Sodium in the structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression (pdb 3h7c)

The binding sites of Sodium atom in the structure of Crystal Structure of Arabidopsis Thaliana Agmatine Deiminase From Cell Free Expression (pdb code 3h7c). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3h7c structure was solved by E.S.BURGIE, C.A.BINGMAN, G.N.PHILLIPS JR., CENTER FOREUKARYOTIC STRUCTURAL GENOMICS (CESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.5 Space group C121 a (A) 123.715 b (A) 69.932 c (A) 50.917 alpha (°) 90.00 beta (°) 98.40 gamma (°) 90.00 Rfactor (%) 14.6 Rfree (%) 17.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3h7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3h7c. 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: X: Arg73, X: Lys74, X: Gln75, X: Leu76, X: Pro77, X: Glu78, X: Hoh602, X: Hoh723, conact list: Atom Atom Distance (A) Na O X:Arg73 2.77 Na CZ X:Arg73 5.00 Na C X:Arg73 3.91 Na NE X:Arg73 4.56 Na NH2 X:Arg73 4.50 Na O X:Lys74 2.98 Na N X:Lys74 4.39 Na C X:Lys74 3.50 Na CA X:Lys74 3.82 Na N X:Gln75 4.42 Na C X:Gln75 4.78 Na O X:Leu76 2.49 Na N X:Leu76 4.10 Na C X:Leu76 3.60 Na CA X:Leu76 4.47 Na N X:Pro77 4.48 Na C X:Pro77 4.64 Na CA X:Pro77 4.47 Na N X:Glu78 4.77 Na O X:Hoh602 3.93 Na O X:Hoh723 2.78 interactive model: Sodium binding site 2 out of 2 in 3h7c Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3h7c. 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: X: Gly304, X: 1pe391, conact list: Atom Atom Distance (A) Na CA X:Gly304 4.62 Na OH2 X:1pe391 3.09 Na C12 X:1pe391 3.86 Na OH3 X:1pe391 2.71 Na OH6 X:1pe391 3.02 Na OH4 X:1pe391 2.84 Na C14 X:1pe391 3.54 Na C24 X:1pe391 3.75 Na OH5 X:1pe391 2.78 Na C25 X:1pe391 3.48 Na C13 X:1pe391 3.60 Na C23 X:1pe391 3.57 Na C26 X:1pe391 4.16 Na C22 X:1pe391 3.73 Na C15 X:1pe391 3.58 interactive model: