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Yttrium in PDB 3bej: Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide

Protein crystallography data

The structure of Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide, PDB code: 3bej was solved by S.M.Soisson, G.Parthasarathy, J.W.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.65 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.642, 90.889, 129.651, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.4

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide (pdb code 3bej). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide, PDB code: 3bej:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 3bej

Go back to Yttrium Binding Sites List in 3bej
Yttrium binding site 1 out of 2 in the Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y1

b:19.1
occ:1.00
O A:HOH603 1.9 16.1 1.0
OE1 A:GLU360 2.4 21.1 1.0
O A:HOH475 2.4 17.7 1.0
O B:HOH734 2.4 17.2 1.0
OD1 A:ASP359 2.4 20.4 1.0
O A:HOH499 2.4 17.6 1.0
O A:HOH474 2.5 18.2 1.0
O A:HOH514 2.7 32.5 1.0
CD A:GLU360 3.4 19.2 1.0
CG A:ASP359 3.5 26.4 1.0
O A:HOH615 3.6 25.9 1.0
Y B:YT32 3.7 18.8 1.0
OD2 A:ASP359 3.8 22.4 1.0
OE2 A:GLU360 3.8 20.0 1.0
N A:GLU360 4.4 18.8 1.0
O B:HOH576 4.5 17.7 1.0
CB A:SER358 4.6 20.9 1.0
N A:ASP359 4.6 17.5 1.0
CG A:GLU360 4.6 10.8 1.0
OE1 B:GLU360 4.6 14.2 1.0
CB A:GLU360 4.7 14.1 1.0
CB A:ASP359 4.9 17.4 1.0
O B:HOH569 4.9 19.0 1.0
O B:HOH590 4.9 23.2 1.0
CB B:GLU360 5.0 15.9 1.0

Yttrium binding site 2 out of 2 in 3bej

Go back to Yttrium Binding Sites List in 3bej
Yttrium binding site 2 out of 2 in the Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of Human Fxr in Complex with Mfa-1 and Co-Activator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y2

b:18.8
occ:1.00
O B:HOH765 2.1 24.1 1.0
OE1 B:GLU360 2.3 14.2 1.0
O B:HOH734 2.3 17.2 1.0
OD2 B:ASP359 2.3 17.1 1.0
O B:HOH576 2.4 17.7 1.0
O B:HOH569 2.5 19.0 1.0
O A:HOH603 2.5 16.1 1.0
O B:HOH590 2.7 23.2 1.0
CD B:GLU360 3.3 16.8 1.0
CG B:ASP359 3.4 17.6 1.0
O B:HOH774 3.6 35.9 1.0
OD1 B:ASP359 3.7 15.3 1.0
Y A:YT31 3.7 19.1 1.0
OE2 B:GLU360 3.8 15.8 1.0
N B:GLU360 4.3 14.1 1.0
CB B:GLU360 4.5 15.9 1.0
CG B:GLU360 4.5 16.3 1.0
O A:HOH474 4.5 18.2 1.0
OE1 A:GLU360 4.6 21.1 1.0
N B:ASP359 4.7 14.7 1.0
CB B:ASP359 4.8 17.0 1.0
O A:HOH514 4.8 32.5 1.0
CB B:SER358 4.8 19.4 1.0
O A:HOH475 4.8 17.7 1.0
O B:HOH611 4.9 34.8 1.0
CA B:GLU360 5.0 15.0 1.0
CD A:GLU360 5.0 19.2 1.0

Reference:

S.M.Soisson, G.Parthasarathy, A.D.Adams, S.Sahoo, A.Sitlani, C.Sparrow, J.Cui, J.W.Becker. Identification of A Potent Synthetic Fxr Agonist with An Unexpected Mode of Binding and Activation. Proc.Natl.Acad.Sci.Usa V. 105 5337 2008.
ISSN: ISSN 0027-8424
PubMed: 18391212
DOI: 10.1073/PNAS.0710981105
Page generated: Wed Dec 16 02:40:51 2020

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