Sodium in the structure of Structure of the V. Cholerae Rtx Cysteine Protease Domain (pdb 3eeb)

The binding sites of Sodium atom in the structure of Structure of the V. Cholerae Rtx Cysteine Protease Domain (pdb code 3eeb). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3eeb structure was solved by P.J.LUPARDUS, A.SHEN, M.BOGYO, K.C.GARCIA, 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) 44.491 b (A) 66.099 c (A) 136.051 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 24.3 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3eeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3eeb. 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: Gly25, A: Glu27, A: Thr28, A: Lys54, A: His55, A: Ihp210, A: Hoh212, A: Hoh284, A: Hoh285, A: Hoh286, conact list: Atom Atom Distance (A) Na O A:Gly25 4.70 Na O A:Glu27 2.40 Na N A:Glu27 4.59 Na C A:Glu27 3.60 Na CA A:Glu27 4.69 Na N A:Thr28 4.35 Na CB A:Thr28 4.82 Na CA A:Thr28 4.23 Na NZ A:Lys54 4.48 Na NE2 A:His55 4.66 Na CE1 A:His55 4.79 Na P2 A:Ihp210 3.41 Na O32 A:Ihp210 1.92 Na C1 A:Ihp210 4.38 Na C2 A:Ihp210 4.08 Na O42 A:Ihp210 4.11 Na O31 A:Ihp210 2.01 Na O12 A:Ihp210 4.18 Na P1 A:Ihp210 3.11 Na O41 A:Ihp210 4.43 Na O22 A:Ihp210 4.30 Na O21 A:Ihp210 3.43 Na O11 A:Ihp210 3.58 Na O A:Hoh212 4.30 Na O A:Hoh284 2.58 Na O A:Hoh285 4.10 Na O A:Hoh286 2.29 interactive model: Sodium binding site 2 out of 2 in 3eeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3eeb. 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: Gly26, B: Glu27, B: Thr28, B: Lys54, B: Ihp210, B: Hoh243, B: Hoh283, B: Hoh293, conact list: Atom Atom Distance (A) Na C B:Gly26 4.71 Na O B:Glu27 2.33 Na N B:Glu27 4.41 Na C B:Glu27 3.54 Na CA B:Glu27 4.56 Na N B:Thr28 4.35 Na CA B:Thr28 4.33 Na NZ B:Lys54 4.89 Na P2 B:Ihp210 3.59 Na O32 B:Ihp210 2.14 Na C1 B:Ihp210 4.26 Na C2 B:Ihp210 3.95 Na O42 B:Ihp210 4.43 Na O31 B:Ihp210 2.06 Na O12 B:Ihp210 4.16 Na P1 B:Ihp210 3.17 Na O41 B:Ihp210 4.49 Na O22 B:Ihp210 4.51 Na O21 B:Ihp210 3.55 Na O11 B:Ihp210 3.58 Na O B:Hoh243 4.21 Na O B:Hoh283 2.40 Na O B:Hoh293 2.51 interactive model: