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Yttrium in PDB 1st0: Structure of Dcps Bound to M7GPPPG

Protein crystallography data

The structure of Structure of Dcps Bound to M7GPPPG, PDB code: 1st0 was solved by M.Gu, C.Fabrega, S.W.Liu, H.Liu, M.Kiledjian, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.446, 94.783, 178.328, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.1

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Structure of Dcps Bound to M7GPPPG (pdb code 1st0). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the Structure of Dcps Bound to M7GPPPG, PDB code: 1st0:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 1st0

Go back to Yttrium Binding Sites List in 1st0
Yttrium binding site 1 out of 3 in the Structure of Dcps Bound to M7GPPPG


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of Dcps Bound to M7GPPPG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y701

b:55.3
occ:1.00
OE2 A:GLU92 2.4 36.8 1.0
O A:HOH955 2.4 39.7 1.0
OE1 A:GLU92 2.6 42.1 1.0
CD A:GLU92 2.8 40.2 1.0
CG A:GLU92 4.3 39.0 1.0
O A:HOH1044 4.5 47.4 1.0
O A:HOH785 4.7 37.5 1.0
O B:HOH900 4.8 50.0 1.0
CB A:GLU92 4.9 35.1 1.0

Yttrium binding site 2 out of 3 in 1st0

Go back to Yttrium Binding Sites List in 1st0
Yttrium binding site 2 out of 3 in the Structure of Dcps Bound to M7GPPPG


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of Dcps Bound to M7GPPPG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y702

b:94.0
occ:1.00
OD2 A:ASP74 2.4 42.0 1.0
O A:HOH943 2.6 45.2 1.0
CG A:ASP74 3.5 33.3 1.0
OD2 A:ASP76 3.6 41.6 1.0
OD1 A:ASP74 4.3 35.1 1.0
CB A:ASP74 4.4 28.2 1.0
CG A:ASP76 4.6 37.4 1.0
CB A:ASP76 4.9 30.6 1.0

Yttrium binding site 3 out of 3 in 1st0

Go back to Yttrium Binding Sites List in 1st0
Yttrium binding site 3 out of 3 in the Structure of Dcps Bound to M7GPPPG


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Structure of Dcps Bound to M7GPPPG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y703

b:66.5
occ:1.00
O A:HOH919 2.5 44.1 1.0
OD1 A:ASP76 2.6 46.9 1.0
O A:HOH932 2.6 51.2 1.0
O A:HOH935 2.8 52.6 1.0
OD2 A:ASP76 2.9 41.6 1.0
CG A:ASP76 3.1 37.4 1.0
O A:HOH912 4.1 43.4 1.0
O A:HOH936 4.5 42.9 1.0
O A:ASP74 4.5 25.8 1.0
CB A:ASP76 4.6 30.6 1.0

Reference:

M.Gu, C.Fabrega, S.W.Liu, H.Liu, M.Kiledjian, C.D.Lima. Insights Into the Structure, Mechanism, and Regulation of Scavenger Mrna Decapping Activity Mol.Cell V. 14 67 2004.
ISSN: ISSN 1097-2765
PubMed: 15068804
DOI: 10.1016/S1097-2765(04)00180-7
Page generated: Wed Dec 16 02:40:49 2020

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