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Iodine 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:

Magnesium (Mg) 2 atoms

Iodine Binding Sites:

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 1yvp

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

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

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

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

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

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

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

Go back to Iodine Binding Sites List in 1yvp
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

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: Sun Jan 24 17:23:03 2021

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