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Magnesium in PDB 1yvp: Ro Autoantigen Complexed with Rnas

Protein crystallography data

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

Other elements in 1yvp:

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

Iodine (I) 8 atoms

Magnesium Binding Sites:

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 1yvp

Go back to Magnesium Binding Sites List in 1yvp
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 1yvp

Go back to Magnesium Binding Sites List in 1yvp
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

Reference:

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
Page generated: Tue Aug 13 19:55:19 2024

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