Sodium in the structure of Structure of Ybbd in Complex With Pugnac (pdb 3nvd)

The binding sites of Sodium atom in the structure of Structure of Ybbd in Complex With Pugnac (pdb code 3nvd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3nvd structure was solved by K.DIEDERICHS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 48.5-1.8 Space group P1 a (A) 58.473 b (A) 73.206 c (A) 83.788 alpha (°) 79.83 beta (°) 69.45 gamma (°) 88.22 Rfactor (%) 18.7 Rfree (%) 24.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3nvd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3nvd. 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: His222, A: His226, A: Ser233, A: Thr268, A: Ala269, A: His270, A: Val271, A: Asp318, A: Met322, A: Oan646, conact list: Atom Atom Distance (A) Na HB2 A:His222 4.92 Na HB3 A:His222 4.50 Na CD2 A:His222 4.78 Na CG A:His222 4.98 Na HD2 A:His222 4.54 Na CD2 A:His226 3.49 Na CG A:His226 4.82 Na HD2 A:His226 2.88 Na NE2 A:His226 3.61 Na CE1 A:His226 4.92 Na HB2 A:Ser233 3.38 Na HG A:Ser233 2.02 Na CB A:Ser233 3.56 Na HB3 A:Ser233 3.82 Na OG A:Ser233 2.76 Na CA A:Ser233 4.96 Na O A:Thr268 4.60 Na HB2 A:Ala269 4.58 Na N A:Ala269 4.92 Na CB A:Ala269 4.31 Na HA A:Ala269 2.95 Na C A:Ala269 3.93 Na CA A:Ala269 3.76 Na HB1 A:Ala269 3.89 Na HB2 A:His270 3.19 Na N A:His270 3.16 Na CB A:His270 3.82 Na HB3 A:His270 4.71 Na CD2 A:His270 4.01 Na C A:His270 4.53 Na CG A:His270 3.92 Na CA A:His270 4.04 Na HD2 A:His270 3.88 Na O A:His270 4.59 Na NE2 A:His270 4.86 Na HA A:His270 4.91 Na ND1 A:His270 4.77 Na H A:His270 2.40 Na CG2 A:Val271 4.76 Na HG21 A:Val271 4.96 Na HG22 A:Val271 4.93 Na HG23 A:Val271 3.92 Na HB2 A:Asp318 3.93 Na CB A:Asp318 4.11 Na HB3 A:Asp318 3.88 Na OD2 A:Asp318 2.76 Na OD1 A:Asp318 4.83 Na CG A:Asp318 3.78 Na HE3 A:Met322 4.46 Na SD A:Met322 4.46 Na CE A:Met322 3.70 Na HE1 A:Met322 2.93 Na HE2 A:Met322 3.71 Na CAH A:Oan646 3.65 Na CAG A:Oan646 4.67 Na NAI A:Oan646 4.58 interactive model: Sodium binding site 2 out of 2 in 3nvd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3nvd. 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: His222, B: His226, B: Ser233, B: Thr268, B: Ala269, B: His270, B: Val271, B: Asp318, B: Met322, B: Oan646, conact list: Atom Atom Distance (A) Na CB B:His222 4.96 Na HB3 B:His222 4.28 Na CD2 B:His222 4.82 Na CG B:His222 4.99 Na HD2 B:His222 4.56 Na CD2 B:His226 3.42 Na CG B:His226 4.74 Na HD2 B:His226 2.79 Na NE2 B:His226 3.57 Na CE1 B:His226 4.90 Na HB2 B:Ser233 3.40 Na HG B:Ser233 2.38 Na CB B:Ser233 3.59 Na HB3 B:Ser233 3.55 Na OG B:Ser233 3.16 Na C B:Thr268 4.98 Na O B:Thr268 4.46 Na O B:Ala269 4.88 Na HB2 B:Ala269 4.25 Na N B:Ala269 4.63 Na CB B:Ala269 3.97 Na HB3 B:Ala269 4.83 Na HA B:Ala269 2.65 Na C B:Ala269 3.68 Na CA B:Ala269 3.44 Na HB1 B:Ala269 3.55 Na HB2 B:His270 3.57 Na N B:His270 3.01 Na CB B:His270 3.97 Na HB3 B:His270 4.93 Na CD2 B:His270 3.80 Na C B:His270 4.34 Na CG B:His270 3.92 Na CA B:His270 3.93 Na HD2 B:His270 3.62 Na O B:His270 4.49 Na NE2 B:His270 4.62 Na HA B:His270 4.80 Na ND1 B:His270 4.76 Na H B:His270 2.34 Na CG2 B:Val271 4.64 Na HG21 B:Val271 4.83 Na HG22 B:Val271 4.86 Na HG23 B:Val271 3.80 Na HB2 B:Asp318 3.89 Na CB B:Asp318 4.08 Na HB3 B:Asp318 3.87 Na OD2 B:Asp318 2.79 Na OD1 B:Asp318 4.86 Na CG B:Asp318 3.77 Na SD B:Met322 4.75 Na CE B:Met322 4.36 Na HE1 B:Met322 3.67 Na HE2 B:Met322 4.37 Na CAH B:Oan646 3.91 Na CAG B:Oan646 4.89 Na NAI B:Oan646 4.82 interactive model: