Sodium in the structure of Crystal Structure of A Putative Beta-1,4-Endoglucanase / Cellulase From Prevotella Bryantii (pdb 3l55)

The binding sites of Sodium atom in the structure of Crystal Structure of A Putative Beta-1,4-Endoglucanase / Cellulase From Prevotella Bryantii (pdb code 3l55). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3l55 structure was solved by P.J.STOGIOS, V.YIM, O.EGOROVA, E.EVDOKIMOVA, A.JOACHIMIAK, A.M.EDWARDS, A.SAVCHENKO, MIDWEST CENTER FOR STRUCTURALGENOMICS (MCSG), ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS(OCSP), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 26.4-1.6 Space group P1211 a (A) 57.911 b (A) 85.256 c (A) 74.561 alpha (°) 90.00 beta (°) 109.15 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 21.9 Sodium Binding Sites: Sodium binding site 1 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3l55. 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: Asp80, A: Asn84, A: Hoh561, A: Hoh617, A: Hoh653, A: Hoh767, A: Hoh778, A: Hoh848, conact list: Atom Atom Distance (A) Na CB A:Asp80 4.38 Na OD2 A:Asp80 2.79 Na OD1 A:Asp80 4.97 Na CG A:Asp80 3.92 Na CB A:Asn84 4.71 Na ND2 A:Asn84 4.52 Na O A:Hoh561 4.33 Na O A:Hoh617 4.06 Na O A:Hoh653 4.05 Na O A:Hoh767 4.86 Na O A:Hoh778 2.84 Na O A:Hoh848 2.99 interactive model: Sodium binding site 2 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3l55. 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: Gly34, A: Cys35, A: Phe47, B: Trp243, A: Hoh432, A: Hoh517, B: Hoh396, B: Hoh646, conact list: Atom Atom Distance (A) Na O A:Gly34 4.67 Na CB A:Cys35 4.94 Na CA A:Cys35 4.65 Na CZ A:Phe47 3.73 Na CE1 A:Phe47 3.75 Na CD1 B:Trp243 4.44 Na O B:Trp243 4.56 Na O A:Hoh432 4.82 Na O A:Hoh517 4.26 Na O B:Hoh396 4.88 Na O B:Hoh646 3.32 interactive model: Sodium binding site 3 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3l55. 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: Ile300, A: Ser339, A: Leu340, A: Pro341, A: Thr342, A: Val343, conact list: Atom Atom Distance (A) Na CB A:Ile300 4.89 Na CD1 A:Ile300 4.60 Na CG2 A:Ile300 3.57 Na O A:Ser339 4.66 Na O A:Leu340 4.11 Na N A:Leu340 4.72 Na CB A:Leu340 3.87 Na CD2 A:Leu340 4.09 Na C A:Leu340 3.49 Na CG A:Leu340 4.64 Na CA A:Leu340 3.43 Na N A:Pro341 3.54 Na CB A:Pro341 4.97 Na CD A:Pro341 3.53 Na C A:Pro341 4.31 Na CG A:Pro341 4.12 Na CA A:Pro341 4.45 Na N A:Thr342 3.33 Na CB A:Thr342 3.78 Na CG2 A:Thr342 3.71 Na OG1 A:Thr342 3.11 Na C A:Thr342 4.74 Na CA A:Thr342 4.06 Na N A:Val343 4.38 Na CG2 A:Val343 4.99 interactive model: Sodium binding site 4 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3l55. 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: Thr261, A: Phe264, A: Ser265, A: Leu313, A: His317, conact list: Atom Atom Distance (A) Na O A:Thr261 3.55 Na CB A:Thr261 3.65 Na CG2 A:Thr261 4.24 Na OG1 A:Thr261 4.78 Na C A:Thr261 4.10 Na CA A:Thr261 3.85 Na CB A:Phe264 4.54 Na N A:Ser265 4.61 Na CB A:Ser265 4.92 Na CB A:Ser265 4.86 Na OG A:Ser265 3.63 Na CD2 A:Leu313 4.49 Na NE2 A:His317 3.65 Na ND1 A:His317 4.25 Na CD2 A:His317 4.97 Na CE1 A:His317 3.09 interactive model: Sodium binding site 5 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3l55. 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: Gly21, B: Leu22, B: Gly23, B: Val311, B: Ala320, B: Thr321, B: Tyr351, B: Hoh385, B: Hoh404, B: Hoh590, B: Hoh910, conact list: Atom Atom Distance (A) Na O B:Gly21 2.84 Na C B:Gly21 3.64 Na CA B:Gly21 4.75 Na N B:Leu22 4.06 Na CB B:Leu22 4.85 Na CD2 B:Leu22 4.07 Na C B:Leu22 4.56 Na CG B:Leu22 4.96 Na CA B:Leu22 3.81 Na N B:Gly23 4.33 Na CG2 B:Val311 4.71 Na CG1 B:Val311 4.70 Na CA B:Val311 4.97 Na C B:Ala320 3.92 Na CB B:Ala320 4.45 Na CA B:Ala320 3.96 Na O B:Thr321 3.54 Na N B:Thr321 3.03 Na CB B:Thr321 3.65 Na CG2 B:Thr321 3.82 Na OG1 B:Thr321 2.90 Na C B:Thr321 4.07 Na CA B:Thr321 3.73 Na CD1 B:Tyr351 4.85 Na CE1 B:Tyr351 4.78 Na O B:Hoh385 2.74 Na O B:Hoh404 4.32 Na O B:Hoh590 4.20 Na O B:Hoh910 4.10 interactive model: Sodium binding site 6 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3l55. 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: His284, B: Ser290, B: Trp324, B: Mse325, B: Ser326, B: Asp329, B: Hoh386, B: Hoh463, B: Hoh508, B: Hoh642, B: Hoh648, B: Hoh683, B: Hoh690, B: Hoh698, B: Hoh773, conact list: Atom Atom Distance (A) Na NE2 B:His284 2.91 Na ND1 B:His284 5.00 Na CD2 B:His284 3.79 Na CE1 B:His284 3.89 Na CG B:His284 4.97 Na OG B:Ser290 4.43 Na CD1 B:Trp324 4.27 Na O B:Trp324 4.80 Na NE1 B:Trp324 4.25 Na SE B:Mse325 3.47 Na CB B:Mse325 3.66 Na CE B:Mse325 3.86 Na CG B:Mse325 4.23 Na CA B:Mse325 4.99 Na N B:Ser326 4.93 Na OG B:Ser326 4.48 Na OD1 B:Asp329 5.00 Na O B:Hoh386 3.67 Na O B:Hoh463 4.48 Na O B:Hoh508 4.20 Na O B:Hoh642 4.20 Na O B:Hoh648 4.14 Na O B:Hoh683 4.15 Na O B:Hoh690 2.98 Na O B:Hoh698 3.05 Na O B:Hoh773 4.53 interactive model: Sodium binding site 7 out of 7 in 3l55 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3l55. 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: Mse91, B: Lys94, B: Ala95, B: Hoh673, conact list: Atom Atom Distance (A) Na SE B:Mse91 3.69 Na O B:Mse91 3.11 Na CB B:Mse91 4.27 Na CB B:Mse91 4.14 Na CE B:Mse91 3.62 Na CE B:Mse91 4.13 Na C B:Mse91 3.96 Na CG B:Mse91 4.71 Na CG B:Mse91 4.68 Na CA B:Mse91 4.10 Na CA B:Mse91 4.09 Na O B:Lys94 4.81 Na CB B:Lys94 3.89 Na CE B:Lys94 4.71 Na CD B:Lys94 3.93 Na C B:Lys94 4.22 Na CG B:Lys94 3.89 Na CA B:Lys94 4.63 Na N B:Ala95 3.77 Na CB B:Ala95 4.12 Na CA B:Ala95 4.10 Na O B:Hoh673 3.51 interactive model: