Sodium in the structure of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S (pdb 2pya)

The binding sites of Sodium atom in the structure of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S (pdb code 2pya). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2pya structure was solved by H.BOENISCH, R.LADENSTEIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-0.9 Space group P212121 a (A) 25.385 b (A) 39.812 c (A) 45.117 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 9.8 Rfree (%) 10.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2pya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2pya. 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: Asn22, A: Pro40, A: Hoh202, A: Hoh205, A: Hoh206, A: Hoh207, A: Hoh215, A: Hoh220, A: Hoh230, A: Hoh254, A: Hoh265, conact list: Atom Atom Distance (A) Na HD21 A:Asn22 4.24 Na CB A:Asn22 4.55 Na HD22 A:Asn22 3.04 Na HB3 A:Asn22 4.58 Na ND2 A:Asn22 3.43 Na OD1 A:Asn22 2.45 Na CG A:Asn22 3.22 Na HB3 A:Pro40 4.74 Na HB3 A:Pro40 4.28 Na CA A:Pro40 4.85 Na O A:Pro40 4.41 Na HA A:Pro40 4.02 Na O A:Hoh202 4.84 Na O A:Hoh205 2.40 Na O A:Hoh206 4.08 Na O A:Hoh207 4.20 Na O A:Hoh215 3.93 Na O A:Hoh220 2.42 Na O A:Hoh220 1.45 Na O A:Hoh230 2.32 Na O A:Hoh254 2.46 Na O A:Hoh254 3.38 Na O A:Hoh265 3.78 interactive model: Sodium binding site 2 out of 2 in 2pya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2pya. 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: Glu31, A: Asp32, A: Leu33, A: Lys46, A: Hoh224, A: Hoh236, A: Hoh238, A: Hoh239, A: Hoh250, A: Hoh270, A: Hoh271, A: Hoh293, conact list: Atom Atom Distance (A) Na HB2 A:Glu31 4.14 Na CB A:Glu31 4.79 Na C A:Glu31 3.47 Na CA A:Glu31 4.45 Na O A:Glu31 2.23 Na HA A:Glu31 4.35 Na N A:Asp32 4.31 Na HA A:Asp32 3.50 Na OD1 A:Asp32 4.47 Na C A:Asp32 4.95 Na CA A:Asp32 4.32 Na O A:Leu33 4.73 Na HZ3 A:Lys46 4.64 Na HZ2 A:Lys46 4.85 Na NZ A:Lys46 4.93 Na HZ1 A:Lys46 4.64 Na O A:Hoh224 2.26 Na O A:Hoh236 4.37 Na O A:Hoh238 2.55 Na O A:Hoh239 4.35 Na O A:Hoh250 2.43 Na O A:Hoh270 2.43 Na O A:Hoh271 2.29 Na O A:Hoh293 4.75 interactive model: