Sodium in the structure of Crystal Structure of The Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed With A Caddie Protein in the Monoclinic Crystal (pdb 1wx5)

The binding sites of Sodium atom in the structure of Crystal Structure of The Copper-Free Streptomyces Castaneoglobisporus Tyrosinase Complexed With A Caddie Protein in the Monoclinic Crystal (pdb code 1wx5). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1wx5 structure was solved by Y.MATOBA, T.KUMAGAI, A.YAMAMOTO, H.YOSHITSU, M.SUGIYAMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.0 Space group P1211 a (A) 58.850 b (A) 93.200 c (A) 65.590 alpha (°) 90.00 beta (°) 93.80 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 29.1 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1wx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1wx5. 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: Gly240, A: Thr241, A: Pro242, A: Asp243, A: Val244, A: Val245, A: Asp246, A: Glu249, A: Hoh322, A: Hoh330, A: Hoh387, A: Hoh423, conact list: Atom Atom Distance (A) Na O A:Gly240 4.84 Na N A:Gly240 4.78 Na C A:Gly240 4.41 Na CA A:Gly240 4.98 Na O A:Thr241 2.29 Na N A:Thr241 3.97 Na CB A:Thr241 4.43 Na C A:Thr241 3.37 Na CA A:Thr241 4.09 Na N A:Pro242 4.36 Na C A:Pro242 4.95 Na CA A:Pro242 4.58 Na N A:Asp243 4.85 Na O A:Val244 2.51 Na N A:Val244 4.40 Na C A:Val244 3.73 Na CA A:Val244 4.61 Na N A:Val245 4.64 Na C A:Val245 4.76 Na CA A:Val245 4.61 Na N A:Asp246 4.06 Na CB A:Asp246 4.23 Na OD2 A:Asp246 4.49 Na OD1 A:Asp246 2.33 Na CG A:Asp246 3.53 Na CA A:Asp246 4.79 Na OE1 A:Glu249 2.50 Na OE2 A:Glu249 2.60 Na CD A:Glu249 2.81 Na CG A:Glu249 4.20 Na O A:Hoh322 2.34 Na O A:Hoh330 4.53 Na O A:Hoh387 4.36 Na O A:Hoh423 2.69 interactive model: Sodium binding site 2 out of 3 in 1wx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1wx5. 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: Gly240, C: Thr241, C: Pro242, C: Asp243, C: Val244, C: Val245, C: Asp246, C: Glu249, C: Hoh361, C: Hoh391, C: Hoh463, conact list: Atom Atom Distance (A) Na C C:Gly240 4.74 Na O C:Thr241 2.23 Na N C:Thr241 4.26 Na CB C:Thr241 4.63 Na C C:Thr241 3.36 Na CA C:Thr241 4.27 Na N C:Pro242 4.23 Na C C:Pro242 4.42 Na CA C:Pro242 4.20 Na N C:Asp243 4.33 Na C C:Asp243 4.92 Na O C:Val244 2.39 Na N C:Val244 3.94 Na C C:Val244 3.48 Na CA C:Val244 4.32 Na N C:Val245 4.38 Na C C:Val245 4.69 Na CA C:Val245 4.46 Na N C:Asp246 4.23 Na CB C:Asp246 4.55 Na OD2 C:Asp246 4.45 Na OD1 C:Asp246 2.40 Na CG C:Asp246 3.64 Na OE1 C:Glu249 2.39 Na OE2 C:Glu249 2.60 Na CD C:Glu249 2.81 Na CG C:Glu249 4.28 Na O C:Hoh361 4.95 Na O C:Hoh391 4.70 Na O C:Hoh463 2.98 interactive model: Sodium binding site 3 out of 3 in 1wx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1wx5. 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: Glu50, C: Arg51, C: Thr52, C: Asp243, C: Val244, C: Val245, C: Hoh449, C: Hoh463, C: Hoh471, conact list: Atom Atom Distance (A) Na OE1 C:Glu50 4.46 Na CB C:Glu50 4.57 Na OE2 C:Glu50 4.86 Na CD C:Glu50 4.12 Na C C:Glu50 4.55 Na CG C:Glu50 3.34 Na CA C:Glu50 4.69 Na O C:Arg51 2.88 Na N C:Arg51 3.72 Na C C:Arg51 3.55 Na CA C:Arg51 4.26 Na N C:Thr52 4.25 Na CB C:Thr52 4.42 Na CG2 C:Thr52 4.56 Na OG1 C:Thr52 3.65 Na CA C:Thr52 4.42 Na O C:Asp243 2.77 Na C C:Asp243 3.25 Na CA C:Asp243 4.14 Na O C:Val244 4.73 Na N C:Val244 3.70 Na C C:Val244 3.92 Na CA C:Val244 3.75 Na N C:Val245 3.76 Na CB C:Val245 4.90 Na CG2 C:Val245 3.88 Na CA C:Val245 4.63 Na O C:Hoh449 3.98 Na O C:Hoh463 3.84 Na O C:Hoh471 4.22 interactive model: