Sodium in the structure of A Human Prolactin Receptor Antagonist in Complex With The Mutant Extracellular Domain H188A of the Human Prolactin Receptor (pdb 3ncc)

The binding sites of Sodium atom in the structure of A Human Prolactin Receptor Antagonist in Complex With The Mutant Extracellular Domain H188A of the Human Prolactin Receptor (pdb code 3ncc). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ncc structure was solved by M.V.KULKARNI, M.C.TETTAMANZI, J.W.MURPHY, C.KEELER, D.G.MYSZKA, N.E.CHAYEN, E.J.LOLIS, M.E.HODSDON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.0-2.5 Space group P65 a (A) 123.411 b (A) 123.411 c (A) 73.148 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.8 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3ncc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ncc. 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: Arg13, B: Pro15, B: Thr19, B: Phe20, B: Thr21, B: His63, B: Hoh250, B: Hoh255, B: Hoh265, conact list: Atom Atom Distance (A) Na O B:Arg13 4.41 Na N B:Pro15 4.76 Na CD B:Pro15 3.35 Na CG B:Pro15 3.84 Na O B:Thr19 4.21 Na CB B:Thr19 3.92 Na OG1 B:Thr19 3.02 Na C B:Thr19 3.92 Na CA B:Thr19 4.60 Na O B:Phe20 3.89 Na N B:Phe20 3.64 Na CB B:Phe20 4.94 Na C B:Phe20 3.52 Na CA B:Phe20 3.51 Na N B:Thr21 3.90 Na CB B:Thr21 4.12 Na OG1 B:Thr21 3.07 Na CA B:Thr21 4.57 Na NE2 B:His63 4.84 Na ND1 B:His63 3.58 Na CE1 B:His63 3.52 Na CG B:His63 4.97 Na O B:Hoh250 4.99 Na O B:Hoh255 3.24 Na O B:Hoh265 4.05 interactive model: Sodium binding site 2 out of 3 in 3ncc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ncc. 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: Asp68, A: Glu70, B: Glu18, B: Lys66, B: Gln67, B: Tyr68, B: Thr69, B: Ser70, A: Hoh230, A: Hoh238, A: Hoh244, B: Hoh252, B: Hoh292, B: Hoh302, B: Hoh331, conact list: Atom Atom Distance (A) Na CB A:Asp68 3.80 Na OD1 A:Asp68 3.34 Na CG A:Asp68 3.95 Na OE2 A:Glu70 4.99 Na O B:Glu18 4.54 Na O B:Lys66 2.30 Na CB B:Lys66 4.67 Na C B:Lys66 3.43 Na CA B:Lys66 4.08 Na N B:Gln67 4.50 Na C B:Gln67 4.82 Na CA B:Gln67 4.68 Na N B:Tyr68 4.91 Na O B:Thr69 2.18 Na N B:Thr69 3.92 Na CB B:Thr69 4.20 Na CG2 B:Thr69 4.83 Na C B:Thr69 3.33 Na CA B:Thr69 3.99 Na N B:Ser70 4.42 Na CB B:Ser70 4.79 Na CA B:Ser70 4.63 Na O A:Hoh230 4.86 Na O A:Hoh238 2.35 Na O A:Hoh244 2.30 Na O B:Hoh252 4.47 Na O B:Hoh292 3.97 Na O B:Hoh302 4.82 Na O B:Hoh331 2.31 interactive model: Sodium binding site 3 out of 3 in 3ncc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ncc. 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: Trp24, B: Tyr54, B: Gly58, B: Pro59, B: Asn60, B: Ser61, B: Cys62, B: Hoh240, B: Hoh309, B: Hoh319, conact list: Atom Atom Distance (A) Na CZ3 B:Trp24 4.74 Na CZ2 B:Trp24 4.14 Na CH2 B:Trp24 3.87 Na O B:Tyr54 2.97 Na CB B:Tyr54 4.13 Na CD2 B:Tyr54 4.02 Na C B:Tyr54 3.93 Na CG B:Tyr54 4.57 Na CA B:Tyr54 4.14 Na O B:Gly58 3.39 Na C B:Gly58 4.52 Na O B:Pro59 4.80 Na C B:Pro59 4.03 Na CA B:Pro59 4.59 Na O B:Asn60 4.96 Na N B:Asn60 3.26 Na C B:Asn60 3.74 Na CA B:Asn60 3.59 Na O B:Ser61 2.78 Na N B:Ser61 2.88 Na CB B:Ser61 4.24 Na OG B:Ser61 3.86 Na C B:Ser61 3.67 Na CA B:Ser61 3.78 Na N B:Cys62 4.97 Na O B:Hoh240 4.75 Na O B:Hoh309 3.12 Na O B:Hoh319 3.17 interactive model: