The binding sites of Sodium atom in the structure of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex (pdb code 2fza). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2fza structure was solved by J.KONDO, T.CIENGSHIN, E.C.M.JUAN, K.MITOMI, A.TAKENAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 10.0-3.6 | | Space group | P63 | | a (A) | 36.368 | | b (A) | 36.368 | | c (A) | 62.826 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 120.00 | | Rfactor (%) | 29.4 | | Rfree (%) | 32.9 |
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Sodium binding site 1 out of 5 in 2fza
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2fza. 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: Dg3, A: Dg4, B: Dg5, A: Ca11, | conact list:
| Atom | Atom | Distance (A) | | Na | O6 A:Dg3 | 4.87 | | Na | C6 A:Dg4 | 4.34 | | Na | O6 A:Dg4 | 3.11 | | Na | O6 B:Dg5 | 4.49 | | Na | CA A:Ca11 | 4.80 |
| interactive model:
| Sodium binding site 2 out of 5 in 2fza
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2fza. 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: Dg5, B: Dg5, | conact list:
| Atom | Atom | Distance (A) | | Na | C6 A:Dg5 | 3.83 | | Na | N1 A:Dg5 | 4.39 | | Na | C5 A:Dg5 | 4.93 | | Na | O6 A:Dg5 | 2.83 | | Na | C6 B:Dg5 | 3.81 | | Na | N1 B:Dg5 | 4.40 | | Na | C5 B:Dg5 | 4.90 | | Na | O6 B:Dg5 | 2.80 |
| interactive model:
| Sodium binding site 3 out of 5 in 2fza
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2fza. 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: Da6, A: Dg7, | conact list:
| Atom | Atom | Distance (A) | | Na | C8 A:Da6 | 4.26 | | Na | N7 A:Da6 | 4.68 | | Na | OP2 A:Da6 | 4.95 | | Na | C8 A:Dg7 | 3.81 | | Na | C6 A:Dg7 | 4.24 | | Na | C5 A:Dg7 | 3.89 | | Na | N7 A:Dg7 | 2.88 | | Na | O6 A:Dg7 | 3.81 |
| interactive model:
| Sodium binding site 4 out of 5 in 2fza
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2fza. 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: Dg5, B: Dg3, B: Dg4, B: Ca12, | conact list:
| Atom | Atom | Distance (A) | | Na | O6 A:Dg5 | 4.49 | | Na | O6 B:Dg3 | 4.85 | | Na | C6 B:Dg4 | 4.32 | | Na | O6 B:Dg4 | 3.09 | | Na | CA B:Ca12 | 4.80 |
| interactive model:
| Sodium binding site 5 out of 5 in 2fza
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2fza. 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: Da6, B: Dg7, | conact list:
| Atom | Atom | Distance (A) | | Na | C8 B:Da6 | 4.25 | | Na | N7 B:Da6 | 4.66 | | Na | OP2 B:Da6 | 4.95 | | Na | C8 B:Dg7 | 3.82 | | Na | C6 B:Dg7 | 4.23 | | Na | C5 B:Dg7 | 3.88 | | Na | N7 B:Dg7 | 2.88 | | Na | O6 B:Dg7 | 3.80 |
| interactive model:
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