The binding sites of Sodium atom in the structure of Crystal Structure of Putative Cystathionine Beta-Lyase Involved in Aluminum Resistance (NP_348457.1) From Clostridium Acetobutylicum At 2.00 A Resolution (pdb code 3hvy). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3hvy structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 30.0-2.0 | | Space group | P1211 | | a (A) | 58.830 | | b (A) | 186.620 | | c (A) | 93.710 | | alpha (°) | 90.00 | | beta (°) | 103.06 | | gamma (°) | 90.00 | | Rfactor (%) | 14.5 | | Rfree (%) | 18.7 |
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Sodium binding site 1 out of 4 in 3hvy
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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 3hvy. 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: Ala83, A: Asn84, A: Ile85, A: Asn87, A: Edo432, A: Hoh455, A: Hoh849, A: Hoh864, | conact list:
| Atom | Atom | Distance (A) | | Na | O A:Ala83 | 4.71 | | Na | O A:Asn84 | 2.32 | | Na | N A:Asn84 | 4.92 | | Na | CB A:Asn84 | 4.19 | | Na | ND2 A:Asn84 | 4.70 | | Na | C A:Asn84 | 3.22 | | Na | OD1 A:Asn84 | 2.46 | | Na | CG A:Asn84 | 3.59 | | Na | CA A:Asn84 | 3.61 | | Na | N A:Ile85 | 4.39 | | Na | C A:Ile85 | 4.96 | | Na | CA A:Ile85 | 4.87 | | Na | N A:Asn87 | 4.33 | | Na | CB A:Asn87 | 4.25 | | Na | ND2 A:Asn87 | 4.27 | | Na | OD1 A:Asn87 | 2.23 | | Na | CG A:Asn87 | 3.38 | | Na | CA A:Asn87 | 4.09 | | Na | O1 A:Edo432 | 4.19 | | Na | O2 A:Edo432 | 2.62 | | Na | C2 A:Edo432 | 3.77 | | Na | C1 A:Edo432 | 4.05 | | Na | O A:Hoh455 | 2.21 | | Na | O A:Hoh849 | 4.88 | | Na | O A:Hoh864 | 2.35 |
| interactive model:
| Sodium binding site 2 out of 4 in 3hvy
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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 3hvy. 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: Ala83, B: Asn84, B: Ile85, B: Asn87, B: Edo430, B: Hoh568, | conact list:
| Atom | Atom | Distance (A) | | Na | O B:Ala83 | 4.65 | | Na | O B:Asn84 | 2.37 | | Na | N B:Asn84 | 4.91 | | Na | CB B:Asn84 | 4.15 | | Na | ND2 B:Asn84 | 4.62 | | Na | C B:Asn84 | 3.27 | | Na | OD1 B:Asn84 | 2.36 | | Na | CG B:Asn84 | 3.52 | | Na | CA B:Asn84 | 3.61 | | Na | N B:Ile85 | 4.46 | | Na | C B:Ile85 | 4.97 | | Na | CA B:Ile85 | 4.96 | | Na | N B:Asn87 | 4.31 | | Na | CB B:Asn87 | 4.28 | | Na | ND2 B:Asn87 | 4.29 | | Na | OD1 B:Asn87 | 2.33 | | Na | CG B:Asn87 | 3.43 | | Na | CA B:Asn87 | 4.07 | | Na | O1 B:Edo430 | 4.62 | | Na | O2 B:Edo430 | 3.67 | | Na | C2 B:Edo430 | 2.84 | | Na | C1 B:Edo430 | 3.98 | | Na | O B:Hoh568 | 2.24 |
| interactive model:
| Sodium binding site 3 out of 4 in 3hvy
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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 3hvy. 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: Ala83, C: Asn84, C: Ile85, C: Asn87, C: Hoh548, C: Hoh874, | conact list:
| Atom | Atom | Distance (A) | | Na | O C:Ala83 | 4.68 | | Na | O C:Asn84 | 2.35 | | Na | N C:Asn84 | 4.93 | | Na | CB C:Asn84 | 4.21 | | Na | ND2 C:Asn84 | 4.70 | | Na | C C:Asn84 | 3.25 | | Na | OD1 C:Asn84 | 2.44 | | Na | CG C:Asn84 | 3.59 | | Na | CA C:Asn84 | 3.62 | | Na | N C:Ile85 | 4.42 | | Na | C C:Ile85 | 4.97 | | Na | CA C:Ile85 | 4.89 | | Na | N C:Asn87 | 4.27 | | Na | CB C:Asn87 | 4.15 | | Na | ND2 C:Asn87 | 4.12 | | Na | OD1 C:Asn87 | 2.09 | | Na | CG C:Asn87 | 3.25 | | Na | CA C:Asn87 | 4.01 | | Na | O C:Hoh548 | 2.31 | | Na | O C:Hoh874 | 4.85 |
| interactive model:
| Sodium binding site 4 out of 4 in 3hvy
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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 3hvy. 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: Ala83, D: Asn84, D: Ile85, D: Asn87, D: Hoh444, D: Hoh549, D: Hoh552, D: Hoh600, D: Hoh621, D: Hoh624, D: Hoh867, | conact list:
| Atom | Atom | Distance (A) | | Na | O D:Ala83 | 4.84 | | Na | O D:Asn84 | 2.33 | | Na | CB D:Asn84 | 4.17 | | Na | ND2 D:Asn84 | 4.57 | | Na | C D:Asn84 | 3.25 | | Na | OD1 D:Asn84 | 2.32 | | Na | CG D:Asn84 | 3.49 | | Na | CA D:Asn84 | 3.67 | | Na | N D:Ile85 | 4.40 | | Na | C D:Ile85 | 4.99 | | Na | CA D:Ile85 | 4.86 | | Na | N D:Asn87 | 4.46 | | Na | CB D:Asn87 | 4.39 | | Na | ND2 D:Asn87 | 4.19 | | Na | OD1 D:Asn87 | 2.28 | | Na | CG D:Asn87 | 3.41 | | Na | CA D:Asn87 | 4.28 | | Na | O D:Hoh444 | 2.65 | | Na | O D:Hoh549 | 3.07 | | Na | O D:Hoh552 | 2.40 | | Na | O D:Hoh600 | 4.24 | | Na | O D:Hoh621 | 4.91 | | Na | O D:Hoh624 | 4.01 | | Na | O D:Hoh867 | 4.24 |
| interactive model:
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