Sodium in the structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna (pdb 3l25)

The binding sites of Sodium atom in the structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna (pdb code 3l25). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3l25 structure was solved by D.W.LEUNG, K.C.PRINS, D.M.BOREK, M.FARAHBAKHSH, J.M.TUFARIELLO, P.RAMANAN, J.C.NIX, L.A.HELGESON, Z.OTWINOWSKI, R.B.HONZATKO, C.F.BASLER, G.K.AMARASINGHE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 44.7-2.0 Space group P212121 a (A) 78.947 b (A) 84.571 c (A) 89.316 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.9 Rfree (%) 20.7 Sodium Binding Sites: Sodium binding site 1 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3l25. 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: Tyr229, A: Leu232, A: Pro233, A: Gly234, A: Phe235, A: His240, A: Hoh32, A: Hoh185, A: Hoh353, conact list: Atom Atom Distance (A) Na O A:Tyr229 4.09 Na O A:Leu232 2.40 Na N A:Leu232 4.91 Na CB A:Leu232 4.87 Na C A:Leu232 3.57 Na CA A:Leu232 4.65 Na O A:Pro233 4.26 Na N A:Pro233 4.30 Na C A:Pro233 3.73 Na CA A:Pro233 4.08 Na O A:Gly234 2.40 Na N A:Gly234 3.51 Na C A:Gly234 3.48 Na CA A:Gly234 4.01 Na N A:Phe235 4.62 Na CE2 A:Phe235 4.27 Na CD1 A:Phe235 4.00 Na CD2 A:Phe235 4.55 Na CZ A:Phe235 3.82 Na CE1 A:Phe235 3.68 Na CG A:Phe235 4.43 Na NE2 A:His240 4.09 Na CE1 A:His240 4.62 Na O A:Hoh32 2.38 Na O A:Hoh185 2.24 Na O A:Hoh353 2.33 interactive model: Sodium binding site 2 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3l25. 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: B: Tyr229, B: Leu232, B: Pro233, B: Gly234, B: Phe235, B: His240, B: Hoh71, B: Hoh346, conact list: Atom Atom Distance (A) Na O B:Tyr229 4.07 Na O B:Leu232 2.46 Na CB B:Leu232 4.90 Na C B:Leu232 3.61 Na CA B:Leu232 4.69 Na O B:Pro233 4.23 Na N B:Pro233 4.32 Na C B:Pro233 3.69 Na CA B:Pro233 4.01 Na O B:Gly234 2.41 Na N B:Gly234 3.47 Na C B:Gly234 3.50 Na CA B:Gly234 4.04 Na N B:Phe235 4.62 Na CE2 B:Phe235 4.14 Na CD1 B:Phe235 3.97 Na CD2 B:Phe235 4.46 Na CZ B:Phe235 3.70 Na CE1 B:Phe235 3.61 Na CG B:Phe235 4.40 Na NE2 B:His240 4.23 Na CE1 B:His240 4.62 Na O B:Hoh71 2.46 Na O B:Hoh346 4.41 interactive model: Sodium binding site 3 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3l25. 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: B: Val314, B: Pro315, B: Pro316, B: Ser317, B: Pro318, B: Hoh29, B: Hoh76, conact list: Atom Atom Distance (A) Na CB B:Val314 4.67 Na CG2 B:Val314 4.05 Na O B:Pro315 2.46 Na N B:Pro315 4.86 Na C B:Pro315 3.52 Na CA B:Pro315 4.83 Na O B:Pro316 2.50 Na N B:Pro316 3.94 Na CB B:Pro316 4.92 Na C B:Pro316 3.14 Na CA B:Pro316 3.46 Na N B:Ser317 4.15 Na CA B:Ser317 4.76 Na CD B:Pro318 3.91 Na CG B:Pro318 4.80 Na O B:Hoh29 2.38 Na O B:Hoh76 4.62 interactive model: Sodium binding site 4 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3l25. 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: A4, C: U5, C: G6, F: A4, F: U5, F: G6, A: Fmt19, D: Fmt20, A: Hoh33, A: Hoh363, C: Hoh89, C: Hoh96, D: Hoh34, D: Hoh357, F: Hoh21, F: Hoh54, conact list: Atom Atom Distance (A) Na C2 C:A4 4.25 Na N1 C:A4 4.78 Na N3 C:U5 4.46 Na C2 C:U5 3.50 Na N1 C:U5 4.30 Na C1' C:U5 4.13 Na O2 C:U5 2.34 Na C2' C:U5 4.61 Na O2' C:U5 4.50 Na O4' C:G6 4.94 Na C2 F:A4 4.29 Na N1 F:A4 4.84 Na N3 F:U5 4.41 Na C2 F:U5 3.49 Na N1 F:U5 4.32 Na C1' F:U5 4.14 Na O2 F:U5 2.33 Na C2' F:U5 4.60 Na O2' F:U5 4.46 Na O4' F:G6 4.92 Na O2 A:Fmt19 3.82 Na C A:Fmt19 4.81 Na O1 D:Fmt20 3.90 Na C D:Fmt20 4.91 Na O A:Hoh33 2.45 Na O A:Hoh363 4.23 Na O C:Hoh89 2.45 Na O C:Hoh96 4.85 Na O D:Hoh34 2.41 Na O D:Hoh357 4.12 Na O F:Hoh21 4.86 Na O F:Hoh54 2.53 interactive model: Sodium binding site 5 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3l25. 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: U5, C: G6, C: C7, F: G2, F: C3, F: A4, B: Hoh105, B: Hoh195, B: Hoh347, C: Hoh37, C: Hoh40, C: Hoh63, C: Hoh68, C: Hoh99, C: Hoh285, C: Hoh291, F: Hoh121, F: Hoh136, F: Hoh266, conact list: Atom Atom Distance (A) Na N3 C:U5 4.31 Na C5 C:U5 3.81 Na C4 C:U5 3.27 Na O4 C:U5 2.46 Na C6 C:G6 3.60 Na N1 C:G6 4.79 Na C5 C:G6 4.16 Na N7 C:G6 4.02 Na O6 C:G6 2.53 Na N4 C:C7 4.30 Na O6 F:G2 4.22 Na N4 F:C3 3.88 Na N6 F:A4 4.25 Na O B:Hoh105 4.57 Na O B:Hoh195 4.62 Na O B:Hoh347 3.89 Na O C:Hoh37 2.55 Na O C:Hoh40 2.41 Na O C:Hoh63 4.72 Na O C:Hoh68 4.29 Na O C:Hoh99 4.66 Na O C:Hoh285 2.45 Na O C:Hoh291 4.14 Na O F:Hoh121 2.39 Na O F:Hoh136 4.89 Na O F:Hoh266 4.86 interactive model: Sodium binding site 6 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3l25. 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: D: Lys309, D: Ser310, D: Lys339, C: G2, C: C3, C: Hoh108, C: Hoh307, D: Hoh80, D: Hoh151, D: Hoh342, D: Hoh344, D: Hoh362, D: Hoh363, conact list: Atom Atom Distance (A) Na O D:Lys309 4.18 Na C D:Lys309 4.68 Na N D:Ser310 4.59 Na CB D:Ser310 3.62 Na OG D:Ser310 2.70 Na CA D:Ser310 3.86 Na O D:Lys339 4.06 Na O2' C:G2 4.76 Na C3' C:C3 4.80 Na C1' C:C3 3.73 Na O4' C:C3 3.40 Na C5' C:C3 4.93 Na C2' C:C3 4.19 Na C4' C:C3 3.88 Na O2' C:C3 3.43 Na O C:Hoh108 4.13 Na O C:Hoh307 2.40 Na O D:Hoh80 4.47 Na O D:Hoh151 2.50 Na O D:Hoh342 4.68 Na O D:Hoh344 2.69 Na O D:Hoh362 2.20 Na O D:Hoh363 3.89 interactive model: Sodium binding site 7 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3l25. 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: D: Tyr229, D: Leu232, D: Pro233, D: Gly234, D: Phe235, D: His240, D: Hoh10, D: Hoh59, D: Hoh343, conact list: Atom Atom Distance (A) Na O D:Tyr229 4.07 Na O D:Leu232 2.42 Na N D:Leu232 4.94 Na CB D:Leu232 4.84 Na C D:Leu232 3.57 Na CA D:Leu232 4.63 Na O D:Pro233 4.32 Na N D:Pro233 4.31 Na C D:Pro233 3.74 Na CA D:Pro233 4.07 Na O D:Gly234 2.36 Na N D:Gly234 3.50 Na C D:Gly234 3.46 Na CA D:Gly234 4.01 Na N D:Phe235 4.60 Na CE2 D:Phe235 4.29 Na CD1 D:Phe235 3.99 Na CD2 D:Phe235 4.56 Na CZ D:Phe235 3.84 Na CE1 D:Phe235 3.68 Na CG D:Phe235 4.42 Na CA D:Phe235 5.00 Na NE2 D:His240 4.00 Na CE1 D:His240 4.49 Na O D:Hoh10 2.35 Na O D:Hoh59 2.27 Na O D:Hoh343 2.40 interactive model: Sodium binding site 8 out of 8 in 3l25 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3l25. 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: G2, C: C3, C: A4, F: U5, F: G6, F: C7, C: Hoh217, C: Hoh241, E: Hoh82, E: Hoh134, F: Hoh10, F: Hoh16, F: Hoh24, F: Hoh58, F: Hoh60, F: Hoh297, conact list: Atom Atom Distance (A) Na O6 C:G2 4.15 Na N4 C:C3 3.78 Na N6 C:A4 4.25 Na N3 F:U5 4.40 Na C5 F:U5 3.89 Na C4 F:U5 3.38 Na O4 F:U5 2.56 Na C6 F:G6 3.53 Na N1 F:G6 4.73 Na C5 F:G6 4.09 Na N7 F:G6 3.95 Na O6 F:G6 2.47 Na N4 F:C7 4.38 Na O C:Hoh217 2.16 Na O C:Hoh241 4.81 Na O E:Hoh82 4.59 Na O E:Hoh134 4.57 Na O F:Hoh10 4.78 Na O F:Hoh16 2.49 Na O F:Hoh24 4.35 Na O F:Hoh58 2.57 Na O F:Hoh60 4.90 Na O F:Hoh297 2.39 interactive model: