The binding sites of Sodium atom in the structure of Crystal Structure of PH1918 Protein From Pyrococcus Horikoshii OT3 (pdb code 2d16). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2d16 structure was solved by N.K.LOKANATH, N.KUNISHIMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICSINITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 33.7-1.6 | | Space group | P3 | | a (A) | 66.120 | | b (A) | 66.120 | | c (A) | 125.072 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 120.00 | | Rfactor (%) | 18.5 | | Rfree (%) | 20.4 |
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Sodium binding site 1 out of 4 in 2d16
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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 2d16. 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: Val129, A: Ile130, A: Gly131, A: Hoh1009, A: Hoh1046, | conact list:
| Atom | Atom | Distance (A) | | Na | O A:Val129 | 4.53 | | Na | O A:Ile130 | 2.43 | | Na | N A:Ile130 | 4.80 | | Na | CB A:Ile130 | 4.19 | | Na | C A:Ile130 | 3.14 | | Na | CA A:Ile130 | 3.55 | | Na | N A:Gly131 | 4.17 | | Na | CA A:Gly131 | 4.59 | | Na | O A:Hoh1009 | 2.41 | | Na | O A:Hoh1046 | 3.91 |
| interactive model:
| Sodium binding site 2 out of 4 in 2d16
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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 2d16. 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: Val129, B: Ile130, B: Gly131, B: Hoh1003, B: Hoh1052, | conact list:
| Atom | Atom | Distance (A) | | Na | O B:Val129 | 4.52 | | Na | O B:Ile130 | 2.42 | | Na | N B:Ile130 | 4.84 | | Na | CB B:Ile130 | 4.27 | | Na | C B:Ile130 | 3.18 | | Na | CA B:Ile130 | 3.61 | | Na | N B:Gly131 | 4.20 | | Na | CA B:Gly131 | 4.61 | | Na | O B:Hoh1003 | 2.45 | | Na | O B:Hoh1052 | 3.78 |
| interactive model:
| Sodium binding site 3 out of 4 in 2d16
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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 2d16. 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: C: Val129, C: Ile130, C: Gly131, C: Hoh1005, C: Hoh1056, | conact list:
| Atom | Atom | Distance (A) | | Na | O C:Val129 | 4.56 | | Na | O C:Ile130 | 2.50 | | Na | N C:Ile130 | 4.86 | | Na | CB C:Ile130 | 4.27 | | Na | C C:Ile130 | 3.20 | | Na | CA C:Ile130 | 3.62 | | Na | N C:Gly131 | 4.20 | | Na | CA C:Gly131 | 4.60 | | Na | O C:Hoh1005 | 2.36 | | Na | O C:Hoh1056 | 3.95 |
| interactive model:
| Sodium binding site 4 out of 4 in 2d16
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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 2d16. 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: Val129, D: Ile130, D: Gly131, D: Hoh1040, D: Hoh1124, | conact list:
| Atom | Atom | Distance (A) | | Na | O D:Val129 | 4.50 | | Na | O D:Ile130 | 2.40 | | Na | N D:Ile130 | 4.82 | | Na | CB D:Ile130 | 4.22 | | Na | C D:Ile130 | 3.15 | | Na | CA D:Ile130 | 3.58 | | Na | N D:Gly131 | 4.17 | | Na | CA D:Gly131 | 4.59 | | Na | O D:Hoh1040 | 3.78 | | Na | O D:Hoh1124 | 2.44 |
| interactive model:
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