Sodium in the structure of Cocaine Hydrolytic Antibody 15A10 (pdb 1nj9)

The binding sites of Sodium atom in the structure of Cocaine Hydrolytic Antibody 15A10 (pdb code 1nj9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1nj9 structure was solved by N.A.LARSEN, P.DE PRADA, S.X.DENG, X.ZHU, D.W.LANDRY, I.A.WILSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.4 Space group P1211 a (A) 37.500 b (A) 108.400 c (A) 111.300 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 28.3 Sodium Binding Sites: Sodium binding site 1 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1nj9. 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: L: Pro59, L: Ala60, L: Arg61, conact list: Atom Atom Distance (A) Na CB L:Pro59 4.34 Na C L:Pro59 4.85 Na CA L:Pro59 4.83 Na N L:Ala60 4.19 Na C L:Ala60 4.79 Na CB L:Ala60 4.63 Na CA L:Ala60 4.78 Na N L:Arg61 3.91 Na CB L:Arg61 3.87 Na CD L:Arg61 4.17 Na CZ L:Arg61 4.72 Na CG L:Arg61 4.08 Na NE L:Arg61 4.92 Na NH1 L:Arg61 3.63 Na CA L:Arg61 4.51 interactive model: Sodium binding site 2 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1nj9. 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: L: Lys39, L: Pro40, L: Asp41, L: Hoh1014, conact list: Atom Atom Distance (A) Na O L:Lys39 4.93 Na CB L:Lys39 3.55 Na CE L:Lys39 4.37 Na CD L:Lys39 4.40 Na C L:Lys39 4.43 Na CG L:Lys39 4.26 Na CA L:Lys39 4.51 Na NZ L:Lys39 4.68 Na O L:Pro40 4.80 Na N L:Pro40 4.36 Na CD L:Pro40 4.20 Na C L:Pro40 4.73 Na CA L:Pro40 4.96 Na N L:Asp41 4.99 Na CB L:Asp41 4.89 Na OD2 L:Asp41 3.66 Na OD1 L:Asp41 2.66 Na CG L:Asp41 3.51 Na O L:Hoh1014 4.73 interactive model: Sodium binding site 3 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1nj9. 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: H: Ala197, H: His198, H: Pro199, H: Ser202, H: Thr203, H: Lys204, conact list: Atom Atom Distance (A) Na C H:Ala197 4.63 Na CB H:Ala197 4.10 Na CA H:Ala197 4.58 Na O H:His198 3.98 Na N H:His198 4.30 Na C H:His198 4.06 Na CA H:His198 4.94 Na O H:Pro199 4.84 Na N H:Pro199 3.98 Na CB H:Pro199 4.78 Na CD H:Pro199 4.81 Na C H:Pro199 4.85 Na CA H:Pro199 3.88 Na O H:Ser202 4.50 Na N H:Ser202 4.88 Na C H:Ser202 4.15 Na CA H:Ser202 4.39 Na O H:Thr203 2.81 Na N H:Thr203 4.17 Na C H:Thr203 3.90 Na CA H:Thr203 4.64 Na N H:Lys204 4.88 Na CE H:Lys204 3.77 Na CD H:Lys204 4.38 Na CG H:Lys204 3.77 interactive model: Sodium binding site 4 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1nj9. 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: H: Pro211, H: Arg212, H: Hoh1017, H: Hoh1023, conact list: Atom Atom Distance (A) Na O H:Pro211 3.85 Na C H:Pro211 4.87 Na O H:Arg212 4.56 Na C H:Arg212 3.97 Na OXT H:Arg212 2.85 Na O H:Hoh1017 2.57 Na O H:Hoh1023 4.46 interactive model: Sodium binding site 5 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1nj9. 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: H: Val151, H: Thr152, H: Trp153, H: Ser155, H: Gly156, H: Ser157, H: Leu158, H: Ser159, H: Val162, H: Hoh1026, conact list: Atom Atom Distance (A) Na O H:Val151 4.96 Na O H:Thr152 4.82 Na N H:Thr152 4.84 Na CB H:Thr152 3.45 Na CG2 H:Thr152 4.23 Na OG1 H:Thr152 4.54 Na C H:Thr152 3.61 Na CA H:Thr152 3.44 Na N H:Trp153 2.83 Na CB H:Trp153 4.12 Na CD1 H:Trp153 4.89 Na C H:Trp153 4.00 Na CG H:Trp153 4.91 Na CA H:Trp153 3.80 Na O H:Trp153 3.44 Na C H:Ser155 4.64 Na O H:Gly156 4.32 Na N H:Gly156 3.34 Na C H:Gly156 3.74 Na CA H:Gly156 2.90 Na N H:Ser157 4.35 Na O H:Leu158 3.00 Na N H:Leu158 4.60 Na C H:Leu158 3.90 Na CA H:Leu158 4.95 Na N H:Ser159 4.41 Na CA H:Ser159 4.40 Na CG2 H:Val162 4.55 Na O H:Hoh1026 3.07 interactive model: Sodium binding site 6 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1nj9. 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: Ile27C, A: Thr28, A: Ser29, A: Asn31, A: Tyr32, A: Ala33, A: Val50, A: Leu66, conact list: Atom Atom Distance (A) Na CD1 A:Ile27C 4.58 Na O A:Thr28 3.46 Na C A:Thr28 4.08 Na O A:Ser29 3.96 Na N A:Ser29 4.30 Na C A:Ser29 4.19 Na CA A:Ser29 3.90 Na O A:Asn31 4.78 Na N A:Asn31 4.54 Na CB A:Asn31 4.56 Na C A:Asn31 4.11 Na CA A:Asn31 4.62 Na O A:Tyr32 4.81 Na N A:Tyr32 3.43 Na C A:Tyr32 3.68 Na CA A:Tyr32 3.58 Na O A:Ala33 4.25 Na N A:Ala33 2.98 Na C A:Ala33 4.58 Na CB A:Ala33 3.67 Na CA A:Ala33 3.88 Na O A:Val50 3.67 Na CB A:Val50 4.77 Na C A:Val50 4.08 Na CG1 A:Val50 4.13 Na CA A:Val50 4.08 Na CD1 A:Leu66 4.12 Na CD2 A:Leu66 4.92 Na CG A:Leu66 4.99 interactive model: Sodium binding site 7 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1nj9. 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: His42, B: Val89, B: Gln105, B: Gly106, B: Thr107, B: Leu108, B: Hoh1015, B: Hoh1029, conact list: Atom Atom Distance (A) Na CD2 A:His42 4.13 Na CG1 B:Val89 4.10 Na O B:Gln105 3.73 Na C B:Gln105 4.53 Na O B:Gly106 3.84 Na N B:Gly106 4.91 Na C B:Gly106 4.05 Na CA B:Gly106 4.55 Na N B:Thr107 4.49 Na C B:Thr107 4.87 Na CA B:Thr107 4.73 Na N B:Leu108 4.49 Na CB B:Leu108 4.96 Na O B:Hoh1015 4.16 Na O B:Hoh1029 4.76 interactive model: Sodium binding site 8 out of 8 in 1nj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1nj9. 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: Val151, B: Thr152, B: Trp153, B: Gly156, B: Leu158, B: Ser159, B: Val162, conact list: Atom Atom Distance (A) Na O B:Val151 4.88 Na CB B:Thr152 4.28 Na CG2 B:Thr152 4.66 Na C B:Thr152 4.57 Na CA B:Thr152 4.10 Na N B:Trp153 3.97 Na CB B:Trp153 4.97 Na CD1 B:Trp153 4.64 Na CA B:Trp153 5.00 Na O B:Trp153 4.92 Na O B:Gly156 4.86 Na N B:Gly156 4.92 Na C B:Gly156 4.68 Na CA B:Gly156 4.12 Na O B:Leu158 3.09 Na C B:Leu158 3.99 Na O B:Ser159 4.91 Na N B:Ser159 4.31 Na CB B:Ser159 4.50 Na C B:Ser159 4.86 Na CA B:Ser159 3.84 Na CB B:Val162 4.86 Na CG2 B:Val162 4.33 Na CG1 B:Val162 4.68 interactive model: