Iodine 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:

Magnesium

(Mg)

2 atoms

The binding sites of Iodine atom in the Ro Autoantigen Complexed with Rnas (pdb code 1yvp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Ro Autoantigen Complexed with Rnas, PDB code: 1yvp:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ C:I3 b:70.8 occ:1.00 I5 C:IU3 0.0 70.8 1.0 C5 C:IU3 2.1 54.9 1.0 C6 C:IU3 3.0 53.7 1.0 C4 C:IU3 3.1 53.3 1.0 O4 C:IU3 3.3 49.9 1.0 C5 C:C2 3.6 39.9 1.0 C4 C:C2 3.7 39.3 1.0 C6 C:C2 3.7 39.8 1.0 O C:HOH140 3.8 48.0 1.0 N1 C:C2 3.9 41.5 1.0 N3 C:C2 3.9 40.3 1.0 CD A:ARG146 3.9 28.9 1.0 NH2 A:ARG146 4.0 22.0 1.0 C2 C:C2 4.1 41.4 1.0 OP2 C:IU3 4.2 39.8 1.0 N4 C:C2 4.2 40.6 1.0 N1 C:IU3 4.3 50.2 1.0 N3 C:IU3 4.3 50.8 1.0 NE A:ARG146 4.4 28.2 1.0 CZ A:ARG146 4.4 27.5 1.0 C2' C:C2 4.5 43.2 1.0 C3' C:C2 4.5 43.0 1.0 C1' C:C2 4.8 42.4 1.0 O2 C:C2 4.8 44.4 1.0 C2 C:IU3 4.9 50.3 1.0

Iodine binding site 2 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ D:I1 b:94.7 occ:1.00 I5 D:IU1 0.0 94.7 1.0 C5 D:IU1 2.1 74.4 1.0 C6 D:IU1 3.0 69.7 1.0 C4 D:IU1 3.1 73.4 1.0 O4 D:IU1 3.3 73.1 1.0 CG A:LYS204 3.6 45.1 1.0 CE A:LYS204 3.7 50.6 1.0 CB A:SER203 4.0 37.6 1.0 I5 D:IU2 4.1 72.2 1.0 O4 D:IU2 4.3 53.4 1.0 CD A:LYS204 4.3 47.8 1.0 N3 D:IU1 4.3 68.6 1.0 N1 D:IU1 4.3 62.8 1.0 O5' D:IU1 4.5 57.3 1.0 NZ A:LYS200 4.6 41.3 1.0 OG A:SER203 4.6 41.9 1.0 CG A:LYS200 4.6 37.5 1.0 C4 D:IU2 4.8 54.0 1.0 CA A:LYS200 4.8 34.4 1.0 C5 D:IU2 4.8 55.2 1.0 OE2 A:GLU208 4.8 58.6 1.0 CB A:LYS204 4.9 42.5 1.0 C2 D:IU1 4.9 64.7 1.0 NZ A:LYS204 5.0 51.6 1.0

Iodine binding site 3 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ D:I2 b:72.2 occ:1.00 I5 D:IU2 0.0 72.2 1.0 C5 D:IU2 2.1 55.2 1.0 C6 D:IU2 3.0 52.4 1.0 C4 D:IU2 3.1 54.0 1.0 O4 D:IU2 3.3 53.4 1.0 C5 D:IU1 4.0 74.4 1.0 C6 D:IU1 4.1 69.7 1.0 OP2 D:IU2 4.1 47.1 1.0 I5 D:IU1 4.1 94.7 1.0 N1 D:IU2 4.3 49.4 1.0 N3 D:IU2 4.3 49.1 1.0 O5' D:IU1 4.4 57.3 1.0 C4 D:IU1 4.6 73.4 1.0 C3' D:IU1 4.7 50.4 1.0 N1 D:IU1 4.7 62.8 1.0 C2 D:IU2 4.9 49.5 1.0 O5' D:IU2 5.0 42.7 1.0

Iodine binding site 4 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ D:I6 b:76.0 occ:1.00 I5 D:IU6 0.0 76.0 1.0 C5 D:IU6 2.1 58.0 1.0 C6 D:IU6 3.0 56.0 1.0 C4 D:IU6 3.1 55.7 1.0 O4 D:IU6 3.3 50.4 1.0 C5 D:C5 3.8 36.7 1.0 OP2 D:IU6 3.8 49.5 1.0 C6 D:C5 3.9 35.8 1.0 N3 D:IU6 4.4 52.3 1.0 N1 D:IU6 4.4 53.8 1.0 C4 D:C5 4.5 37.2 1.0 C3' D:C5 4.5 44.6 1.0 N1 D:C5 4.6 37.3 1.0 O5' D:C5 4.6 50.4 1.0 OP2 D:C5 4.7 50.6 1.0 O5' D:IU6 4.7 49.8 1.0 P D:IU6 4.9 50.9 1.0 C2' D:C5 4.9 42.6 1.0 C2 D:IU6 4.9 51.9 1.0

Iodine binding site 5 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ E:I3 b:72.3 occ:1.00 I5 E:IU3 0.0 72.3 1.0 C5 E:IU3 2.1 60.4 1.0 C6 E:IU3 3.0 58.9 1.0 C4 E:IU3 3.1 60.3 1.0 O4 E:IU3 3.3 59.2 1.0 C5 E:C2 3.6 37.7 1.0 C6 E:C2 3.7 39.1 1.0 C4 E:C2 3.8 37.5 1.0 O B:HOH2078 3.8 42.8 1.0 O E:HOH291 3.9 42.8 1.0 NH2 B:ARG146 4.0 31.3 1.0 CD B:ARG146 4.0 30.3 1.0 N1 E:C2 4.0 40.8 1.0 N3 E:C2 4.1 38.2 1.0 C2 E:C2 4.2 39.4 1.0 OP2 E:IU3 4.3 46.9 1.0 N1 E:IU3 4.3 55.8 1.0 N3 E:IU3 4.3 58.8 1.0 N4 E:C2 4.4 37.8 1.0 NE B:ARG146 4.4 30.3 1.0 CZ B:ARG146 4.4 31.8 1.0 C3' E:C2 4.5 47.4 1.0 C2' E:C2 4.6 45.9 1.0 O5' E:C2 4.8 47.2 1.0 C1' E:C2 4.9 43.2 1.0 C2 E:IU3 4.9 57.8 1.0

Iodine binding site 6 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ F:I1 b:85.9 occ:1.00 I5 F:IU1 0.0 85.9 1.0 C5 F:IU1 2.1 68.8 1.0 C6 F:IU1 3.0 65.9 1.0 NZ B:LYS204 3.1 61.5 1.0 C4 F:IU1 3.1 68.2 1.0 O4 F:IU1 3.3 66.8 1.0 CE B:LYS204 3.7 62.8 1.0 CG B:LYS204 3.7 61.5 1.0 O4 F:IU2 4.0 55.9 1.0 I5 F:IU2 4.1 73.5 1.0 CG B:LYS200 4.1 43.2 1.0 CB B:SER203 4.2 51.4 1.0 CD B:LYS204 4.3 62.1 1.0 N1 F:IU1 4.3 60.8 1.0 N3 F:IU1 4.3 64.4 1.0 NZ B:LYS200 4.4 45.8 1.0 CA B:LYS200 4.5 37.8 1.0 C4 F:IU2 4.5 59.4 1.0 C5 F:IU2 4.6 59.6 1.0 O5' F:IU1 4.6 56.1 1.0 OG B:SER203 4.7 55.1 1.0 OE2 B:GLU208 4.8 82.3 1.0 OE1 B:GLU208 4.8 82.4 1.0 CB B:LYS200 4.9 40.3 1.0 C2 F:IU1 4.9 62.5 1.0 CB B:LYS204 4.9 60.1 1.0 CE B:LYS200 5.0 46.0 1.0

Iodine binding site 7 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ F:I2 b:73.5 occ:1.00 I5 F:IU2 0.0 73.5 1.0 C5 F:IU2 2.1 59.6 1.0 C6 F:IU2 3.0 59.1 1.0 C4 F:IU2 3.1 59.4 1.0 O F:HOH313 3.2 50.3 1.0 O4 F:IU2 3.3 55.9 1.0 OP2 F:IU2 3.9 49.7 1.0 I5 F:IU1 4.1 85.9 1.0 C5 F:IU1 4.1 68.8 1.0 C6 F:IU1 4.1 65.9 1.0 N1 F:IU2 4.3 56.8 1.0 N3 F:IU2 4.3 57.1 1.0 C3' F:IU1 4.6 53.5 1.0 O5' F:IU1 4.6 56.1 1.0 NZ B:LYS204 4.7 61.5 1.0 N1 F:IU1 4.8 60.8 1.0 C4 F:IU1 4.8 68.2 1.0 O5' F:IU2 4.8 49.9 1.0 C2 F:IU2 4.9 57.6 1.0 P F:IU2 4.9 50.8 1.0

Iodine binding site 8 out of 8 in the Ro Autoantigen Complexed with Rnas


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Ro Autoantigen Complexed with Rnas within 5.0Å range: probe atom residue distance (Å) B Occ F:I6 b:83.4 occ:1.00 I5 F:IU6 0.0 83.4 1.0 C5 F:IU6 2.1 68.3 1.0 C6 F:IU6 3.0 66.1 1.0 C4 F:IU6 3.1 65.8 1.0 O4 F:IU6 3.3 64.2 1.0 OP2 F:IU6 3.7 51.3 1.0 C5 F:C5 3.8 36.0 1.0 C6 F:C5 3.8 37.5 1.0 N3 F:IU6 4.3 62.5 1.0 N1 F:IU6 4.3 61.4 1.0 C3' F:C5 4.4 46.4 1.0 C4 F:C5 4.4 35.7 1.0 N1 F:C5 4.5 37.8 1.0 O5' F:C5 4.6 49.9 1.0 OP2 F:C5 4.7 53.0 1.0 O5' F:IU6 4.7 52.9 1.0 P F:IU6 4.7 51.7 1.0 C2' F:C5 4.9 43.5 1.0 C2 F:IU6 4.9 61.6 1.0 N3 F:C5 5.0 33.0 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