Sodium in the structure of Crystal Structure Of D141E Mutant of Bpkatg At pH 8.0 (pdb 2dv2)

The binding sites of Sodium atom in the structure of Crystal Structure Of D141E Mutant of Bpkatg At pH 8.0 (pdb code 2dv2). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2dv2 structure was solved by T.DEEMAGARN, B.WISEMAN, X.CARPENA, A.IVANCICH, I.FITA, P.C.LOEWEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.1 Space group P212121 a (A) 100.327 b (A) 114.824 c (A) 174.310 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.8 Rfree (%) 18.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2dv2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2dv2. 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: Tyr117, A: Gly122, A: Arg123, A: Gly124, A: Gly125, A: Glu128, A: Glu198, A: Asp427, A: Ser494, A: Asp495, A: Hoh1507, A: Hoh1508, A: Hoh1570, A: Hoh1609, conact list: Atom Atom Distance (A) Na CD1 A:Tyr117 4.75 Na CE1 A:Tyr117 4.97 Na O A:Gly122 2.53 Na C A:Gly122 3.64 Na CA A:Gly122 4.91 Na O A:Arg123 4.20 Na N A:Arg123 4.10 Na CB A:Arg123 4.96 Na C A:Arg123 3.60 Na CA A:Arg123 3.63 Na O A:Gly124 2.39 Na N A:Gly124 3.56 Na C A:Gly124 3.51 Na CA A:Gly124 4.15 Na N A:Gly125 4.59 Na CA A:Gly125 4.87 Na OE2 A:Glu128 4.62 Na OE2 A:Glu198 4.65 Na CB A:Asp427 4.16 Na OD2 A:Asp427 4.03 Na CG A:Asp427 4.62 Na O A:Ser494 2.44 Na CB A:Ser494 4.25 Na C A:Ser494 3.29 Na CA A:Ser494 4.03 Na N A:Asp495 4.15 Na CB A:Asp495 4.58 Na CA A:Asp495 4.44 Na O A:Hoh1507 2.43 Na O A:Hoh1508 2.26 Na O A:Hoh1570 4.16 Na O A:Hoh1609 3.86 interactive model: Sodium binding site 2 out of 2 in 2dv2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2dv2. 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: Tyr117, B: Gly122, B: Arg123, B: Gly124, B: Gly125, B: Glu128, B: Glu198, B: Asp427, B: Ser494, B: Asp495, B: Hoh2009, B: Hoh2010, B: Hoh2063, B: Hoh2112, B: Hoh2254, conact list: Atom Atom Distance (A) Na CD1 B:Tyr117 4.67 Na CE1 B:Tyr117 4.88 Na O B:Gly122 2.57 Na C B:Gly122 3.64 Na CA B:Gly122 4.88 Na O B:Arg123 4.11 Na N B:Arg123 4.12 Na CB B:Arg123 4.97 Na C B:Arg123 3.63 Na CA B:Arg123 3.69 Na O B:Gly124 2.34 Na N B:Gly124 3.61 Na C B:Gly124 3.49 Na CA B:Gly124 4.12 Na N B:Gly125 4.58 Na CA B:Gly125 4.87 Na OE2 B:Glu128 4.58 Na OE2 B:Glu198 4.66 Na CB B:Asp427 4.20 Na OD2 B:Asp427 4.15 Na CG B:Asp427 4.71 Na O B:Ser494 2.47 Na CB B:Ser494 4.25 Na C B:Ser494 3.33 Na CA B:Ser494 4.05 Na N B:Asp495 4.19 Na CB B:Asp495 4.63 Na CA B:Asp495 4.50 Na O B:Hoh2009 2.20 Na O B:Hoh2010 2.35 Na O B:Hoh2063 4.24 Na O B:Hoh2112 3.95 Na O B:Hoh2254 4.90 interactive model: