Sodium in the structure of Crystal Structure of the Factor Xa/NAP5 Complex (pdb 2p3f)

The binding sites of Sodium atom in the structure of Crystal Structure of the Factor Xa/NAP5 Complex (pdb code 2p3f). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2p3f structure was solved by J.L.RIOS-STEINER, M.T.MURAKAMI, A.TULINSKY, R.K.ARNI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-3.1 Space group P6122 a (A) 137.170 b (A) 137.170 c (A) 167.670 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18 Rfree (%) 28 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2p3f Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2p3f. 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: H: Tyr185, H: Asp185A, H: Thr185B, H: Lys186, H: Ala221, H: Arg222, H: Lys223, H: Gly223A, H: Lys224, H: Hoh256, conact list: Atom Atom Distance (A) Na O H:Tyr185 2.39 Na N H:Tyr185 4.67 Na CB H:Tyr185 4.57 Na C H:Tyr185 3.40 Na CA H:Tyr185 4.41 Na O H:Asp185A 2.53 Na N H:Asp185A 4.09 Na C H:Asp185A 3.19 Na CA H:Asp185A 3.98 Na O H:Thr185B 4.32 Na N H:Thr185B 3.88 Na C H:Thr185B 4.20 Na CA H:Thr185B 4.07 Na O H:Lys186 4.13 Na N H:Lys186 4.78 Na O H:Ala221 3.30 Na C H:Ala221 3.65 Na CA H:Ala221 4.16 Na O H:Arg222 2.78 Na N H:Arg222 4.24 Na C H:Arg222 3.66 Na CA H:Arg222 4.58 Na N H:Lys223 4.34 Na C H:Lys223 4.51 Na CA H:Lys223 4.23 Na N H:Gly223A 4.29 Na O H:Lys224 2.75 Na N H:Lys224 3.98 Na C H:Lys224 3.93 Na CA H:Lys224 4.53 Na O H:Hoh256 4.58 interactive model: