Sodium in the structure of Contribution Of Hydrogen Bonds to the Conformational Stability of Human Lysozyme (pdb 1wqp)

The binding sites of Sodium atom in the structure of Contribution Of Hydrogen Bonds to the Conformational Stability of Human Lysozyme (pdb code 1wqp). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1wqp structure was solved by Y.YAMAGATA, M.KUBOTA, Y.SUMIKAWA, J.FUNAHASHI, S.FUJII, K.YUTANI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.8 Space group P212121 a (A) 56.780 b (A) 60.970 c (A) 33.810 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.4 Rfree (%) n/a Sodium Binding Sites: Sodium binding site 1 out of 1 in 1wqp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1wqp. 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: Ser61, A: Arg62, A: Tyr63, A: Trp64, A: Cys65, A: Asn66, A: Asp67, A: Ala73, A: Val74, A: Asn75, A: Hoh138, A: Hoh146, A: Hoh154, A: Hoh206, conact list: Atom Atom Distance (A) Na O A:Ser61 1.98 Na CB A:Ser61 4.37 Na C A:Ser61 3.15 Na CA A:Ser61 3.96 Na O A:Arg62 4.15 Na N A:Arg62 4.13 Na C A:Arg62 4.08 Na CA A:Arg62 4.27 Na N A:Tyr63 4.42 Na C A:Tyr63 4.86 Na CA A:Tyr63 4.98 Na N A:Trp64 4.92 Na O A:Cys65 2.13 Na N A:Cys65 4.19 Na C A:Cys65 3.20 Na CA A:Cys65 4.32 Na N A:Asn66 3.84 Na CB A:Asn66 4.47 Na C A:Asn66 4.71 Na OD1 A:Asn66 4.52 Na CA A:Asn66 3.67 Na N A:Asp67 4.64 Na O A:Ala73 4.76 Na C A:Ala73 4.10 Na CB A:Ala73 3.26 Na CA A:Ala73 4.27 Na O A:Val74 2.44 Na N A:Val74 3.86 Na C A:Val74 3.51 Na CA A:Val74 4.33 Na N A:Asn75 4.39 Na CB A:Asn75 4.75 Na CA A:Asn75 4.50 Na O A:Hoh138 2.39 Na O A:Hoh146 4.57 Na O A:Hoh154 2.14 Na O A:Hoh206 4.78 interactive model: