Sodium in PDB 1qy2: 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: 1qy2 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 / 1.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.248, 53.248, 137.703, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.5

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 1qy2). 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: 1qy2:
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:15.9 occ:1.00 O A:HOH429 2.1 28.3 1.0 O A:HOH529 2.3 39.7 1.0 O A:HOH579 2.4 47.8 1.0 ND1 A:HIS104 2.5 25.4 1.0 O A:HOH516 2.5 29.8 1.0 CE1 A:HIS104 3.1 20.2 1.0 CG A:HIS104 3.4 23.2 1.0 NA A:NA204 3.5 16.3 1.0 O A:HOH483 3.6 35.4 1.0 OG1 A:THR91 3.6 21.5 1.0 CB A:HIS104 3.9 18.4 1.0 NE2 A:HIS104 4.1 20.9 1.0 O A:HOH578 4.2 43.9 1.0 CD2 A:HIS104 4.2 25.6 1.0 CE1 A:HIS141 4.5 24.2 1.0 O A:HIS104 4.7 18.3 1.0 O A:HOH435 4.7 34.9 1.0 CB A:THR91 4.8 18.3 1.0 CG2 A:THR91 4.9 18.6 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:23.5 occ:1.00 O A:HOH536 2.2 47.9 1.0 O A:HOH479 2.3 39.6 1.0 CE A:LYS76 2.9 72.3 1.0 NZ A:LYS76 3.0 75.8 1.0 CD A:LYS76 3.8 72.6 1.0 OE1 A:GLU79 4.2 38.1 1.0 O A:HOH567 4.3 31.1 1.0 O A:HOH572 4.3 41.4 1.0 O A:HOH561 4.4 43.2 1.0 O A:HOH515 4.5 26.8 1.0 OE2 A:GLU79 4.6 39.0 1.0 CD A:GLU79 4.8 39.9 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:16.3 occ:1.00 O A:HOH516 2.4 29.8 1.0 CE1 A:HIS141 2.5 24.2 1.0 O A:HOH450 2.6 32.1 1.0 NE2 A:HIS141 3.1 28.1 1.0 NA A:NA202 3.5 15.9 1.0 ND1 A:HIS141 3.7 28.7 1.0 O A:HOH483 4.0 35.4 1.0 O A:HOH408 4.0 24.3 1.0 O A:HOH538 4.3 42.0 1.0 CD2 A:HIS141 4.4 21.2 1.0 CG A:HIS141 4.7 23.0 1.0 O A:HOH529 4.8 39.7 1.0 O A:HOH578 4.9 43.9 1.0 ND1 A:HIS104 5.0 25.4 1.0 CG A:HIS104 5.0 23.2 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