Sodium in the structure of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex With Cdp and PO4 (pdb 2vbt)

The binding sites of Sodium atom in the structure of Riboflavin Kinase MJ0056 From Methanocaldococcus Jannaschii in Complex With Cdp and PO4 (pdb code 2vbt). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2vbt structure was solved by M.D.HARTMANN, M.AMMELBURG, S.DJURANOVIC, J.MARTIN, A.N.LUPAS, K.ZETH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.7 Space group P43212 a (A) 77.720 b (A) 77.720 c (A) 106.868 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 26.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2vbt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2vbt. 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: Gly16, A: Glu17, A: Gly18, A: Thr43, A: Asn45, A: Glu107, A: Cdp1137, A: Po41139, A: Hoh2030, conact list: Atom Atom Distance (A) Na N A:Gly16 4.72 Na C A:Gly16 4.96 Na CA A:Gly16 4.85 Na N A:Glu17 4.42 Na N A:Gly18 4.16 Na CA A:Gly18 4.67 Na O A:Thr43 3.08 Na N A:Thr43 4.28 Na CB A:Thr43 3.71 Na CG2 A:Thr43 4.67 Na OG1 A:Thr43 2.34 Na C A:Thr43 3.91 Na CA A:Thr43 4.21 Na N A:Asn45 4.90 Na CB A:Asn45 4.83 Na ND2 A:Asn45 3.48 Na OD1 A:Asn45 2.64 Na CG A:Asn45 3.40 Na OE1 A:Glu107 3.97 Na CD A:Glu107 4.66 Na CG A:Glu107 4.93 Na O3B A:Cdp1137 4.40 Na PA A:Cdp1137 3.48 Na O2A A:Cdp1137 4.52 Na O1B A:Cdp1137 3.51 Na PB A:Cdp1137 3.05 Na O5' A:Cdp1137 4.59 Na O2B A:Cdp1137 2.36 Na O3A A:Cdp1137 2.74 Na O1A A:Cdp1137 3.01 Na O1 A:Po41139 2.84 Na P A:Po41139 3.98 Na O4 A:Po41139 4.87 Na O3 A:Po41139 3.93 Na O A:Hoh2030 4.81 interactive model: