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Barium in PDB 2hol: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions

Protein crystallography data

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions, PDB code: 2hol was solved by T.E.Edwards, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 65.500, 65.500, 101.700, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 24.4

Other elements in 2hol:

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 4 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions (pdb code 2hol). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions, PDB code: 2hol:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 2hol

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Barium binding site 1 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba106

b:78.5
occ:1.00
O1B A:TPP105 1.9 55.6 1.0
O2A A:TPP105 2.2 58.8 1.0
O A:HOH102 2.6 42.6 1.0
O A:HOH104 3.2 25.8 1.0
O A:HOH98 3.2 33.1 1.0
PB A:TPP105 3.4 49.4 1.0
PA A:TPP105 3.5 55.4 1.0
O1A A:TPP105 3.8 59.0 1.0
N4 A:C77 3.9 39.9 1.0
N7 A:A75 4.0 32.0 1.0
O3A A:TPP105 4.1 57.2 1.0
O2B A:TPP105 4.2 51.6 1.0
O3B A:TPP105 4.3 54.8 1.0
N6 A:A75 4.6 36.7 1.0
C5 A:A75 4.7 33.5 1.0
C8 A:A75 4.7 31.8 1.0
N7 A:G76 4.8 39.0 1.0
O7 A:TPP105 4.8 56.6 1.0
O6 A:G76 4.9 41.9 1.0
OP2 A:A75 4.9 34.5 1.0
C6 A:A75 4.9 33.6 1.0
O A:HOH96 4.9 17.6 1.0

Barium binding site 2 out of 9 in 2hol

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Barium binding site 2 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba107

b:67.8
occ:1.00
O6 A:G60 2.2 26.2 1.0
O A:HOH96 2.4 17.6 1.0
O6 A:G78 2.5 30.4 1.0
O A:HOH97 2.5 30.1 1.0
O2B A:TPP105 2.6 51.6 1.0
O A:HOH99 2.6 18.9 1.0
C6 A:G60 3.2 23.1 1.0
C6 A:G78 3.4 26.9 1.0
O3A A:TPP105 3.5 57.2 1.0
PB A:TPP105 3.6 49.4 1.0
N1 A:G60 3.7 22.8 1.0
O4 A:U59 3.7 29.2 1.0
N1 A:G78 3.7 23.2 1.0
N1 A:A61 4.2 21.4 1.0
N3 A:C77 4.3 39.1 1.0
O A:HOH102 4.4 42.6 1.0
C2 A:A61 4.4 20.5 1.0
C4 A:U59 4.5 29.1 1.0
N4 A:C77 4.5 39.9 1.0
C5 A:G60 4.5 20.9 1.0
O1B A:TPP105 4.5 55.6 1.0
O1A A:TPP105 4.6 59.0 1.0
PA A:TPP105 4.7 55.4 1.0
C5 A:G78 4.7 30.2 1.0
O3B A:TPP105 4.8 54.8 1.0
C4 A:C77 4.8 39.3 1.0
N6 A:A80 4.9 37.4 1.0

Barium binding site 3 out of 9 in 2hol

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Barium binding site 3 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba108

b:70.7
occ:1.00
OP1 A:C63 2.2 22.8 1.0
OP2 A:U64 2.4 20.9 1.0
O A:HOH101 2.5 34.4 1.0
P A:C63 3.6 21.5 1.0
P A:U64 3.7 15.4 1.0
OP1 A:U64 4.2 15.5 1.0
O3' A:U62 4.2 21.9 1.0
OP2 A:C63 4.2 20.1 1.0
O3' A:C63 4.4 17.8 1.0
C3' A:C63 4.6 20.3 1.0
O5' A:C63 4.6 22.1 1.0
O5' A:U64 4.8 16.2 1.0
C5' A:C63 4.9 23.9 1.0

Barium binding site 4 out of 9 in 2hol

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Barium binding site 4 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba109

b:1.0
occ:1.00
N7 A:A41 2.5 24.8 1.0
C8 A:A41 3.4 25.1 1.0
C5 A:A41 3.6 22.6 1.0
N6 A:A41 3.9 26.5 1.0
C6 A:A41 4.2 22.8 1.0
O2' A:G40 4.3 18.0 1.0
O6 A:G42 4.3 25.3 1.0
N9 A:A41 4.6 23.4 1.0
C4 A:A41 4.8 24.5 1.0

Barium binding site 5 out of 9 in 2hol

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Barium binding site 5 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba110

b:93.0
occ:1.00
N7 A:G40 2.5 27.1 1.0
C8 A:G40 3.5 26.2 1.0
C5 A:G40 3.5 27.3 1.0
O6 A:G40 3.6 32.9 1.0
O A:HOH93 3.8 29.1 1.0
C6 A:G40 3.9 29.1 1.0
OP2 A:G40 4.2 18.4 1.0
OP2 A:U39 4.5 16.9 1.0
N9 A:G40 4.7 23.6 1.0
C4 A:G40 4.7 26.6 1.0
C5 A:U39 4.7 18.3 1.0
OP2 A:G42 5.0 21.5 1.0

Barium binding site 6 out of 9 in 2hol

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Barium binding site 6 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba111

b:0.0
occ:1.00
OP2 A:A80 3.2 60.4 1.0
N7 A:G81 3.9 43.5 1.0
OP1 A:A80 4.1 59.8 1.0
P A:A80 4.2 59.7 1.0
N7 A:G82 4.3 36.5 1.0
O6 A:G83 4.3 37.9 1.0
OP2 A:G81 4.6 50.6 1.0
C8 A:G81 4.7 44.2 1.0
O6 A:G81 4.7 42.0 1.0
C5 A:G81 4.8 43.9 1.0
O6 A:G82 4.8 37.2 1.0
C6 A:G83 4.9 37.4 1.0

Barium binding site 7 out of 9 in 2hol

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Barium binding site 7 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba112

b:0.0
occ:1.00
N7 A:G36 2.7 33.5 1.0
O A:HOH95 3.0 12.5 1.0
C8 A:G36 3.7 31.8 1.0
O6 A:G36 3.7 36.9 1.0
C5 A:G36 3.7 31.9 1.0
OP2 A:A35 3.9 69.6 1.0
C6 A:G36 4.1 32.7 1.0
N7 A:A35 4.1 40.0 1.0
OP2 A:A34 4.3 77.0 1.0
C8 A:A35 4.5 40.7 1.0
OP2 A:G36 4.6 43.3 1.0
N9 A:G36 4.9 31.0 1.0
C4 A:G36 4.9 31.8 1.0
C5 A:A35 4.9 39.9 1.0

Barium binding site 8 out of 9 in 2hol

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Barium binding site 8 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba113

b:0.0
occ:1.00
N7 A:G66 3.7 40.9 1.0
O6 A:G66 4.0 43.0 1.0
N6 A:A67 4.3 41.1 1.0
C5 A:G66 4.5 42.0 1.0
C6 A:G66 4.6 42.8 1.0
C8 A:G66 4.7 39.8 1.0
N7 A:A67 4.8 43.7 1.0

Barium binding site 9 out of 9 in 2hol

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Barium binding site 9 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba114

b:85.4
occ:1.00
O6 A:G40 2.9 32.9 1.0
OP2 A:A43 3.0 24.4 1.0
C6 A:G40 3.8 29.1 1.0
N1 A:G40 3.8 27.3 1.0
P A:A43 4.2 21.2 1.0
OP1 A:A43 4.5 23.8 1.0
O4 A:U39 4.9 19.5 1.0
O5' A:A43 4.9 25.4 1.0

Reference:

T.E.Edwards, A.R.Ferre-D'amare. Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive Rna-Small Molecule Recognition Structure V. 14 1459 2006.
ISSN: ISSN 0969-2126
PubMed: 16962976
DOI: 10.1016/J.STR.2006.07.008
Page generated: Wed Jul 10 15:03:14 2024

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