Sodium in the structure of Structure of Udp-Galactose-4-Epimerase Complexed With Udp-4-Deoxy-4- Fluoro-Alpha-D-Glucose (pdb 1udb)

The binding sites of Sodium atom in the structure of Structure of Udp-Galactose-4-Epimerase Complexed With Udp-4-Deoxy-4- Fluoro-Alpha-D-Glucose (pdb code 1udb). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1udb structure was solved by J.B.THODEN, H.M.HOLDEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.6 Space group P3221 a (A) 83.500 b (A) 83.500 c (A) 108.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 3 in 1udb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1udb. 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: Val90, A: Gln91, A: Hoh564, A: Hoh656, A: Hoh723, A: Hoh811, conact list: Atom Atom Distance (A) Na O A:Val90 4.81 Na O A:Gln91 4.82 Na NE2 A:Gln91 3.55 Na OE1 A:Gln91 2.07 Na CB A:Gln91 4.56 Na CD A:Gln91 3.10 Na CG A:Gln91 4.39 Na CA A:Gln91 4.31 Na O A:Hoh564 2.42 Na O A:Hoh656 2.49 Na O A:Hoh723 2.30 Na O A:Hoh811 3.96 interactive model: Sodium binding site 2 out of 3 in 1udb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1udb. 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: Asn35, A: Pro193, A: Gln194, A: Gly195, A: Ile196, A: Hoh551, A: Hoh597, A: Hoh598, A: Hoh679, A: Hoh766, A: Hoh785, A: Hoh788, A: Hoh793, A: Hoh827, A: Hoh985, A: Hoh1050, conact list: Atom Atom Distance (A) Na OD1 A:Asn35 4.80 Na CB A:Pro193 4.99 Na C A:Pro193 4.79 Na O A:Gln194 2.36 Na N A:Gln194 3.77 Na CB A:Gln194 4.25 Na C A:Gln194 3.47 Na CA A:Gln194 4.03 Na N A:Gly195 4.60 Na CA A:Gly195 4.88 Na O A:Ile196 4.56 Na O A:Hoh551 2.50 Na O A:Hoh597 4.19 Na O A:Hoh598 4.67 Na O A:Hoh679 2.28 Na O A:Hoh766 4.85 Na O A:Hoh785 4.81 Na O A:Hoh788 4.57 Na O A:Hoh793 2.51 Na O A:Hoh827 4.28 Na O A:Hoh985 2.48 Na O A:Hoh1050 4.42 interactive model: Sodium binding site 3 out of 3 in 1udb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1udb. 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: Lys37, A: Asp192, A: Gln194, A: Gln334, A: Gly335, A: Tyr336, A: Asp338, A: Hoh632, A: Hoh640, A: Hoh838, A: Hoh844, A: Hoh889, A: Hoh923, A: Hoh944, A: Hoh961, A: Hoh1016, conact list: Atom Atom Distance (A) Na CE A:Lys37 4.91 Na NZ A:Lys37 4.14 Na OD2 A:Asp192 4.58 Na OD1 A:Asp192 4.53 Na NE2 A:Gln194 4.53 Na OE1 A:Gln194 4.59 Na O A:Gln334 2.22 Na NE2 A:Gln334 4.50 Na CB A:Gln334 4.38 Na C A:Gln334 3.30 Na CA A:Gln334 4.14 Na N A:Gly335 4.24 Na C A:Gly335 4.64 Na CA A:Gly335 4.41 Na O A:Tyr336 3.87 Na N A:Tyr336 4.69 Na C A:Tyr336 4.87 Na OD1 A:Asp338 4.73 Na O A:Hoh632 2.51 Na O A:Hoh640 2.27 Na O A:Hoh838 3.03 Na O A:Hoh844 4.69 Na O A:Hoh889 2.45 Na O A:Hoh923 4.76 Na O A:Hoh944 3.90 Na O A:Hoh961 2.32 Na O A:Hoh1016 2.74 interactive model: