Sodium in the structure of Calcium-Free (Apo) S100A12 (pdb 2wce)

The binding sites of Sodium atom in the structure of Calcium-Free (Apo) S100A12 (pdb code 2wce). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wce structure was solved by O.V.MOROZ, E.V.BLAGOVA, A.J.WILKINSON, K.S.WILSON, I.B.BRONSTEIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 55.6-1.8 Space group H3 a (A) 77.516 b (A) 77.516 c (A) 99.076 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.3 Rfree (%) 20.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2wce Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wce. 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: Tyr17, A: Ser18, A: Val19, A: Arg20, A: Lys21, A: Gly22, A: His23, A: Phe24, A: Asp25, A: Thr26, A: Leu27, A: Gln67, A: Hoh2038, A: Hoh2050, A: Hoh2052, A: Hoh2085, conact list: Atom Atom Distance (A) Na O A:Tyr17 4.86 Na O A:Ser18 2.20 Na CB A:Ser18 4.32 Na C A:Ser18 3.28 Na CA A:Ser18 3.81 Na N A:Val19 4.41 Na C A:Val19 4.73 Na CA A:Val19 4.73 Na N A:Arg20 4.79 Na O A:Lys21 2.30 Na N A:Lys21 4.06 Na CB A:Lys21 4.76 Na C A:Lys21 3.48 Na CA A:Lys21 4.31 Na O A:Gly22 4.39 Na N A:Gly22 4.42 Na C A:Gly22 4.09 Na CA A:Gly22 4.47 Na O A:His23 2.35 Na N A:His23 4.01 Na C A:His23 3.52 Na CA A:His23 4.37 Na O A:Phe24 4.66 Na N A:Phe24 4.45 Na C A:Phe24 4.47 Na CA A:Phe24 4.50 Na N A:Asp25 4.86 Na O A:Thr26 2.31 Na N A:Thr26 4.25 Na OG1 A:Thr26 4.72 Na C A:Thr26 3.49 Na CA A:Thr26 4.47 Na N A:Leu27 4.32 Na CB A:Leu27 4.67 Na CA A:Leu27 4.18 Na OE1 A:Gln67 4.52 Na O A:Hoh2038 4.68 Na O A:Hoh2050 4.41 Na O A:Hoh2052 2.63 Na O A:Hoh2085 2.42 interactive model: Sodium binding site 2 out of 2 in 2wce Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wce. 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: Tyr17, B: Ser18, B: Val19, B: Arg20, B: Lys21, B: Gly22, B: His23, B: Phe24, B: Asp25, B: Thr26, B: Leu27, B: Gln67, B: Hoh2034, B: Hoh2035, B: Hoh2049, B: Hoh2050, B: Hoh2086, conact list: Atom Atom Distance (A) Na O B:Tyr17 4.89 Na O B:Ser18 2.27 Na CB B:Ser18 4.41 Na C B:Ser18 3.36 Na CA B:Ser18 3.88 Na N B:Val19 4.53 Na C B:Val19 4.87 Na CA B:Val19 4.90 Na N B:Arg20 4.86 Na O B:Lys21 2.30 Na N B:Lys21 4.13 Na CB B:Lys21 4.87 Na C B:Lys21 3.47 Na CA B:Lys21 4.36 Na O B:Gly22 4.51 Na N B:Gly22 4.39 Na C B:Gly22 4.08 Na CA B:Gly22 4.46 Na O B:His23 2.32 Na O B:His23 2.34 Na N B:His23 3.85 Na N B:His23 3.89 Na CB B:His23 4.84 Na C B:His23 3.46 Na C B:His23 3.49 Na CA B:His23 4.22 Na CA B:His23 4.30 Na O B:Phe24 4.81 Na N B:Phe24 4.46 Na C B:Phe24 4.56 Na CA B:Phe24 4.59 Na N B:Asp25 4.84 Na O B:Thr26 2.23 Na N B:Thr26 4.20 Na OG1 B:Thr26 4.52 Na C B:Thr26 3.45 Na CA B:Thr26 4.45 Na N B:Leu27 4.30 Na CB B:Leu27 4.65 Na CA B:Leu27 4.20 Na OE1 B:Gln67 4.59 Na O B:Hoh2034 4.96 Na O B:Hoh2035 4.78 Na O B:Hoh2049 2.67 Na O B:Hoh2050 4.49 Na O B:Hoh2086 2.40 interactive model: