29 Na OE2 A:Glu4 3.41 Na CD A:Glu4 4.27 Na CB A:Asn65 4.44 Na ND2 A:Asn65 3.86 Na CG A:Asn65 4.67 Na ND2 A:Asn67 4.04 Na OD1 A:Asn67 4.04 Na CG A:Asn67 4.49 Na CD A:Arg284 4.13 Na CZ A:Arg284 4.77 Na NE A:Arg284 4.88 Na NH1 A:Arg284 3.82 Na O A:Hoh546 3.89 interactive model: Sodium binding site 2 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ddk. 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: Lys38, A: Lys376, A: Asp397, A: Glu400, A: Ser401, A: Hoh695, conact list: Atom Atom Distance (A) Na CE A:Lys38 4.42 Na CD A:Lys38 4.37 Na NZ A:Lys38 3.68 Na NZ A:Lys376 4.50 Na O A:Asp397 3.95 Na CB A:Asp397 4.21 Na C A:Asp397 4.58 Na OD1 A:Asp397 3.99 Na CG A:Asp397 4.49 Na CA A:Asp397 4.37 Na CB A:Glu400 4.22 Na CG A:Glu400 4.89 Na N A:Ser401 4.89 Na O A:Hoh695 4.39 interactive model: Sodium binding site 3 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ddk. 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: Arg188, A: Tyr195, A: Ser292, A: Gly293, A: So4923, A: Hoh565, conact list: Atom Atom Distance (A) Na CD A:Arg188 4.31 Na CZ A:Arg188 4.57 Na CG A:Arg188 4.10 Na NE A:Arg188 4.86 Na NH1 A:Arg188 3.55 Na CE2 A:Tyr195 3.93 Na CD2 A:Tyr195 4.33 Na CZ A:Tyr195 4.64 Na OH A:Tyr195 4.86 Na CB A:Ser292 3.85 Na OG A:Ser292 3.16 Na C A:Ser292 4.15 Na CA A:Ser292 3.77 Na N A:Gly293 3.53 Na CA A:Gly293 4.50 Na S A:So4923 4.00 Na O1 A:So4923 4.67 Na O2 A:So4923 3.37 Na O3 A:So4923 3.45 Na O A:Hoh565 3.03 interactive model: Sodium binding site 4 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3ddk. 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: His228, A: Leu229, A: Glu366, A: Val367, A: So4924, A: Hoh625, A: Hoh627, A: Hoh675, A: Hoh754, conact list: Atom Atom Distance (A) Na O A:His228 4.95 Na CB A:His228 4.31 Na ND1 A:His228 4.62 Na C A:His228 4.15 Na CG A:His228 4.97 Na CA A:His228 4.42 Na O A:Leu229 2.91 Na N A:Leu229 3.54 Na CB A:Leu229 4.20 Na C A:Leu229 3.81 Na CA A:Leu229 4.01 Na OE1 A:Glu366 3.47 Na OE2 A:Glu366 3.23 Na CD A:Glu366 3.47 Na C A:Glu366 4.79 Na CG A:Glu366 4.53 Na CA A:Glu366 4.97 Na O A:Val367 2.90 Na N A:Val367 3.83 Na CB A:Val367 4.20 Na C A:Val367 3.91 Na CA A:Val367 4.24 Na S A:So4924 4.21 Na O1 A:So4924 4.70 Na O2 A:So4924 4.14 Na O3 A:So4924 3.21 Na O A:Hoh625 3.01 Na O A:Hoh627 3.80 Na O A:Hoh675 4.73 Na O A:Hoh754 4.80 interactive model: Sodium binding site 5 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3ddk. 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: His69, A: Asp71, A: Glu72, A: Hoh548, conact list: Atom Atom Distance (A) Na NE2 A:His69 3.91 Na CE1 A:His69 4.33 Na CB A:Asp71 3.69 Na C A:Asp71 4.05 Na CA A:Asp71 3.76 Na N A:Glu72 3.40 Na CB A:Glu72 4.11 Na OE2 A:Glu72 4.24 Na CD A:Glu72 4.60 Na CG A:Glu72 4.07 Na CA A:Glu72 4.34 Na O A:Hoh548 2.90 interactive model: Sodium binding site 6 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3ddk. 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: His199, A: Val210, A: Ser295, A: Ile296, A: Hoh565, A: Hoh568, A: Hoh594, A: Hoh655, A: Hoh656, conact list: Atom Atom Distance (A) Na NE2 A:His199 2.90 Na ND1 A:His199 4.73 Na CD2 A:His199 4.10 Na CE1 A:His199 3.47 Na CB A:Val210 4.98 Na CG1 A:Val210 3.50 Na CB A:Ser295 4.82 Na CD1 A:Ile296 4.46 Na CG1 A:Ile296 4.68 Na O A:Hoh565 3.07 Na O A:Hoh568 4.70 Na O A:Hoh594 2.76 Na O A:Hoh655 3.15 Na O A:Hoh656 4.17 interactive model: Sodium binding site 7 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3ddk. 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: Val33, A: Phe34, A: Glu35, A: His399, A: Lys436, A: Hoh713, conact list: Atom Atom Distance (A) Na O A:Val33 4.77 Na CB A:Phe34 4.10 Na CD1 A:Phe34 3.76 Na C A:Phe34 4.08 Na CE1 A:Phe34 4.75 Na CG A:Phe34 4.41 Na CA A:Phe34 3.83 Na O A:Glu35 4.63 Na N A:Glu35 3.31 Na CB A:Glu35 4.08 Na OE2 A:Glu35 4.90 Na CD A:Glu35 4.93 Na C A:Glu35 4.95 Na CG A:Glu35 3.83 Na CA A:Glu35 4.26 Na NE2 A:His399 4.14 Na CB A:His399 4.79 Na ND1 A:His399 3.45 Na CD2 A:His399 4.46 Na CE1 A:His399 3.52 Na CG A:His399 4.07 Na CD A:Lys436 4.99 Na NZ A:Lys436 4.00 Na O A:Hoh713 3.36 interactive model: Sodium binding site 8 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3ddk. 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: Tyr385, A: Arg455, A: Leu459, conact list: Atom Atom Distance (A) Na CZ A:Tyr385 4.27 Na CE1 A:Tyr385 4.21 Na OH A:Tyr385 3.37 Na NE A:Arg455 4.92 Na CD1 A:Leu459 4.66 interactive model: Sodium binding site 9 out of 9 in 3ddk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3ddk. 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: Val313, A: Tyr314, A: Lys315, A: Gly316, A: Hoh659, conact list: Atom Atom Distance (A) Na O A:Val313 4.85 Na O A:Tyr314 4.27 Na CB A:Tyr314 4.13 Na CD1 A:Tyr314 4.26 Na C A:Tyr314 3.72 Na CG A:Tyr314 4.66 Na CA A:Tyr314 3.76 Na O A:Lys315 2.70 Na N A:Lys315 3.75 Na C A:Lys315 3.70 Na CA A:Lys315 4.42 Na N A:Gly316 4.60 Na C A:Gly316 4.87 Na CA A:Gly316 4.66 Na O A:Hoh659 3.01 interactive model: