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Barium in PDB 5fk4: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu, PDB code: 5fk4 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.370 / 2.43
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.550, 57.550, 155.620, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.83

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu (pdb code 5fk4). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 17 binding sites of Barium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu, PDB code: 5fk4:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 17 in 5fk4

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Barium binding site 1 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1095

b:54.2
occ:0.72
O A:HOH2008 2.8 38.2 1.0
N7 A:G13 2.8 60.4 1.0
C8 A:G13 3.5 62.7 1.0
C5 A:G13 4.0 58.4 1.0
OP2 A:A61 4.4 52.4 1.0
O6 A:G13 4.6 59.8 1.0
C6 A:G13 4.7 57.7 1.0
N9 A:G13 4.8 69.8 1.0
OP2 A:G13 4.8 65.7 1.0
C2' A:C60 4.9 55.8 1.0

Barium binding site 2 out of 17 in 5fk4

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Barium binding site 2 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1096

b:56.7
occ:0.80
OP1 A:A62 2.7 68.3 1.0
O A:HOH2003 2.8 16.4 1.0
OP2 A:G11 2.8 44.7 1.0
O A:HOH2005 2.9 44.8 1.0
OP1 A:A10 3.1 68.2 1.0
O A:HOH2002 3.6 16.4 1.0
OP2 A:A10 3.6 52.1 1.0
P A:A10 3.8 51.7 1.0
P A:A62 3.8 49.6 1.0
OP2 A:A62 4.2 41.6 1.0
P A:G11 4.3 55.4 1.0
O A:HOH2022 4.3 17.0 1.0
O5' A:A62 4.3 51.3 1.0
O5' A:A10 4.6 54.1 1.0
N7 A:G11 4.6 41.8 1.0
C5' A:A62 4.8 49.6 1.0
C8 A:G11 4.9 45.5 1.0
O5' A:G11 5.0 43.5 1.0

Barium binding site 3 out of 17 in 5fk4

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Barium binding site 3 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1097

b:0.6
occ:0.84
N7 A:G56 2.9 96.1 1.0
O6 A:G56 3.0 96.8 1.0
N1 A:A45 3.6 57.6 1.0
C5 A:G56 3.6 93.8 1.0
C6 A:G56 3.6 92.9 1.0
C8 A:G56 4.0 95.4 1.0
N6 A:A45 4.0 46.5 1.0
OP2 A:G55 4.1 0.6 1.0
N7 A:G55 4.1 0.9 1.0
C6 A:A45 4.3 52.6 1.0
C5 A:G55 4.4 98.0 1.0
O6 A:G55 4.4 98.2 1.0
OP2 A:G56 4.4 0.6 1.0
C2 A:A45 4.5 52.8 1.0
C6 A:G55 4.5 95.7 1.0
C2 A:A46 4.5 88.1 1.0
N1 A:A46 4.7 86.4 1.0
C8 A:G55 4.7 0.7 1.0
C4 A:G56 4.9 90.1 1.0
N1 A:G56 5.0 87.3 1.0

Barium binding site 4 out of 17 in 5fk4

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Barium binding site 4 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1098

b:73.9
occ:0.61
O A:HOH2032 3.0 49.8 1.0
O6 A:G86 3.0 47.0 1.0
N7 A:G86 3.3 33.5 1.0
N7 A:A85 3.6 44.2 1.0
C6 A:G86 3.7 38.5 1.0
C5 A:G86 3.8 32.5 1.0
N6 A:A85 4.1 33.7 1.0
C5 A:A85 4.2 46.3 1.0
N6 A:A87 4.4 40.2 1.0
C8 A:A85 4.4 49.7 1.0
C6 A:A85 4.4 48.1 1.0
C8 A:G86 4.5 35.1 1.0
OP2 A:A85 4.6 60.4 1.0
OP2 A:A84 4.8 54.3 1.0
O4 A:U7 4.9 50.3 1.0

Barium binding site 5 out of 17 in 5fk4

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Barium binding site 5 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1099

b:51.4
occ:0.51
O A:HOH2027 2.6 31.9 1.0
O4 A:U80 2.7 44.6 1.0
O6 A:G79 2.7 34.6 1.0
O6 A:G71 3.0 33.4 1.0
N6 A:A70 3.1 33.1 1.0
C4 A:U80 3.6 42.1 1.0
C6 A:G79 3.7 42.4 1.0
N4 A:C72 3.8 32.6 1.0
N3 A:U80 3.9 43.8 1.0
C6 A:A70 4.0 44.0 1.0
C6 A:G71 4.1 37.9 1.0
O4 A:U81 4.5 30.3 1.0
C5 A:G79 4.6 42.4 1.0
N7 A:G71 4.6 48.1 1.0
C5 A:A70 4.6 39.2 1.0
N1 A:G79 4.7 43.2 1.0
N1 A:A70 4.7 45.7 1.0
C5 A:G71 4.7 43.7 1.0
N7 A:G79 4.8 46.1 1.0
N7 A:A70 4.8 38.7 1.0
C4 A:C72 4.8 37.7 1.0
OP1 A:G68 4.9 39.9 1.0
O A:HOH2028 4.9 39.9 1.0
C5 A:U80 4.9 41.8 1.0

Barium binding site 6 out of 17 in 5fk4

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Barium binding site 6 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1100

b:0.2
occ:1.00
N7 A:G50 2.9 0.5 1.0
O6 A:G50 3.1 0.3 1.0
C5 A:G50 3.4 0.2 1.0
C6 A:G50 3.5 0.0 1.0
C8 A:G50 4.0 0.0 1.0
N7 A:A49 4.2 92.0 1.0
OP2 A:A49 4.6 0.8 1.0
C4 A:G50 4.7 0.1 1.0
C5 A:A49 4.7 87.2 1.0
C8 A:A49 4.8 88.5 1.0
N1 A:G50 4.8 0.1 1.0
N6 A:A49 4.9 91.4 1.0
N9 A:G50 5.0 0.5 1.0

Barium binding site 7 out of 17 in 5fk4

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Barium binding site 7 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1101

b:73.9
occ:0.92
O6 A:G82 2.8 40.5 1.0
BA A:BA1110 2.9 0.6 0.8
O A:HOH2026 3.0 46.0 1.0
O A:HOH2031 3.1 29.9 1.0
O A:HOH2025 3.2 39.9 1.0
O4 A:U81 3.3 30.3 1.0
C6 A:G82 3.9 39.4 1.0
C4 A:U81 4.0 30.9 1.0
N4 A:C69 4.1 36.3 1.0
C5 A:U81 4.2 32.3 1.0
N7 A:G82 4.2 32.4 1.0
OP1 A:U67 4.3 47.3 1.0
OP2 A:G68 4.3 44.1 1.0
C5 A:G82 4.4 42.5 1.0
OP2 A:U67 4.4 59.9 1.0
N6 A:A83 4.5 47.2 1.0
P A:U67 4.8 36.6 1.0
N6 A:A70 5.0 33.1 1.0

Barium binding site 8 out of 17 in 5fk4

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Barium binding site 8 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1102

b:50.3
occ:1.00
O A:HOH2013 2.4 39.9 1.0
O6 A:G27 2.6 40.5 1.0
N7 A:G27 3.0 54.3 1.0
O6 A:G28 3.2 52.5 1.0
O A:HOH2016 3.2 28.7 1.0
C6 A:G27 3.3 42.5 1.0
C5 A:G27 3.5 47.9 1.0
N7 A:G28 3.5 41.6 1.0
C6 A:G28 3.8 45.4 1.0
C5 A:U26 3.8 45.4 1.0
C5 A:G28 3.9 39.6 1.0
C4 A:U26 4.1 43.2 1.0
C8 A:G27 4.2 64.1 1.0
O4 A:U26 4.2 42.7 1.0
C6 A:U26 4.4 50.5 1.0
OP2 A:U26 4.6 64.1 1.0
C8 A:G28 4.6 47.5 1.0
N1 A:G27 4.6 48.5 1.0
N4 A:C65 4.7 36.8 1.0
N4 A:C66 4.8 34.3 1.0
C4 A:G27 4.8 41.4 1.0
N3 A:U26 4.9 52.8 1.0
O6 A:G23 4.9 39.5 1.0

Barium binding site 9 out of 17 in 5fk4

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Barium binding site 9 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1103

b:0.1
occ:0.99
O A:HOH2015 2.9 28.7 1.0
O2' A:U64 3.0 34.5 1.0
O4 A:U67 3.0 34.9 1.0
O2 A:U64 3.3 38.1 1.0
C4 A:U67 3.8 34.5 1.0
O A:HOH2023 4.0 60.5 1.0
O A:HOH2014 4.0 21.0 1.0
C2 A:U64 4.0 31.6 1.0
OP2 A:C66 4.0 33.0 1.0
C5 A:U67 4.0 33.7 1.0
C2' A:U64 4.2 41.4 1.0
C1' A:U64 4.4 35.5 1.0
N1 A:U64 4.6 42.0 1.0
N4 A:C25 4.6 43.5 1.0
O6 A:G68 4.7 37.6 1.0
N3 A:U64 4.8 45.7 1.0
C5 A:C66 4.9 32.2 1.0
N7 A:A24 4.9 35.3 1.0
C2 A:A85 4.9 39.5 1.0
N6 A:A24 5.0 40.4 1.0

Barium binding site 10 out of 17 in 5fk4

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Barium binding site 10 out of 17 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uu


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 Kt-7 Variant 3BN Is Uu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1104

b:60.5
occ:0.72
O A:HOH2004 2.4 16.0 1.0
O A:HOH2006 2.4 44.0 1.0
O6 A:G11 2.6 52.9 1.0
OP1 A:U64 3.2 64.5 1.0
O A:HOH2002 3.5 16.4 1.0
OP2 A:U64 3.6 61.8 1.0
P A:U64 3.6 53.8 1.0
C6 A:G11 3.8 40.4 1.0
O5' A:U64 3.9 41.7 1.0
O2' A:C8 4.4 55.2 1.0
N6 A:A10 4.5 56.3 1.0
O A:SAM1094 4.5 54.4 1.0
N1 A:G11 4.6 40.8 1.0
N7 A:A10 4.7 40.3 1.0
C5' A:U64 4.8 37.0 1.0
C5 A:G11 4.8 39.4 1.0
N6 A:A12 4.8 41.9 1.0
OP2 A:A10 4.9 52.1 1.0

Reference:

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201
Page generated: Sat Dec 12 01:57:25 2020

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