Sodium in the structure of Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog Without Calcium (pdb 2wg4)

The binding sites of Sodium atom in the structure of Crystal Structure of the Complex Between Human Hedgehog- Interacting Protein Hip and Sonic Hedgehog Without Calcium (pdb code 2wg4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2wg4 structure was solved by B.BISHOP, A.R.ARICESCU, K.HARLOS, C.A.O'CALLAGHAN, E.Y.JONES, C.SIEBOLD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.8-3.1 Space group P3221 a (A) 88.055 b (A) 88.055 c (A) 171.946 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.35 Rfree (%) 29.2 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2wg4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2wg4. 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: Arg410, B: Ser411, B: Asn412, B: Pro413, B: Phe415, B: Asp473, B: Tyr474, B: Glu475, conact list: Atom Atom Distance (A) Na O B:Arg410 2.51 Na C B:Arg410 3.72 Na CA B:Arg410 4.76 Na O B:Ser411 3.52 Na N B:Ser411 4.53 Na C B:Ser411 3.81 Na CA B:Ser411 4.42 Na O B:Asn412 2.47 Na N B:Asn412 4.23 Na C B:Asn412 3.57 Na CA B:Asn412 4.50 Na O B:Pro413 4.32 Na N B:Pro413 4.41 Na C B:Pro413 4.62 Na CA B:Pro413 4.47 Na N B:Phe415 4.95 Na CB B:Phe415 4.21 Na CD2 B:Phe415 4.66 Na CG B:Phe415 4.92 Na O B:Asp473 4.97 Na CB B:Asp473 4.82 Na OD2 B:Asp473 3.96 Na C B:Asp473 4.51 Na OD1 B:Asp473 2.44 Na CG B:Asp473 3.54 Na CA B:Asp473 4.93 Na O B:Tyr474 2.53 Na N B:Tyr474 4.17 Na C B:Tyr474 3.68 Na CA B:Tyr474 4.46 Na N B:Glu475 4.67 Na OE1 B:Glu475 4.80 Na CA B:Glu475 4.86 interactive model: Sodium binding site 2 out of 4 in 2wg4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2wg4. 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: His440, B: Pro441, B: Asp443, B: Ile444, B: Ile446, B: Asn447, conact list: Atom Atom Distance (A) Na C B:His440 4.71 Na CA B:His440 4.81 Na O B:Pro441 3.63 Na N B:Pro441 4.34 Na CB B:Pro441 4.75 Na CD B:Pro441 4.08 Na C B:Pro441 4.63 Na CG B:Pro441 4.77 Na CA B:Pro441 4.87 Na O B:Asp443 3.49 Na C B:Asp443 4.68 Na O B:Ile444 4.66 Na O B:Ile446 3.48 Na C B:Ile446 4.43 Na O B:Asn447 4.65 Na N B:Asn447 4.73 Na CB B:Asn447 4.82 Na ND2 B:Asn447 3.79 Na C B:Asn447 4.69 Na CG B:Asn447 4.78 Na CA B:Asn447 4.07 interactive model: Sodium binding site 3 out of 4 in 2wg4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2wg4. 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: Leu233, B: Ser286, B: Leu287, B: Ala288, B: Leu357, conact list: Atom Atom Distance (A) Na CD1 B:Leu233 4.24 Na CD2 B:Leu233 4.60 Na CG B:Leu233 4.84 Na OG B:Ser286 3.67 Na O B:Leu287 3.26 Na N B:Leu287 4.68 Na C B:Leu287 4.29 Na CB B:Ala288 4.89 Na CA B:Ala288 4.95 Na O B:Leu357 3.26 Na C B:Leu357 4.41 interactive model: Sodium binding site 4 out of 4 in 2wg4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2wg4. 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: His269, B: Val272, B: Gln273, B: Ser274, conact list: Atom Atom Distance (A) Na O B:His269 3.54 Na C B:His269 4.73 Na O B:Val272 3.44 Na C B:Val272 4.55 Na NE2 B:Gln273 3.68 Na CD B:Gln273 4.65 Na CG B:Gln273 4.83 Na CA B:Gln273 4.48 Na N B:Ser274 4.73 Na OG B:Ser274 4.96 interactive model: