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Osmium in PDB 2cky: Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand

Protein crystallography data

The structure of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand, PDB code: 2cky was solved by S.Thore, M.Leibundgut, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.850, 98.670, 54.550, 90.00, 104.80, 90.00
R / Rfree (%) 18.3 / 25

Other elements in 2cky:

The structure of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Osmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Osmium atom in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand (pdb code 2cky). This binding sites where shown within 5.0 Angstroms radius around Osmium atom.
In total 12 binding sites of Osmium where determined in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand, PDB code: 2cky:
Jump to Osmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Osmium binding site 1 out of 12 in 2cky

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Osmium binding site 1 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 1 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Os1083

b:0.3
occ:0.50
N7 A:G10 3.8 31.6 1.0
O6 A:G10 4.0 32.0 1.0
O6 A:G9 4.6 31.8 1.0
C5 A:G10 4.6 30.3 1.0
C6 A:G10 4.7 31.3 1.0
N7 A:G9 4.7 32.8 1.0
C8 A:G10 4.8 30.9 1.0
C6 A:G9 4.9 30.9 1.0
C5 A:G9 5.0 31.3 1.0

Osmium binding site 2 out of 12 in 2cky

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Osmium binding site 2 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 2 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Os1085

b:0.7
occ:1.00
N7 A:G24 4.4 30.6 1.0
O6 A:G24 4.5 28.5 1.0
O6 A:G25 4.6 25.3 1.0
N6 A:A23 4.7 38.7 1.0
OP1 A:A32 4.8 37.9 1.0
N7 A:A23 5.0 40.5 1.0

Osmium binding site 3 out of 12 in 2cky

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Osmium binding site 3 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 3 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Os1086

b:0.9
occ:1.00
O6 A:G54 4.0 43.4 1.0
O6 A:G55 4.5 48.8 1.0
N7 A:G54 4.6 46.0 1.0
O6 A:G53 4.8 49.7 1.0
N7 A:G53 4.8 52.9 1.0
C6 A:G54 4.9 44.0 1.0

Osmium binding site 4 out of 12 in 2cky

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Osmium binding site 4 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 4 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Os1087

b:0.2
occ:1.00
O6 A:G28 4.3 35.5 1.0
N7 A:G28 4.4 33.4 1.0
C6 A:G28 5.0 34.3 1.0

Osmium binding site 5 out of 12 in 2cky

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Osmium binding site 5 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 5 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Os1088

b:0.9
occ:0.50
N7 A:G75 4.4 59.3 1.0
O4 A:U76 4.7 53.1 1.0
O6 A:G75 4.9 60.7 1.0
OP1 A:G1 5.0 69.3 1.0

Osmium binding site 6 out of 12 in 2cky

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Osmium binding site 6 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 6 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Os1081

b:0.7
occ:1.00
O6 B:G55 3.6 48.6 1.0
O6 B:G54 3.7 50.6 1.0
N7 B:G54 4.3 53.0 1.0
C6 B:G55 4.6 47.2 1.0
O6 B:G53 4.6 52.3 1.0
C6 B:G54 4.6 51.1 1.0
C5 B:G54 4.9 52.3 1.0

Osmium binding site 7 out of 12 in 2cky

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Osmium binding site 7 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 7 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Os1085

b:0.1
occ:0.50
O6 B:G2 4.0 55.6 1.0
N7 B:G2 4.1 51.2 1.0
P B:G1 4.2 67.7 1.0
OP2 B:G1 4.2 65.8 1.0
OS B:OS1086 4.7 0.6 1.0
C6 B:G2 4.8 54.5 1.0
C5 B:G2 4.9 52.0 1.0
OP1 B:G1 4.9 66.9 1.0
N7 B:G1 4.9 57.0 1.0

Osmium binding site 8 out of 12 in 2cky

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Osmium binding site 8 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 8 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Os1086

b:0.6
occ:1.00
N7 B:G1 3.9 57.0 1.0
C8 B:G1 4.6 55.7 1.0
OS B:OS1085 4.7 0.1 0.5
O6 B:G1 4.8 61.5 1.0
OP1 B:G1 4.8 66.9 1.0
C5 B:G1 4.9 56.5 1.0

Osmium binding site 9 out of 12 in 2cky

Go back to Osmium Binding Sites List in 2cky
Osmium binding site 9 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 9 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Os1087

b:0.5
occ:0.50
N7 B:G10 3.9 33.5 1.0
O6 B:G10 4.1 33.6 1.0
C5 B:G10 4.7 32.2 1.0
C6 B:G10 4.8 32.5 1.0
C8 B:G10 4.9 33.6 1.0

Osmium binding site 10 out of 12 in 2cky

Go back to Osmium Binding Sites List in 2cky
Osmium binding site 10 out of 12 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Osmium with other atoms in the Os binding site number 10 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Os1088

b:0.5
occ:1.00
N7 B:G28 3.9 39.4 1.0
O6 B:G28 4.4 41.5 1.0
C5 B:G28 4.8 40.1 1.0
C8 B:G28 4.8 39.4 1.0
C6 B:G28 4.9 40.9 1.0
OP1 B:G30 5.0 31.6 1.0

Reference:

S.Thore, M.Leibundgut, N.Ban. Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand. Science V. 312 1208 2006.
ISSN: ISSN 0036-8075
PubMed: 16675665
DOI: 10.1126/SCIENCE.1128451
Page generated: Wed Dec 16 02:01:16 2020

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