Sodium in the structure of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) (pdb 2hb6)

The binding sites of Sodium atom in the structure of Structure of Caenorhabditis Elegans Leucine Aminopeptidase (LAP1) (pdb code 2hb6). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2hb6 structure was solved by Y.PATSKOVSKY, C.ZHAN, B.C.WENGERTER, U.RAMAGOPAL, S.MILSTEIN, M.VIDAL, S.C.ALMO, S.K.BURLEY, NEW YORK SGX RESEARCH CENTER FOR STRUCTURALGENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group P63 a (A) 131.820 b (A) 131.820 c (A) 125.573 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 14.7 Rfree (%) 18.3 Sodium Binding Sites: Sodium binding site 1 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2hb6. 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: Lys252, A: Val254, A: Asp257, A: Asp275, A: Glu336, A: Gly337, A: Thr362, A: So4492, A: Na3002, A: Hoh3379, conact list: Atom Atom Distance (A) Na CE A:Lys252 3.10 Na CD A:Lys252 4.53 Na NZ A:Lys252 2.32 Na CB A:Val254 4.41 Na CG2 A:Val254 4.37 Na CG1 A:Val254 4.34 Na CB A:Asp257 3.92 Na OD2 A:Asp257 2.79 Na OD1 A:Asp257 4.53 Na CG A:Asp257 3.59 Na CB A:Asp275 4.20 Na OD2 A:Asp275 1.85 Na OD1 A:Asp275 3.32 Na CG A:Asp275 2.91 Na OE1 A:Glu336 2.28 Na OE2 A:Glu336 3.72 Na CD A:Glu336 3.35 Na CG A:Glu336 4.66 Na N A:Gly337 4.48 Na CA A:Gly337 4.57 Na O A:Thr362 4.53 Na S A:So4492 4.29 Na O1 A:So4492 4.04 Na O4 A:So4492 3.27 Na NA A:Na3002 2.76 Na O A:Hoh3379 4.62 interactive model: Sodium binding site 2 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2hb6. 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: Lys252, A: Asp257, A: Lys264, A: Asp275, A: Asp334, A: Ala335, A: Glu336, A: Gly337, A: Leu363, A: So4492, A: Na3001, A: Hoh3379, conact list: Atom Atom Distance (A) Na NZ A:Lys252 4.43 Na CB A:Asp257 4.55 Na OD2 A:Asp257 2.26 Na OD1 A:Asp257 4.09 Na CG A:Asp257 3.47 Na CE A:Lys264 4.52 Na NZ A:Lys264 4.07 Na OD2 A:Asp275 4.20 Na O A:Asp334 2.68 Na CB A:Asp334 4.60 Na OD2 A:Asp334 4.63 Na C A:Asp334 3.52 Na OD1 A:Asp334 2.93 Na CG A:Asp334 3.88 Na CA A:Asp334 4.11 Na N A:Ala335 4.44 Na CA A:Ala335 4.66 Na N A:Glu336 4.51 Na OE1 A:Glu336 3.29 Na OE2 A:Glu336 2.74 Na CD A:Glu336 3.41 Na CG A:Glu336 4.89 Na N A:Gly337 4.96 Na O A:Leu363 4.78 Na S A:So4492 3.98 Na O1 A:So4492 4.63 Na O4 A:So4492 2.73 Na O3 A:So4492 4.25 Na NA A:Na3001 2.76 Na O A:Hoh3379 2.94 interactive model: Sodium binding site 3 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2hb6. 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: Ser139, A: Gly140, A: Arg142, A: So4494, A: Hoh3477, conact list: Atom Atom Distance (A) Na CB A:Ser139 4.54 Na OG A:Ser139 4.68 Na C A:Ser139 4.73 Na N A:Gly140 3.87 Na CA A:Gly140 3.85 Na NH2 A:Arg142 4.18 Na S A:So4494 3.35 Na O1 A:So4494 3.91 Na O2 A:So4494 4.57 Na O4 A:So4494 3.47 Na O3 A:So4494 2.28 Na O A:Hoh3477 4.95 interactive model: Sodium binding site 4 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2hb6. 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: Lys252, B: Val254, B: Asp257, B: Asp275, B: Glu336, B: Gly337, B: Thr362, B: So4492, B: Na3004, B: Hoh3300, conact list: Atom Atom Distance (A) Na CE B:Lys252 3.15 Na CD B:Lys252 4.58 Na NZ B:Lys252 2.32 Na CB B:Val254 4.45 Na CG2 B:Val254 4.41 Na CG1 B:Val254 4.35 Na CB B:Asp257 3.90 Na OD2 B:Asp257 2.74 Na OD1 B:Asp257 4.53 Na CG B:Asp257 3.57 Na CB B:Asp275 4.21 Na OD2 B:Asp275 1.86 Na OD1 B:Asp275 3.33 Na CG B:Asp275 2.92 Na OE1 B:Glu336 2.30 Na OE2 B:Glu336 3.69 Na CD B:Glu336 3.35 Na CG B:Glu336 4.67 Na N B:Gly337 4.51 Na CA B:Gly337 4.62 Na O B:Thr362 4.55 Na S B:So4492 4.26 Na O4 B:So4492 3.27 Na O3 B:So4492 4.02 Na NA B:Na3004 2.75 Na O B:Hoh3300 4.52 interactive model: Sodium binding site 5 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2hb6. 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: Lys252, B: Asp257, B: Lys264, B: Asp275, B: Asp334, B: Ala335, B: Glu336, B: Gly337, B: Leu363, B: So4492, B: Na3003, B: Hoh3300, conact list: Atom Atom Distance (A) Na NZ B:Lys252 4.43 Na CB B:Asp257 4.57 Na OD2 B:Asp257 2.28 Na OD1 B:Asp257 4.11 Na CG B:Asp257 3.49 Na CE B:Lys264 4.52 Na NZ B:Lys264 4.05 Na OD2 B:Asp275 4.23 Na O B:Asp334 2.69 Na CB B:Asp334 4.56 Na OD2 B:Asp334 4.57 Na C B:Asp334 3.51 Na OD1 B:Asp334 2.88 Na CG B:Asp334 3.83 Na CA B:Asp334 4.09 Na N B:Ala335 4.43 Na CA B:Ala335 4.65 Na N B:Glu336 4.51 Na OE1 B:Glu336 3.32 Na OE2 B:Glu336 2.75 Na CD B:Glu336 3.43 Na CG B:Glu336 4.90 Na N B:Gly337 4.99 Na O B:Leu363 4.78 Na S B:So4492 3.97 Na O2 B:So4492 4.23 Na O4 B:So4492 2.72 Na O3 B:So4492 4.62 Na NA B:Na3003 2.75 Na O B:Hoh3300 2.84 interactive model: Sodium binding site 6 out of 6 in 2hb6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 2hb6. 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: Ser139, B: Gly140, B: Arg142, B: So4493, conact list: Atom Atom Distance (A) Na CB B:Ser139 4.63 Na OG B:Ser139 4.80 Na C B:Ser139 4.80 Na N B:Gly140 3.88 Na CA B:Gly140 3.88 Na CZ B:Arg142 4.90 Na NH2 B:Arg142 4.04 Na S B:So4493 3.23 Na O1 B:So4493 2.31 Na O2 B:So4493 3.68 Na O4 B:So4493 3.26 Na O3 B:So4493 4.52 interactive model: