Sodium in the structure of Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal (pdb 1tae)

The binding sites of Sodium atom in the structure of Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal (pdb code 1tae). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1tae structure was solved by K.S.GAJIWALA, C.PINKO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.8-2.7 Space group P1211 a (A) 62.296 b (A) 135.179 c (A) 115.797 alpha (°) 90.00 beta (°) 102.29 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 2 in 1tae Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1tae. 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: Glu38, B: Asp39, B: Asn200, B: Pro318, B: Hoh550, conact list: Atom Atom Distance (A) Na OE1 B:Glu38 4.82 Na CB B:Glu38 4.70 Na OE2 B:Glu38 2.82 Na CD B:Glu38 4.07 Na C B:Glu38 4.56 Na CA B:Glu38 4.41 Na N B:Asp39 3.68 Na CB B:Asp39 4.02 Na OD2 B:Asp39 4.66 Na OD1 B:Asp39 3.63 Na CG B:Asp39 3.91 Na CA B:Asp39 4.49 Na CB B:Asn200 4.78 Na ND2 B:Asn200 3.11 Na CG B:Asn200 4.34 Na CG B:Pro318 4.88 Na O B:Hoh550 3.56 interactive model: Sodium binding site 2 out of 2 in 1tae Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1tae. 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: Glu38, D: Asp39, D: Asn200, D: Pro318, D: Hoh559, conact list: Atom Atom Distance (A) Na OE1 D:Glu38 4.06 Na CD D:Glu38 4.46 Na CG D:Glu38 4.10 Na CA D:Glu38 4.93 Na N D:Asp39 4.05 Na CB D:Asp39 4.05 Na OD2 D:Asp39 4.78 Na OD1 D:Asp39 3.79 Na CG D:Asp39 4.03 Na CA D:Asp39 4.71 Na ND2 D:Asn200 3.74 Na CG D:Asn200 4.83 Na CD D:Pro318 5.00 Na CG D:Pro318 4.38 Na O D:Hoh559 3.27 interactive model: