Sodium in the structure of Effect of Alcohols on Protein Hydration (pdb 1yl1)

The binding sites of Sodium atom in the structure of Effect of Alcohols on Protein Hydration (pdb code 1yl1). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1yl1 structure was solved by A.A.DESHPANDE, S.NIMSADKAR, S.C.MANDE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.2-1.9 Space group P43212 a (A) 79.288 b (A) 79.288 c (A) 37.957 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 25.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 1yl1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1yl1. 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: X: Ser60, X: Arg61, X: Trp62, X: Trp63, X: Cys64, X: Asn65, X: Ser72, X: Arg73, X: Asn74, X: Leu75, X: Hoh1948, conact list: Atom Atom Distance (A) Na O X:Ser60 2.66 Na C X:Ser60 3.70 Na CA X:Ser60 4.55 Na O X:Arg61 3.76 Na N X:Arg61 4.53 Na C X:Arg61 3.85 Na CA X:Arg61 4.54 Na N X:Trp62 4.01 Na C X:Trp62 3.93 Na CA X:Trp62 4.15 Na O X:Trp62 4.22 Na N X:Trp63 4.09 Na C X:Trp63 4.41 Na CA X:Trp63 4.71 Na O X:Cys64 2.69 Na N X:Cys64 3.78 Na C X:Cys64 3.46 Na CA X:Cys64 4.20 Na N X:Asn65 4.23 Na CB X:Asn65 4.93 Na CA X:Asn65 4.39 Na O X:Ser72 4.25 Na CB X:Ser72 2.90 Na OG X:Ser72 3.15 Na C X:Ser72 3.52 Na CA X:Ser72 3.67 Na O X:Arg73 4.77 Na N X:Arg73 3.23 Na CB X:Arg73 5.00 Na C X:Arg73 3.68 Na CA X:Arg73 3.97 Na N X:Asn74 2.63 Na CB X:Asn74 3.79 Na C X:Asn74 4.62 Na OD1 X:Asn74 4.97 Na CG X:Asn74 4.69 Na CA X:Asn74 3.22 Na N X:Leu75 4.97 Na O X:Hoh1948 3.75 interactive model: