Sodium in the structure of Thermodynamics Of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein (pdb 1qy0)

The binding sites of Sodium atom in the structure of Thermodynamics Of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein (pdb code 1qy0). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1qy0 structure was solved by R.J.BINGHAM, J.B.C.FINDLAY, S.-Y.HSIEH, A.P.KALVERDA, A.KJELLBERG, C.PERAZZOLO, S.E.V.PHILLIPS, K.SESHADRI, C.H.TRINH, W.B.TURNBULL, G.BODENHAUSEN, S.W.HOMANS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-1.8 Space group P43212 a (A) 53.627 b (A) 53.627 c (A) 137.008 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 21.8 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1qy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1qy0. 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: Glu30, A: Hoh536, conact list: Atom Atom Distance (A) Na OE1 A:Glu30 2.53 Na CB A:Glu30 4.83 Na OE2 A:Glu30 2.94 Na CD A:Glu30 3.02 Na CG A:Glu30 4.40 Na O A:Hoh536 4.30 interactive model: Sodium binding site 2 out of 3 in 1qy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1qy0. 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: Gln136, A: Glu140, A: Hoh459, A: Hoh512, A: Hoh515, A: Hoh528, A: Hoh542, A: Hoh555, conact list: Atom Atom Distance (A) Na O A:Gln136 4.40 Na NE2 A:Gln136 3.92 Na CB A:Gln136 4.51 Na C A:Gln136 4.93 Na OE1 A:Glu140 4.27 Na OE2 A:Glu140 2.59 Na CD A:Glu140 3.30 Na CG A:Glu140 3.61 Na O A:Hoh459 2.53 Na O A:Hoh512 2.41 Na O A:Hoh515 4.24 Na O A:Hoh528 4.40 Na O A:Hoh542 4.74 Na O A:Hoh555 2.37 interactive model: Sodium binding site 3 out of 3 in 1qy0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1qy0. 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: Asp125, A: Hoh463, A: Hoh467, A: Hoh496, A: Hoh505, conact list: Atom Atom Distance (A) Na CB A:Asp125 3.35 Na OD2 A:Asp125 2.52 Na OD1 A:Asp125 4.58 Na CG A:Asp125 3.36 Na CA A:Asp125 4.88 Na O A:Hoh463 2.80 Na O A:Hoh467 4.45 Na O A:Hoh496 4.87 Na O A:Hoh505 4.46 interactive model: