Yttrium in PDB 1dde: Structure of the Dnag Catalytic Core

The structure of Structure of the Dnag Catalytic Core, PDB code: 1dde was solved by J.L.Keck, D.D.Roche, A.S.Lynch, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.020, 55.890, 139.490, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.3

The binding sites of Yttrium atom in the Structure of the Dnag Catalytic Core (pdb code 1dde). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the Structure of the Dnag Catalytic Core, PDB code: 1dde:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in the Structure of the Dnag Catalytic Core


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Structure of the Dnag Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Y1 b:21.6 occ:1.00 OD2 A:ASP331 2.3 15.1 1.0 OE2 A:GLU405 2.5 23.6 1.0 OE1 A:GLU405 2.5 25.9 1.0 O A:HOH528 2.6 23.5 1.0 O A:HOH445 2.7 22.6 1.0 O A:HOH535 2.8 36.1 1.0 O A:HOH457 2.9 34.5 1.0 CD A:GLU405 2.9 25.7 1.0 CG A:ASP331 3.3 19.9 1.0 CB A:ASP331 3.6 18.9 1.0 OG1 A:THR406 4.2 25.4 1.0 CG A:GLU405 4.4 24.9 1.0 OD1 A:ASP331 4.4 18.6 1.0 O A:HOH582 4.5 50.3 1.0 O A:HOH613 4.5 43.8 1.0 N A:GLU405 4.6 17.8 1.0 N A:THR406 4.7 20.8 1.0 CB A:THR406 4.9 24.1 1.0 O A:HOH619 5.0 39.2 1.0

Yttrium binding site 2 out of 4 in the Structure of the Dnag Catalytic Core


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Structure of the Dnag Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Y2 b:22.0 occ:0.33 Y A:Y13 1.9 18.2 0.3 Y A:Y14 2.5 27.5 0.4 OE1 A:GLU265 2.6 26.8 1.0 OD2 A:ASP309 3.0 31.6 1.0 O A:HOH596 3.2 33.2 1.0 CD A:GLU265 3.5 27.1 1.0 O A:HOH559 4.0 59.0 1.0 OE2 A:GLU265 4.0 22.3 1.0 CG A:ASP309 4.1 29.5 1.0 OD2 A:ASP311 4.2 35.7 1.0 CB A:ASP309 4.4 21.4 1.0 O A:HOH604 4.4 25.8 1.0 CB A:GLU265 4.5 23.9 1.0 CG A:GLU265 4.6 24.3 1.0 OD1 A:ASP311 4.8 26.6 1.0 CG A:ASP311 4.9 33.6 1.0

Yttrium binding site 3 out of 4 in the Structure of the Dnag Catalytic Core


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Structure of the Dnag Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Y3 b:18.2 occ:0.33 Y A:Y12 1.9 22.0 0.3 OE1 A:GLU265 2.4 26.8 1.0 O A:HOH596 2.8 33.2 1.0 CD A:GLU265 3.5 27.1 1.0 OE2 A:GLU265 3.9 22.3 1.0 Y A:Y14 4.2 27.5 0.4 OD2 A:ASP311 4.4 35.7 1.0 OD2 A:ASP309 4.4 31.6 1.0 O A:HOH699 4.4 45.5 1.0 OD1 A:ASP311 4.5 26.6 1.0 CB A:ALA313 4.7 29.2 1.0 CG A:GLU265 4.7 24.3 1.0 CB A:GLU265 4.9 23.9 1.0 CG A:ASP311 4.9 33.6 1.0 O A:HOH559 5.0 59.0 1.0

Yttrium binding site 4 out of 4 in the Structure of the Dnag Catalytic Core


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Structure of the Dnag Catalytic Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Y4 b:27.5 occ:0.40 OD2 A:ASP309 2.4 31.6 1.0 Y A:Y12 2.5 22.0 0.3 CB A:ASP309 3.0 21.4 1.0 O A:HOH585 3.0 56.8 1.0 O A:HOH559 3.0 59.0 1.0 CG A:ASP309 3.0 29.5 1.0 O A:HOH596 4.0 33.2 1.0 OD2 A:ASP311 4.0 35.7 1.0 O A:HOH604 4.1 25.8 1.0 OD1 A:ASP309 4.1 27.3 1.0 Y A:Y13 4.2 18.2 0.3 OE1 A:GLU265 4.2 26.8 1.0 CB A:ASP345 4.4 21.4 1.0 CA A:ASP309 4.5 28.3 1.0 O A:HOH643 4.5 44.1 1.0 CG A:ASP311 4.6 33.6 1.0 CD A:GLU265 4.6 27.1 1.0 OD1 A:ASP311 4.7 26.6 1.0 OE2 A:GLU265 4.7 22.3 1.0 O A:GLU344 4.8 18.4 1.0 OD2 A:ASP345 4.9 30.5 1.0

J.L.Keck, D.D.Roche, A.S.Lynch, J.M.Berger. Structure of the Rna Polymerase Domain of E. Coli Primase. Science V. 287 2482 2000.
ISSN: ISSN 0036-8075
PubMed: 10741967
DOI: 10.1126/SCIENCE.287.5462.2482