Sodium in PDB 1qy0: Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein

The structure of Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein, PDB code: 1qy0 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. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.627, 53.627, 137.008, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The structure of Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein also contains other interesting chemical elements:

Cadmium

(Cd)

2 atoms

The binding sites of Sodium atom in the 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 within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein, PDB code: 1qy0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:42.2 occ:1.00 OE1 A:GLU30 2.5 96.7 1.0 OE2 A:GLU30 2.9 88.8 1.0 CD A:GLU30 3.0 78.7 1.0 O A:HOH536 4.3 47.6 1.0 CG A:GLU30 4.4 50.5 1.0 CB A:GLU30 4.8 29.1 1.0

Sodium binding site 2 out of 3 in the Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:19.2 occ:1.00 O A:HOH555 2.4 36.6 1.0 O A:HOH512 2.4 40.2 1.0 O A:HOH459 2.5 37.4 1.0 OE2 A:GLU140 2.6 61.8 1.0 CD A:GLU140 3.3 39.1 1.0 CG A:GLU140 3.6 17.0 1.0 NE2 A:GLN136 3.9 9.7 1.0 O A:HOH515 4.2 44.9 1.0 OE1 A:GLU140 4.3 34.6 1.0 O A:HOH528 4.4 43.9 1.0 O A:GLN136 4.4 13.8 1.0 CB A:GLN136 4.5 15.8 1.0 O A:HOH542 4.7 18.7 1.0 C A:GLN136 4.9 17.4 1.0

Sodium binding site 3 out of 3 in the Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:25.4 occ:1.00 OD2 A:ASP125 2.5 20.0 1.0 O A:HOH463 2.8 27.6 1.0 CB A:ASP125 3.4 17.9 1.0 CG A:ASP125 3.4 30.0 1.0 O A:HOH467 4.5 17.3 1.0 O A:HOH505 4.5 36.6 1.0 OD1 A:ASP125 4.6 20.7 1.0 O A:HOH496 4.9 30.6 1.0 CA A:ASP125 4.9 17.8 1.0

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. Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2-Methoxy-3-Isobutylpyrazine to the Major Urinary Protein. J.Am.Chem.Soc. V. 126 1675 2004.
ISSN: ISSN 0002-7863
PubMed: 14871097