Sodium in the structure of Metallo-Beta-Lactamase (Cadmium-Bound Form) (pdb 2znb)

The binding sites of Sodium atom in the structure of Metallo-Beta-Lactamase (Cadmium-Bound Form) (pdb code 2znb). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2znb structure was solved by N.O.CONCHA, O.HERZBERG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.1 Space group P43212 a (A) 78.086 b (A) 78.086 c (A) 139.746 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 25.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2znb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2znb. 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: Ser54, A: Asn55, A: Gly56, A: Asp69, A: Thr70, A: Asp103, A: Cys104, A: Phe178, A: Gly222, A: Hoh255, A: Hoh256, A: Hoh261, conact list: Atom Atom Distance (A) Na CB A:Ser54 4.41 Na OG A:Ser54 4.91 Na C A:Ser54 4.66 Na O A:Asn55 2.39 Na N A:Asn55 4.00 Na C A:Asn55 3.54 Na CA A:Asn55 4.30 Na N A:Gly56 4.57 Na CA A:Gly56 4.80 Na CB A:Asp69 3.35 Na OD2 A:Asp69 2.55 Na OD1 A:Asp69 4.47 Na CG A:Asp69 3.30 Na CA A:Asp69 4.82 Na O A:Thr70 4.58 Na O A:Asp103 2.42 Na CB A:Asp103 4.34 Na OD2 A:Asp103 4.33 Na C A:Asp103 3.63 Na CG A:Asp103 4.55 Na CA A:Asp103 4.56 Na N A:Cys104 4.52 Na SG A:Cys104 4.67 Na CA A:Cys104 4.55 Na CZ A:Phe178 4.60 Na O A:Gly222 4.40 Na O A:Hoh255 2.15 Na O A:Hoh256 3.63 Na O A:Hoh261 2.74 interactive model: Sodium binding site 2 out of 2 in 2znb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2znb. 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: Tyr40, B: Ser54, B: Asn55, B: Gly56, B: Asp69, B: Thr70, B: Asp103, B: Cys104, B: Phe178, B: Gly222, B: Hoh267, B: Hoh286, B: Hoh300, conact list: Atom Atom Distance (A) Na OH B:Tyr40 4.89 Na CB B:Ser54 4.47 Na OG B:Ser54 4.47 Na C B:Ser54 4.65 Na O B:Asn55 2.22 Na N B:Asn55 4.04 Na C B:Asn55 3.35 Na CA B:Asn55 4.26 Na N B:Gly56 4.33 Na CA B:Gly56 4.51 Na CB B:Asp69 3.35 Na OD2 B:Asp69 2.44 Na OD1 B:Asp69 4.35 Na CG B:Asp69 3.21 Na CA B:Asp69 4.77 Na O B:Thr70 4.61 Na O B:Asp103 2.47 Na CB B:Asp103 4.28 Na OD2 B:Asp103 4.45 Na C B:Asp103 3.68 Na CG B:Asp103 4.61 Na CA B:Asp103 4.58 Na N B:Cys104 4.54 Na SG B:Cys104 4.72 Na CA B:Cys104 4.53 Na CZ B:Phe178 4.57 Na O B:Gly222 4.34 Na O B:Hoh267 2.36 Na O B:Hoh286 3.70 Na O B:Hoh300 2.71 interactive model: