The binding sites of Sodium atom in the structure of Quinol:Fumarate Reductase From Wolinella Succinogenes (pdb code 2bs2). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2bs2 structure was solved by C.R.D.LANCASTER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 28.7-1.8 | | Space group | P1211 | | a (A) | 85.104 | | b (A) | 188.766 | | c (A) | 117.817 | | alpha (°) | 90.00 | | beta (°) | 104.47 | | gamma (°) | 90.00 | | Rfactor (%) | 22.9 | | Rfree (%) | 23.7 |
|
Sodium binding site 1 out of 2 in 2bs2
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2bs2. 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: Tyr370, A: Ser371, A: Met372, A: Gly373, A: Gly374, A: Gly392, A: Glu393, A: Ala394, A: Ala395, A: Cys396, A: Hoh2158, A: Hoh2159, A: Hoh2169, A: Hoh2175, | conact list:
| Atom | Atom | Distance (A) | | Na | CE2 A:Tyr370 | 4.76 | | Na | CZ A:Tyr370 | 4.72 | | Na | OH A:Tyr370 | 4.28 | | Na | O A:Ser371 | 2.49 | | Na | CB A:Ser371 | 4.71 | | Na | C A:Ser371 | 3.57 | | Na | CA A:Ser371 | 4.78 | | Na | O A:Met372 | 2.71 | | Na | N A:Met372 | 4.11 | | Na | C A:Met372 | 3.13 | | Na | CA A:Met372 | 3.71 | | Na | O A:Gly373 | 2.59 | | Na | N A:Gly373 | 3.83 | | Na | C A:Gly373 | 3.41 | | Na | CA A:Gly373 | 4.18 | | Na | N A:Gly374 | 4.17 | | Na | CA A:Gly374 | 4.32 | | Na | O A:Gly392 | 4.47 | | Na | O A:Glu393 | 2.36 | | Na | CB A:Glu393 | 4.71 | | Na | C A:Glu393 | 3.34 | | Na | CG A:Glu393 | 4.27 | | Na | CA A:Glu393 | 3.89 | | Na | O A:Ala394 | 4.94 | | Na | N A:Ala394 | 4.39 | | Na | C A:Ala394 | 4.43 | | Na | CA A:Ala394 | 4.75 | | Na | O A:Ala395 | 2.57 | | Na | N A:Ala395 | 4.14 | | Na | C A:Ala395 | 3.74 | | Na | CA A:Ala395 | 4.54 | | Na | N A:Cys396 | 4.71 | | Na | CA A:Cys396 | 4.89 | | Na | O A:Hoh2158 | 2.45 | | Na | O A:Hoh2159 | 4.20 | | Na | O A:Hoh2169 | 3.81 | | Na | O A:Hoh2175 | 3.99 |
| interactive model:
| Sodium binding site 2 out of 2 in 2bs2
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2bs2. 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: D: Tyr370, D: Ser371, D: Met372, D: Gly373, D: Gly374, D: Gly392, D: Glu393, D: Ala394, D: Ala395, D: Cys396, D: Hoh2156, D: Hoh2157, D: Hoh2168, D: Hoh2174, | conact list:
| Atom | Atom | Distance (A) | | Na | CE2 D:Tyr370 | 4.73 | | Na | CZ D:Tyr370 | 4.69 | | Na | OH D:Tyr370 | 4.24 | | Na | O D:Ser371 | 2.52 | | Na | CB D:Ser371 | 4.76 | | Na | C D:Ser371 | 3.59 | | Na | CA D:Ser371 | 4.81 | | Na | O D:Met372 | 2.72 | | Na | N D:Met372 | 4.11 | | Na | C D:Met372 | 3.15 | | Na | CA D:Met372 | 3.71 | | Na | O D:Gly373 | 2.68 | | Na | N D:Gly373 | 3.87 | | Na | C D:Gly373 | 3.46 | | Na | CA D:Gly373 | 4.22 | | Na | N D:Gly374 | 4.22 | | Na | CA D:Gly374 | 4.36 | | Na | O D:Gly392 | 4.41 | | Na | O D:Glu393 | 2.38 | | Na | CB D:Glu393 | 4.71 | | Na | C D:Glu393 | 3.34 | | Na | CG D:Glu393 | 4.28 | | Na | CA D:Glu393 | 3.88 | | Na | O D:Ala394 | 4.94 | | Na | N D:Ala394 | 4.40 | | Na | C D:Ala394 | 4.45 | | Na | CA D:Ala394 | 4.78 | | Na | O D:Ala395 | 2.55 | | Na | N D:Ala395 | 4.15 | | Na | C D:Ala395 | 3.73 | | Na | CA D:Ala395 | 4.53 | | Na | N D:Cys396 | 4.71 | | Na | CA D:Cys396 | 4.88 | | Na | O D:Hoh2156 | 2.32 | | Na | O D:Hoh2157 | 4.18 | | Na | O D:Hoh2168 | 3.76 | | Na | O D:Hoh2174 | 3.94 |
| interactive model:
|
|