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Cadmium in PDB 1qy1: Thermodynamics of Binding of 2-Methoxy-3-Isopropylpyrazine and 2- Methoxy-3-Isobutylpyrazine to the Major Urinary Protein

Protein crystallography data

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

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 2 binding sites of Cadmium 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 Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1qy1

Go back to Cadmium Binding Sites List in 1qy1
Cadmium binding site 1 out of 2 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 Cadmium with other atoms in the Cd 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:Cd200

b:12.8
occ:1.00
O A:HOH625 2.2 17.7 1.0
OE1 A:GLU139 2.3 12.5 1.0
O A:HOH624 2.3 15.4 1.0
O A:HOH622 2.4 12.8 1.0
OE2 A:GLU139 2.4 10.2 1.0
CD A:GLU139 2.7 8.2 1.0
CG A:GLU139 4.2 12.6 1.0
NE2 A:GLN136 4.2 10.3 1.0
O A:HOH436 4.3 24.8 1.0
O A:HOH487 4.4 20.6 1.0
OE1 A:GLN136 4.5 15.4 1.0
CD A:GLN136 4.8 10.7 1.0

Cadmium binding site 2 out of 2 in 1qy1

Go back to Cadmium Binding Sites List in 1qy1
Cadmium binding site 2 out of 2 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 Cadmium with other atoms in the Cd 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:Cd201

b:20.4
occ:1.00
O A:HOH463 2.2 33.9 1.0
O A:HOH568 2.2 23.1 1.0
OE1 A:GLU13 2.3 19.3 1.0
OE2 A:GLU13 2.5 34.3 1.0
CD A:GLU13 2.7 22.4 1.0
CG A:GLU13 4.2 25.0 1.0
O A:HOH505 4.7 51.5 1.0

Reference:

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
Page generated: Fri Aug 28 12:23:54 2020
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