Sodium in the structure of Crystal Structure of Thiamine-Monophosphate Kinase (MFLA_0573) From Methylobacillus Flagellatus Kt At 1.91 A Resolution (pdb 3mcq)

The binding sites of Sodium atom in the structure of Crystal Structure of Thiamine-Monophosphate Kinase (MFLA_0573) From Methylobacillus Flagellatus Kt At 1.91 A Resolution (pdb code 3mcq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3mcq 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) 29.1-1.9 Space group P3121 a (A) 59.225 b (A) 59.225 c (A) 159.766 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.7 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3mcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3mcq. 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: Pro235, A: Lys236, A: Asp284, A: 1pe328, A: Hoh357, conact list: Atom Atom Distance (A) Na CA A:Pro235 4.97 Na O A:Lys236 4.75 Na N A:Lys236 4.89 Na OD2 A:Asp284 4.23 Na OD1 A:Asp284 4.22 Na CG A:Asp284 4.67 Na OH2 A:1pe328 2.46 Na C12 A:1pe328 3.39 Na OH7 A:1pe328 4.96 Na OH3 A:1pe328 2.59 Na OH6 A:1pe328 2.84 Na OH4 A:1pe328 2.66 Na C14 A:1pe328 3.58 Na C16 A:1pe328 4.18 Na C24 A:1pe328 3.64 Na OH5 A:1pe328 2.53 Na C25 A:1pe328 3.38 Na C13 A:1pe328 3.65 Na C23 A:1pe328 3.58 Na C26 A:1pe328 3.95 Na C22 A:1pe328 3.35 Na C15 A:1pe328 3.46 Na O A:Hoh357 2.36 interactive model: Sodium binding site 2 out of 2 in 3mcq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3mcq. 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: Lys63, A: Asp258, A: Pg4327, A: Hoh400, conact list: Atom Atom Distance (A) Na CE A:Lys63 4.13 Na CD A:Lys63 4.65 Na NZ A:Lys63 4.01 Na OD2 A:Asp258 4.07 Na C6 A:Pg4327 3.60 Na O5 A:Pg4327 4.90 Na C5 A:Pg4327 3.75 Na O2 A:Pg4327 2.86 Na C7 A:Pg4327 4.89 Na C4 A:Pg4327 3.81 Na C1 A:Pg4327 3.57 Na O1 A:Pg4327 2.52 Na C3 A:Pg4327 3.78 Na O4 A:Pg4327 3.59 Na O3 A:Pg4327 2.85 Na C2 A:Pg4327 3.69 Na O A:Hoh400 2.55 interactive model: