Sodium in the structure of Crystal Structure of Putative Mandelate Racemase / Muconate Lactonizing Enzyme From Vibrionales Bacterium Swat-3 (pdb 3dfh)

The binding sites of Sodium atom in the structure of Crystal Structure of Putative Mandelate Racemase / Muconate Lactonizing Enzyme From Vibrionales Bacterium Swat-3 (pdb code 3dfh). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3dfh structure was solved by V.N.MALASHKEVICH, R.TORO, S.R.WASSERMAN, A.J.MEYER, J.M.SAUDER, S.K.BURLEY, S.C.ALMO, NEW YORK SGX RESEARCH CENTER FOR STRUCTURALGENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.6-2.2 Space group I422 a (A) 121.836 b (A) 121.836 c (A) 319.347 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.3 Rfree (%) 23.4 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3dfh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3dfh. 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: Ser249, A: Gln250, A: Hoh541, conact list: Atom Atom Distance (A) Na O A:Ser249 2.66 Na CB A:Ser249 4.40 Na OG A:Ser249 4.81 Na C A:Ser249 3.77 Na CA A:Ser249 4.53 Na N A:Gln250 4.73 Na CG A:Gln250 4.97 Na CA A:Gln250 4.80 Na O A:Hoh541 2.68 interactive model: Sodium binding site 2 out of 3 in 3dfh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3dfh. 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: Ser249, B: Gln250, B: Hoh659, conact list: Atom Atom Distance (A) Na O B:Ser249 2.55 Na CB B:Ser249 4.41 Na OG B:Ser249 4.70 Na C B:Ser249 3.67 Na CA B:Ser249 4.51 Na N B:Gln250 4.56 Na CG B:Gln250 4.87 Na CA B:Gln250 4.62 Na O B:Hoh659 2.39 interactive model: Sodium binding site 3 out of 3 in 3dfh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3dfh. 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: Ser249, C: Gln250, C: Hoh626, conact list: Atom Atom Distance (A) Na O C:Ser249 2.54 Na CB C:Ser249 4.66 Na OG C:Ser249 4.58 Na C C:Ser249 3.70 Na CA C:Ser249 4.67 Na N C:Gln250 4.50 Na CG C:Gln250 4.57 Na CA C:Gln250 4.37 Na O C:Hoh626 2.11 interactive model: