Sodium in the structure of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex With Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside (pdb 2bfg)

The binding sites of Sodium atom in the structure of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex With Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside (pdb code 2bfg). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2bfg structure was solved by M.CZJZEK, T.BRAVMAN, B.HENRISSAT, Y.SHOHAM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.1-2.4 Space group P212121 a (A) 88.950 b (A) 162.160 c (A) 308.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 27 Sodium Binding Sites: Sodium binding site 1 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2bfg. 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: Gly25, D: Arg26, D: Leu29, D: Trp117, D: Phe322, D: Glu323, D: Glu324, D: Hoh2013, D: Hoh2106, conact list: Atom Atom Distance (A) Na C D:Gly25 4.18 Na CA D:Gly25 3.97 Na N D:Arg26 3.38 Na CB D:Arg26 3.95 Na CD D:Arg26 4.65 Na CG D:Arg26 3.89 Na NH1 D:Arg26 4.06 Na CA D:Arg26 4.27 Na CD1 D:Leu29 3.92 Na CG D:Leu29 4.78 Na CD1 D:Trp117 3.95 Na CG D:Trp117 4.98 Na CZ2 D:Trp117 4.44 Na CE2 D:Trp117 4.06 Na NE1 D:Trp117 3.26 Na CB D:Phe322 4.70 Na CE2 D:Phe322 4.46 Na CD1 D:Phe322 4.13 Na CD2 D:Phe322 4.28 Na CZ D:Phe322 4.47 Na C D:Phe322 4.11 Na CE1 D:Phe322 4.29 Na CG D:Phe322 4.11 Na CA D:Phe322 4.07 Na N D:Glu323 3.24 Na CB D:Glu323 4.23 Na C D:Glu323 4.17 Na CA D:Glu323 4.03 Na N D:Glu324 3.63 Na CB D:Glu324 4.69 Na OE2 D:Glu324 4.77 Na CD D:Glu324 4.83 Na CG D:Glu324 3.87 Na CA D:Glu324 4.48 Na O D:Hoh2013 4.86 Na O D:Hoh2106 3.31 interactive model: Sodium binding site 2 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2bfg. 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: E: Gly25, E: Arg26, E: Leu29, E: Trp117, E: Phe322, E: Glu323, E: Glu324, E: Hoh2010, E: Hoh2124, conact list: Atom Atom Distance (A) Na C E:Gly25 4.22 Na CA E:Gly25 3.95 Na N E:Arg26 3.46 Na CB E:Arg26 4.06 Na CD E:Arg26 4.38 Na CG E:Arg26 4.05 Na NH1 E:Arg26 4.36 Na CA E:Arg26 4.36 Na CD1 E:Leu29 3.91 Na CG E:Leu29 4.87 Na CD1 E:Trp117 3.98 Na CZ2 E:Trp117 4.57 Na CE2 E:Trp117 4.15 Na NE1 E:Trp117 3.27 Na CB E:Phe322 4.60 Na CE2 E:Phe322 4.27 Na CD1 E:Phe322 4.16 Na CD2 E:Phe322 4.08 Na CZ E:Phe322 4.38 Na C E:Phe322 4.06 Na CE1 E:Phe322 4.34 Na CG E:Phe322 4.03 Na CA E:Phe322 3.99 Na O E:Glu323 4.95 Na N E:Glu323 3.24 Na CB E:Glu323 4.33 Na C E:Glu323 4.05 Na CA E:Glu323 4.04 Na N E:Glu324 3.59 Na CB E:Glu324 4.57 Na OE2 E:Glu324 4.88 Na CD E:Glu324 4.88 Na CG E:Glu324 3.91 Na CA E:Glu324 4.42 Na O E:Hoh2010 4.69 Na O E:Hoh2124 3.10 interactive model: Sodium binding site 3 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2bfg. 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: G: Gly25, G: Arg26, G: Leu29, G: Trp117, G: Phe322, G: Glu323, G: Glu324, G: Hoh2024, G: Hoh2110, conact list: Atom Atom Distance (A) Na C G:Gly25 4.10 Na CA G:Gly25 3.83 Na N G:Arg26 3.35 Na CB G:Arg26 4.15 Na CD G:Arg26 4.60 Na CG G:Arg26 3.97 Na NH1 G:Arg26 4.01 Na CA G:Arg26 4.35 Na CD1 G:Leu29 3.69 Na CG G:Leu29 4.85 Na CD1 G:Trp117 4.05 Na CZ2 G:Trp117 4.63 Na CE2 G:Trp117 4.22 Na NE1 G:Trp117 3.42 Na CB G:Phe322 4.59 Na CE2 G:Phe322 4.29 Na CD1 G:Phe322 4.10 Na CD2 G:Phe322 4.12 Na CZ G:Phe322 4.36 Na C G:Phe322 4.07 Na CE1 G:Phe322 4.28 Na CG G:Phe322 4.01 Na CA G:Phe322 3.96 Na O G:Glu323 4.95 Na N G:Glu323 3.21 Na CB G:Glu323 4.15 Na C G:Glu323 4.04 Na CA G:Glu323 3.98 Na N G:Glu324 3.64 Na CB G:Glu324 4.63 Na CD G:Glu324 4.83 Na CG G:Glu324 3.95 Na CA G:Glu324 4.43 Na O G:Hoh2024 4.96 Na O G:Hoh2110 3.14 interactive model: Sodium binding site 4 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2bfg. 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: Gly25, C: Arg26, C: Leu29, C: Trp117, C: Phe322, C: Glu323, C: Glu324, C: Hoh2012, C: Hoh2121, conact list: Atom Atom Distance (A) Na C C:Gly25 4.10 Na CA C:Gly25 3.88 Na N C:Arg26 3.34 Na CB C:Arg26 3.99 Na CD C:Arg26 4.33 Na CZ C:Arg26 4.95 Na CG C:Arg26 3.85 Na NH1 C:Arg26 3.94 Na CA C:Arg26 4.28 Na CD1 C:Leu29 3.75 Na CG C:Leu29 4.75 Na CD1 C:Trp117 3.87 Na CD2 C:Trp117 4.97 Na CG C:Trp117 4.89 Na CZ2 C:Trp117 4.50 Na CE2 C:Trp117 4.05 Na NE1 C:Trp117 3.23 Na CB C:Phe322 4.68 Na CE2 C:Phe322 4.50 Na CD1 C:Phe322 4.12 Na CD2 C:Phe322 4.31 Na CZ C:Phe322 4.49 Na C C:Phe322 4.07 Na CE1 C:Phe322 4.30 Na CG C:Phe322 4.13 Na CA C:Phe322 4.01 Na N C:Glu323 3.26 Na CB C:Glu323 4.14 Na C C:Glu323 4.12 Na CA C:Glu323 3.99 Na N C:Glu324 3.66 Na CB C:Glu324 4.68 Na CD C:Glu324 4.95 Na CG C:Glu324 4.01 Na CA C:Glu324 4.49 Na O C:Hoh2012 4.80 Na O C:Hoh2121 3.22 interactive model: Sodium binding site 5 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2bfg. 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: Gly25, B: Arg26, B: Leu29, B: Trp117, B: Phe322, B: Glu323, B: Glu324, B: Hoh2010, B: Hoh2104, conact list: Atom Atom Distance (A) Na C B:Gly25 4.05 Na CA B:Gly25 3.83 Na N B:Arg26 3.30 Na CB B:Arg26 4.02 Na CD B:Arg26 4.61 Na CG B:Arg26 3.76 Na NH1 B:Arg26 4.18 Na CA B:Arg26 4.26 Na CD1 B:Leu29 3.87 Na CG B:Leu29 4.71 Na CD1 B:Trp117 3.87 Na CG B:Trp117 4.92 Na CZ2 B:Trp117 4.57 Na CE2 B:Trp117 4.11 Na NE1 B:Trp117 3.24 Na CB B:Phe322 4.65 Na CE2 B:Phe322 4.32 Na CD1 B:Phe322 4.08 Na CD2 B:Phe322 4.19 Na CZ B:Phe322 4.36 Na C B:Phe322 4.17 Na CE1 B:Phe322 4.25 Na CG B:Phe322 4.06 Na CA B:Phe322 4.02 Na N B:Glu323 3.39 Na CB B:Glu323 4.40 Na C B:Glu323 4.15 Na CA B:Glu323 4.18 Na N B:Glu324 3.60 Na CB B:Glu324 4.55 Na OE2 B:Glu324 4.83 Na CD B:Glu324 4.80 Na CG B:Glu324 3.86 Na CA B:Glu324 4.36 Na O B:Hoh2010 4.81 Na O B:Hoh2104 3.00 interactive model: Sodium binding site 6 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 2bfg. 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: Gly25, H: Arg26, H: Leu29, H: Trp117, H: Phe322, H: Glu323, H: Glu324, H: Hoh2010, H: Hoh2122, conact list: Atom Atom Distance (A) Na C H:Gly25 4.01 Na CA H:Gly25 3.90 Na N H:Arg26 3.17 Na CB H:Arg26 3.79 Na CD H:Arg26 4.25 Na CG H:Arg26 3.78 Na NH1 H:Arg26 4.35 Na CA H:Arg26 4.07 Na CD1 H:Leu29 3.85 Na CG H:Leu29 4.81 Na CD1 H:Trp117 3.79 Na CD2 H:Trp117 4.81 Na CG H:Trp117 4.79 Na CZ2 H:Trp117 4.20 Na CE2 H:Trp117 3.81 Na NE1 H:Trp117 3.04 Na CB H:Phe322 4.85 Na CE2 H:Phe322 4.56 Na CD1 H:Phe322 4.39 Na CD2 H:Phe322 4.39 Na CZ H:Phe322 4.65 Na C H:Phe322 4.19 Na CE1 H:Phe322 4.57 Na CG H:Phe322 4.29 Na CA H:Phe322 4.19 Na N H:Glu323 3.28 Na CB H:Glu323 4.32 Na C H:Glu323 4.13 Na CA H:Glu323 4.06 Na N H:Glu324 3.75 Na CB H:Glu324 4.79 Na OE2 H:Glu324 4.98 Na CD H:Glu324 4.94 Na CG H:Glu324 4.00 Na CA H:Glu324 4.55 Na O H:Hoh2010 4.77 Na O H:Hoh2122 3.08 interactive model: Sodium binding site 7 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 2bfg. 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: Gly25, A: Arg26, A: Leu29, A: Trp117, A: Phe322, A: Glu323, A: Glu324, A: Hoh2008, A: Hoh2119, conact list: Atom Atom Distance (A) Na C A:Gly25 4.16 Na CA A:Gly25 3.89 Na N A:Arg26 3.42 Na CB A:Arg26 4.16 Na CD A:Arg26 4.73 Na CG A:Arg26 3.83 Na NH1 A:Arg26 4.19 Na CA A:Arg26 4.39 Na CD1 A:Leu29 3.90 Na CG A:Leu29 4.87 Na CD1 A:Trp117 3.89 Na CG A:Trp117 4.92 Na CZ2 A:Trp117 4.53 Na CE2 A:Trp117 4.08 Na NE1 A:Trp117 3.24 Na CB A:Phe322 4.68 Na CE2 A:Phe322 4.32 Na CD1 A:Phe322 4.17 Na CD2 A:Phe322 4.17 Na CZ A:Phe322 4.40 Na C A:Phe322 4.10 Na CE1 A:Phe322 4.34 Na CG A:Phe322 4.10 Na CA A:Phe322 4.07 Na O A:Glu323 4.92 Na N A:Glu323 3.21 Na CB A:Glu323 4.37 Na C A:Glu323 4.00 Na CA A:Glu323 4.02 Na N A:Glu324 3.51 Na CB A:Glu324 4.51 Na OE2 A:Glu324 4.84 Na CD A:Glu324 4.76 Na CG A:Glu324 3.78 Na CA A:Glu324 4.29 Na O A:Hoh2008 4.77 Na O A:Hoh2119 3.12 interactive model: Sodium binding site 8 out of 8 in 2bfg Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 2bfg. 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: F: Gly25, F: Arg26, F: Leu29, F: Trp117, F: Phe322, F: Glu323, F: Glu324, F: Hoh2006, F: Hoh2094, conact list: Atom Atom Distance (A) Na C F:Gly25 4.12 Na CA F:Gly25 3.96 Na N F:Arg26 3.31 Na CB F:Arg26 3.93 Na CD F:Arg26 4.47 Na CG F:Arg26 3.93 Na NH1 F:Arg26 4.12 Na CA F:Arg26 4.22 Na CD1 F:Leu29 3.77 Na CG F:Leu29 4.64 Na CD1 F:Trp117 3.87 Na CG F:Trp117 4.96 Na CZ2 F:Trp117 4.44 Na CE2 F:Trp117 4.02 Na NE1 F:Trp117 3.15 Na CB F:Phe322 4.78 Na CE2 F:Phe322 4.49 Na CD1 F:Phe322 4.18 Na CD2 F:Phe322 4.34 Na CZ F:Phe322 4.49 Na C F:Phe322 4.19 Na CE1 F:Phe322 4.34 Na CG F:Phe322 4.19 Na CA F:Phe322 4.16 Na N F:Glu323 3.29 Na CB F:Glu323 4.34 Na C F:Glu323 4.17 Na CA F:Glu323 4.09 Na N F:Glu324 3.70 Na CB F:Glu324 4.61 Na OE2 F:Glu324 4.80 Na CD F:Glu324 4.77 Na CG F:Glu324 3.86 Na CA F:Glu324 4.48 Na O F:Hoh2006 4.84 Na O F:Hoh2094 3.12 interactive model: