Sodium in the structure of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli With A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix (pdb 2zj9)

The binding sites of Sodium atom in the structure of X-Ray Crystal Structure of Ampc Beta-Lactamase (Ampc(D)) From An Escherichia Coli With A Tripeptide Deletion (GLY286 SER287 ASP288) on the H10 Helix (pdb code 2zj9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2zj9 structure was solved by Y.YAMAGUCHI, G.SATO, Y.YAMAGATA, J.WACHINO, Y.ARAKAWA, H.KUROSAKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.2-1.7 Space group P1 a (A) 47.065 b (A) 47.381 c (A) 81.461 alpha (°) 82.62 beta (°) 80.91 gamma (°) 65.40 Rfactor (%) 16.3 Rfree (%) 20.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2zj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2zj9. 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: Gln100, A: Gln136, A: Asn137, A: Trp138, A: Gln139, A: Hoh426, A: Hoh457, A: Hoh468, A: Hoh486, conact list: Atom Atom Distance (A) Na NE2 A:Gln100 3.46 Na OE1 A:Gln100 2.53 Na CD A:Gln100 3.32 Na CG A:Gln100 4.70 Na O A:Gln136 2.66 Na C A:Gln136 3.73 Na O A:Asn137 3.02 Na N A:Asn137 4.15 Na C A:Asn137 3.18 Na CA A:Asn137 3.67 Na N A:Trp138 3.70 Na C A:Trp138 3.31 Na CA A:Trp138 4.13 Na O A:Trp138 2.44 Na NE2 A:Gln139 2.25 Na N A:Gln139 4.08 Na OE1 A:Gln139 4.49 Na CB A:Gln139 4.90 Na CB A:Gln139 4.78 Na CD A:Gln139 3.50 Na CG A:Gln139 4.32 Na CG A:Gln139 4.07 Na CA A:Gln139 4.29 Na CA A:Gln139 4.27 Na O A:Hoh426 3.95 Na O A:Hoh457 4.55 Na O A:Hoh468 2.21 Na O A:Hoh486 3.98 interactive model: Sodium binding site 2 out of 2 in 2zj9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2zj9. 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: Gln100, B: Gln136, B: Asn137, B: Trp138, B: Gln139, B: Hoh397, B: Hoh536, B: Hoh601, conact list: Atom Atom Distance (A) Na NE2 B:Gln100 3.43 Na OE1 B:Gln100 2.49 Na CD B:Gln100 3.27 Na CG B:Gln100 4.65 Na O B:Gln136 2.71 Na C B:Gln136 3.81 Na O B:Asn137 3.06 Na N B:Asn137 4.28 Na C B:Asn137 3.33 Na CA B:Asn137 3.83 Na N B:Trp138 3.90 Na C B:Trp138 3.45 Na CA B:Trp138 4.29 Na O B:Trp138 2.58 Na NE2 B:Gln139 4.30 Na N B:Gln139 4.20 Na OE1 B:Gln139 2.17 Na CB B:Gln139 4.84 Na CD B:Gln139 3.31 Na CG B:Gln139 4.09 Na CA B:Gln139 4.34 Na O B:Hoh397 3.84 Na O B:Hoh536 3.89 Na O B:Hoh601 4.31 interactive model: