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 |
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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:
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