Sodium in the structure of A Mutant Human Prolactin Receptor Antagonist H27A in Complex With The Extracellular Domain of the Human Prolactin Receptor (pdb 3n06)

The binding sites of Sodium atom in the structure of A Mutant Human Prolactin Receptor Antagonist H27A in Complex With The Extracellular Domain of the Human Prolactin Receptor (pdb code 3n06). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3n06 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) 30.9-2.0 Space group P65 a (A) 123.419 b (A) 123.419 c (A) 72.665 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3n06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3n06. 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: Hoh245, A: Hoh276, B: Hoh277, B: Hoh319, B: Hoh328, B: Hoh332, B: Hoh333, conact list: Atom Atom Distance (A) Na CB A:Asp68 3.89 Na OD1 A:Asp68 3.70 Na CG A:Asp68 4.24 Na OE2 A:Glu70 4.81 Na O B:Glu18 4.51 Na O B:Lys66 2.25 Na CB B:Lys66 4.46 Na C B:Lys66 3.32 Na CA B:Lys66 3.96 Na N B:Gln67 4.38 Na C B:Gln67 4.68 Na CA B:Gln67 4.55 Na N B:Tyr68 4.84 Na O B:Thr69 2.22 Na N B:Thr69 3.96 Na CB B:Thr69 4.31 Na C B:Thr69 3.40 Na CA B:Thr69 4.10 Na N B:Ser70 4.49 Na CB B:Ser70 4.99 Na CA B:Ser70 4.70 Na O A:Hoh245 4.98 Na O A:Hoh276 2.31 Na O B:Hoh277 4.40 Na O B:Hoh319 4.01 Na O B:Hoh328 2.48 Na O B:Hoh332 2.42 Na O B:Hoh333 4.78 interactive model: Sodium binding site 2 out of 3 in 3n06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3n06. 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: Hoh275, B: Hoh279, B: Hoh289, conact list: Atom Atom Distance (A) Na O B:Arg13 4.43 Na N B:Pro15 4.80 Na CD B:Pro15 3.43 Na CG B:Pro15 3.88 Na O B:Thr19 4.20 Na CB B:Thr19 3.90 Na OG1 B:Thr19 3.09 Na C B:Thr19 3.88 Na CA B:Thr19 4.60 Na O B:Phe20 3.84 Na N B:Phe20 3.59 Na CB B:Phe20 4.96 Na C B:Phe20 3.50 Na CA B:Phe20 3.52 Na N B:Thr21 3.91 Na CB B:Thr21 4.05 Na OG1 B:Thr21 3.11 Na CA B:Thr21 4.56 Na NE2 B:His63 4.86 Na ND1 B:His63 3.66 Na CE1 B:His63 3.57 Na O B:Hoh275 4.91 Na O B:Hoh279 3.31 Na O B:Hoh289 4.25 interactive model: Sodium binding site 3 out of 3 in 3n06 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3n06. 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: Hoh323, B: Hoh340, B: Hoh359, B: Hoh364, conact list: Atom Atom Distance (A) Na CZ3 B:Trp24 4.58 Na CZ2 B:Trp24 3.83 Na CE2 B:Trp24 4.92 Na CH2 B:Trp24 3.66 Na O B:Tyr54 3.19 Na CB B:Tyr54 4.22 Na CD2 B:Tyr54 4.04 Na C B:Tyr54 4.13 Na CG B:Tyr54 4.62 Na CA B:Tyr54 4.29 Na O B:Gly58 3.67 Na C B:Gly58 4.79 Na O B:Pro59 4.85 Na C B:Pro59 4.16 Na CA B:Pro59 4.80 Na O B:Asn60 4.75 Na N B:Asn60 3.34 Na CB B:Asn60 4.89 Na C B:Asn60 3.56 Na OD1 B:Asn60 4.95 Na CA B:Asn60 3.43 Na O B:Ser61 2.86 Na N B:Ser61 2.78 Na CB B:Ser61 4.41 Na OG B:Ser61 4.03 Na C B:Ser61 3.71 Na CA B:Ser61 3.78 Na O B:Hoh323 2.01 Na O B:Hoh340 3.07 Na O B:Hoh359 3.08 Na O B:Hoh364 4.78 interactive model: