The binding sites of Sodium atom in the structure of Hyaluronic Acid, Molecular Conformations and Interactions in Two Sodium Salts (pdb code 2hya). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2hya structure was solved by S.ARNOTT, with Fiber diffraction technique. |
Sodium binding site 1 out of 4 in 2hya
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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 2hya. 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: Gcu1, A: Nag2, | conact list:
| Atom | Atom | Distance (A) | | Na | O5 A:Gcu1 | 3.44 | | Na | H5 A:Gcu1 | 3.39 | | Na | O6B A:Gcu1 | 2.73 | | Na | C1 A:Gcu1 | 4.59 | | Na | O6A A:Gcu1 | 2.70 | | Na | C6 A:Gcu1 | 2.58 | | Na | C5 A:Gcu1 | 3.37 | | Na | H1 A:Gcu1 | 4.62 | | Na | C4 A:Gcu1 | 4.82 | | Na | HN2 A:Nag2 | 4.53 | | Na | H82 A:Nag2 | 4.86 |
| interactive model:
| Sodium binding site 2 out of 4 in 2hya
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Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2hya. 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: Nag2, A: Gcu3, A: Nag4, | conact list:
| Atom | Atom | Distance (A) | | Na | H5 A:Nag2 | 3.92 | | Na | H3 A:Nag2 | 3.55 | | Na | C5 A:Nag2 | 4.77 | | Na | H1 A:Nag2 | 4.98 | | Na | C4 A:Nag2 | 4.62 | | Na | C3 A:Nag2 | 4.49 | | Na | O4 A:Nag2 | 3.92 | | Na | O5 A:Gcu3 | 3.44 | | Na | H5 A:Gcu3 | 3.39 | | Na | O6B A:Gcu3 | 2.73 | | Na | C1 A:Gcu3 | 4.59 | | Na | O6A A:Gcu3 | 2.70 | | Na | C6 A:Gcu3 | 2.58 | | Na | C5 A:Gcu3 | 3.37 | | Na | H1 A:Gcu3 | 4.62 | | Na | C4 A:Gcu3 | 4.82 | | Na | HN2 A:Nag4 | 4.53 | | Na | H82 A:Nag4 | 4.86 |
| interactive model:
| Sodium binding site 3 out of 4 in 2hya
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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 2hya. 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: Nag4, A: Gcu5, A: Nag6, | conact list:
| Atom | Atom | Distance (A) | | Na | H5 A:Nag4 | 3.92 | | Na | H3 A:Nag4 | 3.55 | | Na | C5 A:Nag4 | 4.77 | | Na | H1 A:Nag4 | 4.98 | | Na | C4 A:Nag4 | 4.62 | | Na | C3 A:Nag4 | 4.49 | | Na | O4 A:Nag4 | 3.92 | | Na | O5 A:Gcu5 | 3.44 | | Na | H5 A:Gcu5 | 3.39 | | Na | O6B A:Gcu5 | 2.73 | | Na | C1 A:Gcu5 | 4.59 | | Na | O6A A:Gcu5 | 2.70 | | Na | C6 A:Gcu5 | 2.58 | | Na | C5 A:Gcu5 | 3.37 | | Na | H1 A:Gcu5 | 4.62 | | Na | C4 A:Gcu5 | 4.82 | | Na | HN2 A:Nag6 | 4.53 | | Na | H82 A:Nag6 | 4.86 |
| interactive model:
| Sodium binding site 4 out of 4 in 2hya
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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 2hya. 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: Nag6, A: Gcu7, A: Nag8, | conact list:
| Atom | Atom | Distance (A) | | Na | H5 A:Nag6 | 3.92 | | Na | H3 A:Nag6 | 3.55 | | Na | C5 A:Nag6 | 4.77 | | Na | H1 A:Nag6 | 4.98 | | Na | C4 A:Nag6 | 4.62 | | Na | C3 A:Nag6 | 4.49 | | Na | O4 A:Nag6 | 3.92 | | Na | O5 A:Gcu7 | 3.44 | | Na | H5 A:Gcu7 | 3.39 | | Na | O6B A:Gcu7 | 2.73 | | Na | C1 A:Gcu7 | 4.59 | | Na | O6A A:Gcu7 | 2.70 | | Na | C6 A:Gcu7 | 2.58 | | Na | C5 A:Gcu7 | 3.37 | | Na | H1 A:Gcu7 | 4.62 | | Na | C4 A:Gcu7 | 4.82 | | Na | HN2 A:Nag8 | 4.53 | | Na | H82 A:Nag8 | 4.86 |
| interactive model:
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