Sodium in the structure of 1.6 Angstrom Structure of Esherichia Coli Aspartate- Semialdehyde Dehydrogenase. (pdb 1t4b)

The binding sites of Sodium atom in the structure of 1.6 Angstrom Structure of Esherichia Coli Aspartate- Semialdehyde Dehydrogenase. (pdb code 1t4b). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1t4b structure was solved by C.E.NICHOLS, B.DHALIWAL, M.LOCKYER, A.R.HAWKINS, D.K.STAMMERS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.4-1.6 Space group P212121 a (A) 56.500 b (A) 70.100 c (A) 180.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 19.9 Sodium Binding Sites: Sodium binding site 1 out of 5 in 1t4b Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1t4b. 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: Met1, A: Gln2, A: Asp67, A: Hoh5129, A: Hoh5131, A: Hoh5198, A: Hoh5391, conact list: Atom Atom Distance (A) Na O A:Met1 3.73 Na N A:Met1 4.93 Na C A:Met1 4.75 Na OE1 A:Gln2 4.24 Na OD2 A:Asp67 4.93 Na O A:Hoh5129 3.55 Na O A:Hoh5131 2.77 Na O A:Hoh5198 4.44 Na O A:Hoh5391 4.59 interactive model: Sodium binding site 2 out of 5 in 1t4b Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1t4b. 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: Asn307, A: Asp308, B: Gln233, A: Hoh5011, A: Hoh5030, A: Hoh5096, A: Hoh5290, A: Hoh5411, A: Hoh5472, A: Hoh5473, A: Hoh5474, B: Hoh5054, B: Hoh5179, B: Hoh5309, B: Hoh5456, conact list: Atom Atom Distance (A) Na O A:Asn307 4.34 Na CB A:Asn307 4.87 Na C A:Asn307 4.97 Na OD2 A:Asp308 4.29 Na OD1 A:Asp308 4.77 Na CG A:Asp308 4.88 Na NE2 B:Gln233 4.93 Na O A:Hoh5011 2.57 Na O A:Hoh5030 4.41 Na O A:Hoh5096 4.16 Na O A:Hoh5290 2.82 Na O A:Hoh5411 4.32 Na O A:Hoh5472 2.65 Na O A:Hoh5473 2.65 Na O A:Hoh5474 2.54 Na O B:Hoh5054 4.15 Na O B:Hoh5179 4.43 Na O B:Hoh5309 4.51 Na O B:Hoh5456 2.85 interactive model: Sodium binding site 3 out of 5 in 1t4b Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1t4b. 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: Asp76, A: Hoh5135, A: Hoh5138, conact list: Atom Atom Distance (A) Na OD2 A:Asp76 4.01 Na OD1 A:Asp76 3.12 Na CG A:Asp76 3.96 Na O A:Hoh5135 2.80 Na O A:Hoh5138 2.77 interactive model: Sodium binding site 4 out of 5 in 1t4b Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1t4b. 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: Gln233, B: Asn307, B: Asp308, A: Hoh5054, A: Hoh5285, A: Hoh5469, B: Hoh5045, B: Hoh5089, B: Hoh5095, B: Hoh5130, B: Hoh5200, B: Hoh5293, B: Hoh5450, B: Hoh5451, B: Hoh5452, conact list: Atom Atom Distance (A) Na NE2 A:Gln233 4.99 Na O B:Asn307 4.47 Na OD2 B:Asp308 4.39 Na OD1 B:Asp308 4.73 Na CG B:Asp308 4.91 Na O A:Hoh5054 4.39 Na O A:Hoh5285 4.28 Na O A:Hoh5469 2.84 Na O B:Hoh5045 2.69 Na O B:Hoh5089 4.13 Na O B:Hoh5095 4.63 Na O B:Hoh5130 2.72 Na O B:Hoh5200 4.34 Na O B:Hoh5293 4.41 Na O B:Hoh5450 2.79 Na O B:Hoh5451 2.72 Na O B:Hoh5452 2.85 interactive model: Sodium binding site 5 out of 5 in 1t4b Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1t4b. 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: Gln2, B: Hoh5228, B: Hoh5249, B: Hoh5255, B: Hoh5391, B: Hoh5457, B: Hoh5458, conact list: Atom Atom Distance (A) Na NE2 B:Gln2 4.39 Na OE1 B:Gln2 4.82 Na O B:Hoh5228 2.96 Na O B:Hoh5249 4.88 Na O B:Hoh5255 4.13 Na O B:Hoh5391 2.89 Na O B:Hoh5457 2.95 Na O B:Hoh5458 3.62 interactive model: