Sodium in the structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea (pdb 3cng)

The binding sites of Sodium atom in the structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea (pdb code 3cng). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3cng structure was solved by J.OSIPIUK, X.XU, H.ZHENG, A.SAVCHENKO, A.M.EDWARDS, A.JOACHIMIAK, MIDWESTCENTER FOR STRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.2-2.0 Space group C121 a (A) 174.781 b (A) 49.506 c (A) 110.190 alpha (°) 90.00 beta (°) 106.28 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 23.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3cng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3cng. 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: Gly70, A: Phe71, A: Arg84, A: Glu85, A: Glu88, A: Glu129, A: Hoh553, A: Hoh554, A: Hoh557, A: Hoh558, A: Hoh573, conact list: Atom Atom Distance (A) Na C A:Gly70 4.77 Na CA A:Gly70 4.28 Na O A:Phe71 4.81 Na N A:Phe71 4.48 Na NH1 A:Arg84 4.30 Na OE1 A:Glu85 3.09 Na OE2 A:Glu85 2.47 Na CD A:Glu85 3.16 Na CG A:Glu85 4.65 Na OE1 A:Glu88 3.86 Na OE1 A:Glu129 3.77 Na CD A:Glu129 4.77 Na O A:Hoh553 2.35 Na O A:Hoh554 2.85 Na O A:Hoh557 2.93 Na O A:Hoh558 2.68 Na O A:Hoh573 2.39 interactive model: Sodium binding site 2 out of 2 in 3cng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3cng. 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: Gly70, B: Phe71, B: Glu73, B: Arg84, B: Glu85, B: Glu88, B: Glu129, A: Edo506, B: Hoh537, B: Hoh541, B: Hoh573, B: Hoh574, B: Hoh584, B: Hoh604, conact list: Atom Atom Distance (A) Na C B:Gly70 4.40 Na CA B:Gly70 4.16 Na O B:Phe71 4.25 Na N B:Phe71 3.94 Na C B:Phe71 5.00 Na CA B:Phe71 4.85 Na OE2 B:Glu73 4.73 Na NH1 B:Arg84 4.44 Na OE1 B:Glu85 3.35 Na OE2 B:Glu85 2.35 Na CD B:Glu85 3.19 Na CG B:Glu85 4.59 Na OE1 B:Glu88 4.42 Na OE2 B:Glu129 4.45 Na O1 A:Edo506 4.91 Na O B:Hoh537 2.37 Na O B:Hoh541 2.96 Na O B:Hoh573 3.03 Na O B:Hoh574 2.42 Na O B:Hoh584 2.18 Na O B:Hoh604 4.36 interactive model: