Sodium in the structure of Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form (pdb 3a6v)

The binding sites of Sodium atom in the structure of Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form (pdb code 3a6v). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3a6v structure was solved by T.NAKAMURA, Y.YAMAGATA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-2.0 Space group P1211 a (A) 35.750 b (A) 55.950 c (A) 74.120 alpha (°) 90.00 beta (°) 96.40 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 22.7 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3a6v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3a6v. 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: Glu34, A: Phe35, A: Pro36, A: Gly37, A: Gly38, A: Glu53, A: Glu57, B: Pro76, B: Asp77, A: Mn1003, A: Hoh133, A: Hoh140, A: Hoh153, A: Hoh155, A: Hoh186, B: Hoh186, conact list: Atom Atom Distance (A) Na OE2 A:Glu34 4.60 Na O A:Phe35 4.73 Na C A:Pro36 4.44 Na CA A:Pro36 4.62 Na O A:Gly37 2.39 Na N A:Gly37 3.55 Na C A:Gly37 3.53 Na CA A:Gly37 4.12 Na N A:Gly38 4.64 Na CA A:Gly38 4.91 Na OE2 A:Glu53 4.82 Na OE1 A:Glu57 2.36 Na OE2 A:Glu57 2.71 Na CD A:Glu57 2.86 Na CG A:Glu57 4.33 Na CB B:Pro76 4.22 Na C B:Pro76 4.32 Na CA B:Pro76 4.41 Na N B:Asp77 3.96 Na CB B:Asp77 4.27 Na OD2 B:Asp77 3.59 Na OD1 B:Asp77 2.41 Na CG B:Asp77 3.18 Na CA B:Asp77 4.52 Na MN A:Mn1003 3.90 Na O A:Hoh133 4.21 Na O A:Hoh140 4.23 Na O A:Hoh153 2.28 Na O A:Hoh155 4.15 Na O A:Hoh186 4.69 Na O B:Hoh186 2.56 interactive model: Sodium binding site 2 out of 2 in 3a6v Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3a6v. 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: Pro76, A: Asp77, B: Glu34, B: Phe35, B: Pro36, B: Gly37, B: Gly38, B: Glu53, B: Glu57, B: Mn1001, A: Hoh163, B: Hoh131, B: Hoh137, B: Hoh140, B: Hoh141, B: Hoh180, B: Hoh183, conact list: Atom Atom Distance (A) Na CB A:Pro76 4.29 Na C A:Pro76 4.33 Na CA A:Pro76 4.48 Na N A:Asp77 3.91 Na CB A:Asp77 4.18 Na OD2 A:Asp77 3.62 Na OD1 A:Asp77 2.35 Na CG A:Asp77 3.14 Na CA A:Asp77 4.42 Na OE2 B:Glu34 4.65 Na O B:Phe35 4.82 Na C B:Pro36 4.49 Na CA B:Pro36 4.65 Na O B:Gly37 2.35 Na N B:Gly37 3.57 Na C B:Gly37 3.50 Na CA B:Gly37 4.14 Na N B:Gly38 4.59 Na CA B:Gly38 4.85 Na OE2 B:Glu53 4.80 Na OE1 B:Glu57 2.27 Na OE2 B:Glu57 2.76 Na CD B:Glu57 2.83 Na CG B:Glu57 4.30 Na MN B:Mn1001 3.85 Na O A:Hoh163 2.50 Na O B:Hoh131 4.05 Na O B:Hoh137 4.09 Na O B:Hoh140 2.28 Na O B:Hoh141 4.18 Na O B:Hoh180 4.62 Na O B:Hoh183 4.62 interactive model: