Sodium in the structure of Udp-Galactose 4-Epimerase Complexed With Udp-Phenol (pdb 1kvu)

The binding sites of Sodium atom in the structure of Udp-Galactose 4-Epimerase Complexed With Udp-Phenol (pdb code 1kvu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1kvu structure was solved by J.B.THODEN, A.GULICK, H.M.HOLDEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.9 Space group P3221 a (A) 83.500 b (A) 83.500 c (A) 108.400 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 1kvu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1kvu. 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: Hoh492, A: Hoh580, A: Hoh796, conact list: Atom Atom Distance (A) Na O A:Val90 4.85 Na NE2 A:Gln91 3.63 Na OE1 A:Gln91 2.34 Na CB A:Gln91 4.74 Na CD A:Gln91 3.28 Na CG A:Gln91 4.56 Na CA A:Gln91 4.45 Na O A:Hoh492 2.72 Na O A:Hoh580 2.28 Na O A:Hoh796 3.12 interactive model: Sodium binding site 2 out of 3 in 1kvu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1kvu. 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: Hoh535, A: Hoh539, A: Hoh611, A: Hoh630, A: Hoh650, A: Hoh679, A: Hoh707, A: Hoh708, A: Hoh792, A: Hoh810, A: Hoh892, conact list: Atom Atom Distance (A) Na OD1 A:Asn35 4.66 Na CB A:Pro193 4.99 Na C A:Pro193 4.74 Na O A:Gln194 2.33 Na N A:Gln194 3.66 Na CB A:Gln194 3.96 Na C A:Gln194 3.41 Na CA A:Gln194 3.90 Na N A:Gly195 4.55 Na CA A:Gly195 4.79 Na O A:Ile196 4.64 Na O A:Hoh535 4.20 Na O A:Hoh539 4.75 Na O A:Hoh611 4.50 Na O A:Hoh630 2.51 Na O A:Hoh650 2.38 Na O A:Hoh679 2.28 Na O A:Hoh707 4.50 Na O A:Hoh708 2.59 Na O A:Hoh792 3.81 Na O A:Hoh810 4.77 Na O A:Hoh892 2.75 interactive model: Sodium binding site 3 out of 3 in 1kvu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1kvu. 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: Hoh451, A: Hoh593, A: Hoh641, A: Hoh723, A: Hoh768, A: Hoh858, A: Hoh871, conact list: Atom Atom Distance (A) Na NZ A:Lys37 4.47 Na OD2 A:Asp192 4.64 Na OD1 A:Asp192 4.62 Na NE2 A:Gln194 4.65 Na OE1 A:Gln194 4.72 Na O A:Gln334 2.25 Na NE2 A:Gln334 4.49 Na CB A:Gln334 4.46 Na C A:Gln334 3.35 Na CA A:Gln334 4.14 Na N A:Gly335 4.33 Na C A:Gly335 4.71 Na CA A:Gly335 4.48 Na O A:Tyr336 3.95 Na N A:Tyr336 4.73 Na C A:Tyr336 4.94 Na OD1 A:Asp338 4.57 Na O A:Hoh451 2.73 Na O A:Hoh593 2.50 Na O A:Hoh641 2.45 Na O A:Hoh723 2.78 Na O A:Hoh768 4.69 Na O A:Hoh858 3.88 Na O A:Hoh871 3.93 interactive model: