Magnesium in PDB 1yvp: Ro Autoantigen Complexed with Rnas

The structure of Ro Autoantigen Complexed with Rnas, PDB code: 1yvp was solved by A.J.Stein, G.Fuchs, C.Fu, S.L.Wolin, K.M.Reinisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.300, 153.650, 80.560, 90.00, 92.80, 90.00
R / Rfree (%)	20.2 / 23.8

The structure of Ro Autoantigen Complexed with Rnas also contains other interesting chemical elements:

Iodine

(I)

8 atoms

The binding sites of Magnesium atom in the Ro Autoantigen Complexed with Rnas (pdb code 1yvp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ro Autoantigen Complexed with Rnas, PDB code: 1yvp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:32.7 occ:1.00 OXT A:ACT2001 1.8 30.5 1.0 O A:HOH2168 2.0 29.0 1.0 O A:HOH2167 2.0 22.2 1.0 OG1 A:THR445 2.2 28.4 1.0 OG A:SER380 2.2 31.5 1.0 OG A:SER378 2.2 26.4 1.0 C A:ACT2001 2.6 28.8 1.0 CB A:SER380 3.0 27.1 1.0 O A:ACT2001 3.0 28.0 1.0 CB A:SER378 3.3 26.2 1.0 CB A:THR445 3.5 29.2 1.0 N A:SER380 3.7 26.0 1.0 OH A:TYR47 3.8 31.0 1.0 CH3 A:ACT2001 3.9 29.7 1.0 CA A:SER380 3.9 28.4 1.0 CG2 A:THR445 4.0 31.3 1.0 OD1 A:ASP469 4.3 29.8 1.0 O A:GLU471 4.3 32.2 1.0 OD2 A:ASP469 4.5 27.2 1.0 C A:SER378 4.5 25.8 1.0 CA A:SER378 4.5 24.7 1.0 CA A:THR445 4.5 31.6 1.0 N A:ALA379 4.6 24.6 1.0 N A:THR445 4.6 31.8 1.0 N A:MET381 4.7 27.0 1.0 C A:SER380 4.7 27.7 1.0 OD2 A:ASP376 4.7 26.3 1.0 OD1 A:ASP376 4.7 28.8 1.0 CE1 A:TYR47 4.7 25.4 1.0 CZ A:TYR47 4.8 26.7 1.0 CG A:ASP469 4.8 30.9 1.0 CB A:GLU471 4.8 31.0 1.0 C A:ALA379 4.9 26.3 1.0 O A:SER378 4.9 26.3 1.0

Magnesium binding site 2 out of 2 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:30.4 occ:1.00 OXT B:ACT2002 1.8 33.7 1.0 O B:HOH2171 2.0 25.5 1.0 O B:HOH2170 2.0 27.8 1.0 OG B:SER380 2.1 23.4 1.0 OG B:SER378 2.1 29.7 1.0 OG1 B:THR445 2.2 31.2 1.0 C B:ACT2002 2.7 33.0 1.0 CB B:SER380 3.0 25.9 1.0 O B:ACT2002 3.1 33.5 1.0 CB B:SER378 3.2 28.5 1.0 CB B:THR445 3.5 31.8 1.0 N B:SER380 3.7 25.1 1.0 CA B:SER380 3.9 26.3 1.0 CG2 B:THR445 4.0 30.4 1.0 CH3 B:ACT2002 4.1 33.1 1.0 OH B:TYR47 4.1 24.4 1.0 OD1 B:ASP469 4.3 28.1 1.0 O B:GLU471 4.3 30.8 1.0 CA B:SER378 4.4 27.0 1.0 C B:SER378 4.4 27.9 1.0 OD1 B:ASP376 4.4 31.3 1.0 OD2 B:ASP469 4.5 29.3 1.0 OD2 B:ASP376 4.6 31.4 1.0 CA B:THR445 4.6 30.7 1.0 N B:ALA379 4.6 27.7 1.0 N B:MET381 4.6 26.5 1.0 C B:SER380 4.7 25.0 1.0 N B:THR445 4.7 32.2 1.0 O B:SER378 4.7 27.5 1.0 ND2 B:ASN473 4.8 29.0 1.0 CB B:GLU471 4.8 28.0 1.0 CG B:ASP469 4.9 29.2 1.0 C B:ALA379 4.9 27.1 1.0 CG B:ASP376 4.9 28.9 1.0 CE1 B:TYR47 5.0 27.3 1.0

A.J.Stein, G.Fuchs, C.Fu, S.L.Wolin, K.M.Reinisch. Structural Insights Into Rna Quality Control: the Ro Autoantigen Binds Misfolded Rnas Via Its Central Cavity Cell(Cambridge,Mass.) V. 121 529 2005.
ISSN: ISSN 0092-8674
PubMed: 15907467
DOI: 10.1016/J.CELL.2005.03.009