Sodium in the structure of The Structure Of the N-Terminal Domain of Rsbr (pdb 2bnl)
The binding sites of Sodium atom in the structure of The Structure Of the N-Terminal Domain of Rsbr (pdb code 2bnl). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2bnl structure was solved by J.W.MURRAY, O.DELUMEAU, R.J.LEWIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 22.2-2.0 | Space group | P3212 | a (A) | 136.062 | b (A) | 136.062 | c (A) | 113.296 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 120.00 | Rfactor (%) | 15.4 | Rfree (%) | 19.8 |
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Sodium Binding Sites:Sodium binding site 1 out of 3 in 2bnl
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2bnl. 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: Ala62, B: Ser65, B: Gln66, C: Asn44, B: Hoh2075, B: Hoh2076, B: Hoh2078, B: Hoh2079, B: Hoh2080, B: Hoh2081, B: Hoh2083, C: Hoh2022, C: Hoh2049, C: Hoh2051, | conact list:
Atom | Atom | Distance (A) | Na | O B:Ala62 | 4.22 | Na | N B:Ser65 | 4.40 | Na | CB B:Ser65 | 3.39 | Na | OG B:Ser65 | 2.46 | Na | CA B:Ser65 | 4.45 | Na | NE2 B:Gln66 | 3.97 | Na | OE1 B:Gln66 | 3.75 | Na | CD B:Gln66 | 4.25 | Na | ND2 C:Asn44 | 4.26 | Na | OD1 C:Asn44 | 4.54 | Na | CG C:Asn44 | 4.81 | Na | O B:Hoh2075 | 4.99 | Na | O B:Hoh2076 | 4.18 | Na | O B:Hoh2078 | 4.29 | Na | O B:Hoh2079 | 2.41 | Na | O B:Hoh2080 | 4.41 | Na | O B:Hoh2081 | 2.55 | Na | O B:Hoh2083 | 2.29 | Na | O C:Hoh2022 | 2.44 | Na | O C:Hoh2049 | 2.28 | Na | O C:Hoh2051 | 4.31 |
| interactive model:
| Sodium binding site 2 out of 3 in 2bnl
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2bnl. 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: Ala62, C: Ser65, C: Gln66, E: Asn44, C: Hoh2069, C: Hoh2070, C: Hoh2071, C: Hoh2075, C: Hoh2076, C: Hoh2078, E: Hoh2018, E: Hoh2043, E: Hoh2044, | conact list:
Atom | Atom | Distance (A) | Na | O C:Ala62 | 4.21 | Na | N C:Ser65 | 4.39 | Na | CB C:Ser65 | 3.52 | Na | OG C:Ser65 | 2.54 | Na | CA C:Ser65 | 4.56 | Na | NE2 C:Gln66 | 4.00 | Na | OE1 C:Gln66 | 3.91 | Na | CD C:Gln66 | 4.36 | Na | ND2 E:Asn44 | 4.13 | Na | OD1 E:Asn44 | 4.34 | Na | CG E:Asn44 | 4.68 | Na | O C:Hoh2069 | 4.81 | Na | O C:Hoh2070 | 2.27 | Na | O C:Hoh2071 | 4.17 | Na | O C:Hoh2075 | 2.40 | Na | O C:Hoh2076 | 2.53 | Na | O C:Hoh2078 | 4.53 | Na | O E:Hoh2018 | 2.37 | Na | O E:Hoh2043 | 2.25 | Na | O E:Hoh2044 | 4.36 |
| interactive model:
| Sodium binding site 3 out of 3 in 2bnl
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2bnl. 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: F: Ala62, F: Ser65, F: Gln66, F: Hoh2032, F: Hoh2083, F: Hoh2084, F: Hoh2087, F: Hoh2088, F: Hoh2089, | conact list:
Atom | Atom | Distance (A) | Na | O F:Ala62 | 3.96 | Na | N F:Ser65 | 4.37 | Na | CB F:Ser65 | 3.63 | Na | OG F:Ser65 | 2.58 | Na | CA F:Ser65 | 4.59 | Na | NE2 F:Gln66 | 3.89 | Na | OE1 F:Gln66 | 3.67 | Na | CD F:Gln66 | 4.18 | Na | O F:Hoh2032 | 2.37 | Na | O F:Hoh2083 | 2.17 | Na | O F:Hoh2084 | 3.87 | Na | O F:Hoh2087 | 4.43 | Na | O F:Hoh2088 | 2.49 | Na | O F:Hoh2089 | 2.54 |
| interactive model:
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