Sodium in PDB 1qy1: 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: 1qy1 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)	28.00 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.575, 53.575, 137.562, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21

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 1qy1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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: 1qy1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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:7.6 occ:1.00 O A:HOH423 2.2 18.3 1.0 O A:HOH534 2.4 28.7 1.0 ND1 A:HIS104 2.4 18.2 1.0 O A:HOH437 2.5 19.5 1.0 O A:HOH578 2.5 43.8 1.0 CE1 A:HIS104 3.0 17.1 1.0 CG A:HIS104 3.4 12.3 1.0 O A:HOH500 3.5 28.7 1.0 NA A:NA205 3.6 10.3 1.0 OG1 A:THR91 3.6 12.5 1.0 CB A:HIS104 3.9 11.7 1.0 NE2 A:HIS104 4.1 13.7 1.0 O A:HOH544 4.2 35.9 1.0 CD2 A:HIS104 4.2 19.4 1.0 O A:HOH609 4.5 51.3 1.0 CE1 A:HIS141 4.5 20.3 1.0 O A:HOH457 4.7 40.1 1.0 O A:HIS104 4.7 11.6 1.0 CB A:THR91 4.8 14.0 1.0 CG2 A:THR91 4.9 12.6 1.0

Sodium binding site 2 out of 4 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:12.1 occ:1.00 O A:HOH451 2.3 24.0 1.0 CE A:LYS76 3.0 58.1 1.0 NZ A:LYS76 3.0 66.2 1.0 CD A:LYS76 3.8 63.9 1.0 OE1 A:GLU79 4.1 34.1 1.0 O A:HOH514 4.3 20.9 1.0 O A:HOH517 4.3 23.5 1.0 O A:HOH510 4.3 35.3 1.0 OE2 A:GLU79 4.5 39.5 1.0 CD A:GLU79 4.8 40.4 1.0

Sodium binding site 3 out of 4 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:27.6 occ:1.00 O A:HOH620 2.1 57.9 1.0 OE2 A:GLU33 2.3 22.8 1.0 OE1 A:GLU33 2.6 24.8 1.0 O A:HOH605 2.6 52.6 1.0 CD A:GLU33 2.8 26.4 1.0 CG A:GLU33 4.3 22.5 1.0 O A:HOH504 4.5 37.4 1.0 NH1 A:ARG29 4.8 58.1 1.0 CD A:ARG29 4.8 20.6 1.0

Sodium binding site 4 out of 4 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 4 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:Na205 b:10.3 occ:1.00 O A:HOH609 2.1 51.3 1.0 O A:HOH437 2.4 19.5 1.0 CE1 A:HIS141 2.5 20.3 1.0 O A:HOH518 2.6 27.9 1.0 NE2 A:HIS141 3.1 21.4 1.0 NA A:NA202 3.6 7.6 1.0 ND1 A:HIS141 3.7 19.3 1.0 O A:HOH500 3.9 28.7 1.0 O A:HOH409 3.9 17.9 1.0 O A:HOH480 4.4 37.9 1.0 CD2 A:HIS141 4.4 11.8 1.0 CG A:HIS141 4.7 11.9 1.0 O A:HOH534 4.8 28.7 1.0 O A:HOH544 4.9 35.9 1.0 ND1 A:HIS104 4.9 18.2 1.0 CG A:PRO93 4.9 31.3 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