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Barium in PDB 4b5r: Sam-I Riboswitch Bearing the H. Marismortui K-T-7

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r was solved by P.Daldrop, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.90 / 2.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.720, 58.720, 154.710, 90.00, 90.00, 90.00
R / Rfree (%) 21.913 / 25.195

Other elements in 4b5r:

The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 also contains other interesting chemical elements:

Potassium (K) 7 atoms

Barium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7 (pdb code 4b5r). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 12 in 4b5r

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Barium binding site 1 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1096

b:48.4
occ:1.00
O6 A:G27 3.0 34.9 1.0
O6 A:G28 3.1 33.5 1.0
N7 A:G27 3.3 40.1 1.0
C6 A:G27 3.8 37.0 1.0
C6 A:G28 3.8 32.5 1.0
N7 A:G28 3.8 35.8 1.0
C5 A:G27 3.9 39.0 1.0
C5 A:U26 3.9 33.7 1.0
C5 A:G28 4.1 33.8 1.0
C4 A:U26 4.3 33.7 1.0
O4 A:U26 4.4 34.4 1.0
C8 A:G27 4.5 39.7 1.0
C6 A:U26 4.5 34.3 1.0
N4 A:C65 4.7 31.2 1.0
OP2 A:U26 4.8 33.2 1.0
O6 A:G23 4.9 24.4 1.0
C8 A:G28 4.9 35.6 1.0
N1 A:G28 4.9 31.0 1.0

Barium binding site 2 out of 12 in 4b5r

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Barium binding site 2 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1099

b:85.1
occ:1.00
O2' A:U64 3.0 31.2 1.0
O2 A:U64 3.1 31.4 1.0
O4 A:U67 3.4 22.3 1.0
C2 A:U64 4.1 31.0 1.0
C2' A:U64 4.2 28.8 1.0
OP2 A:C66 4.3 27.1 1.0
C1' A:U64 4.4 29.6 1.0
N7 A:A24 4.4 24.3 1.0
C4 A:U67 4.4 23.5 1.0
N4 A:C25 4.5 29.7 1.0
C2 A:A85 4.5 31.8 1.0
O3' A:U64 4.6 25.1 1.0
N1 A:U64 4.7 29.8 1.0
C5 A:U67 4.9 23.9 1.0

Barium binding site 3 out of 12 in 4b5r

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Barium binding site 3 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1101

b:82.4
occ:1.00
O6 A:G11 2.7 31.9 1.0
OP1 A:U64 3.4 37.1 1.0
C6 A:G11 3.9 29.8 1.0
P A:U64 4.1 37.0 1.0
OP2 A:U64 4.1 34.6 1.0
O A:SAM1095 4.2 32.0 1.0
C5' A:U64 4.3 33.5 1.0
O2' A:C8 4.3 33.5 1.0
O5' A:U64 4.6 34.4 1.0
N6 A:A10 4.6 32.5 1.0
N7 A:A10 4.8 33.6 1.0
N1 A:G11 4.8 28.4 1.0
N6 A:A12 4.9 30.6 1.0
C5 A:G11 4.9 29.4 1.0

Barium binding site 4 out of 12 in 4b5r

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Barium binding site 4 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1104

b:63.9
occ:1.00
O6 A:G16 2.9 38.5 1.0
N7 A:G16 3.0 38.8 1.0
O6 A:G15 3.4 38.8 1.0
C6 A:G16 3.6 39.0 1.0
C5 A:G16 3.6 39.2 1.0
N7 A:G15 3.8 37.3 1.0
C6 A:G15 3.8 37.9 1.0
C5 A:G15 4.0 37.9 1.0
C8 A:G16 4.2 38.5 1.0
N4 A:C40 4.7 29.2 1.0
C8 A:G15 4.7 38.8 1.0
N7 A:G17 4.8 35.0 1.0
O6 A:G17 4.8 35.0 1.0
N1 A:G15 4.9 37.6 1.0
OP2 A:G15 4.9 58.7 1.0
C4 A:G16 4.9 38.9 1.0
N1 A:G16 4.9 40.0 1.0

Barium binding site 5 out of 12 in 4b5r

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Barium binding site 5 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1105

b:35.4
occ:1.00
C4' A:G42 4.5 34.1 1.0
O3' A:G42 4.8 34.8 1.0
C5' A:G42 4.8 34.8 1.0

Barium binding site 6 out of 12 in 4b5r

Go back to Barium Binding Sites List in 4b5r
Barium binding site 6 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1106

b:0.3
occ:1.00
BA A:BA1112 4.7 0.5 1.0

Barium binding site 7 out of 12 in 4b5r

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Barium binding site 7 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1107

b:49.7
occ:1.00
O6 A:G18 3.0 37.0 1.0
C6 A:G18 4.0 35.7 1.0
O6 A:G19 4.2 40.4 1.0
N7 A:G18 4.4 35.7 1.0
C5 A:G18 4.6 36.0 1.0
OP2 A:G17 4.7 36.0 1.0
OP2 A:G16 4.9 36.7 1.0
C5' A:G35 5.0 35.0 1.0
N7 A:G17 5.0 35.0 1.0

Barium binding site 8 out of 12 in 4b5r

Go back to Barium Binding Sites List in 4b5r
Barium binding site 8 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1108

b:98.4
occ:1.00
O4 A:U88 3.4 35.3 1.0
C4 A:U88 4.3 33.6 1.0
O4 A:U4 4.3 43.0 1.0
O4 A:U5 4.4 41.6 1.0
C5 A:U88 4.5 33.5 1.0
O6 A:G89 4.7 45.4 1.0
N6 A:A6 4.9 38.9 1.0
N7 A:A87 5.0 28.0 1.0

Barium binding site 9 out of 12 in 4b5r

Go back to Barium Binding Sites List in 4b5r
Barium binding site 9 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1109

b:75.6
occ:1.00
OP2 A:C31 4.6 24.1 1.0
N7 A:G32 4.7 27.5 1.0
OP1 A:G32 4.8 24.6 1.0

Barium binding site 10 out of 12 in 4b5r

Go back to Barium Binding Sites List in 4b5r
Barium binding site 10 out of 12 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1110

b:0.3
occ:1.00
N7 A:G1 3.2 62.9 1.0
C8 A:G1 3.8 65.6 1.0
OP2 A:G1 3.8 72.9 1.0
C5 A:G1 4.2 60.5 1.0
OP3 A:G1 4.3 83.4 1.0
O6 A:G1 4.6 59.0 1.0
P A:G1 4.6 82.7 1.0
C6 A:G1 4.8 58.8 1.0
O5' A:G1 4.8 75.8 1.0
N7 A:G2 5.0 38.3 1.0

Reference:

P.Daldrop, D.M.J.Lilley. The Plasticity of A Structural Motif in Rna: Structural Polymorphism of A Kink Turn As A Function of Its Environment. Rna V. 19 357 2013.
ISSN: ISSN 1355-8382
PubMed: 23325110
DOI: 10.1261/RNA.036657.112
Page generated: Sat Dec 12 01:56:03 2020

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