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Potassium 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:

Barium (Ba) 12 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1097

b:48.8
occ:1.00
OP2 A:G11 2.7 35.9 1.0
OP1 A:A62 2.7 36.8 1.0
OP2 A:A10 3.5 39.3 1.0
P A:G11 4.1 35.8 1.0
P A:A62 4.2 37.6 1.0
O5' A:A62 4.5 36.1 1.0
C5' A:A62 4.6 34.4 1.0
O5' A:G11 4.6 34.6 1.0
P A:A10 4.7 37.3 1.0
OP1 A:G11 4.7 37.2 1.0
N7 A:G11 4.9 28.9 1.0
O5' A:A10 4.9 35.8 1.0
C8 A:G11 5.0 28.8 1.0
O3' A:A61 5.0 32.4 1.0

Potassium binding site 2 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1098

b:48.1
occ:1.00
O6 A:G50 2.9 87.7 1.0
C6 A:G50 3.7 84.0 1.0
N1 A:G50 4.0 80.8 1.0
OP1 A:A52 4.1 63.0 1.0
C5 A:G50 5.0 82.7 1.0

Potassium binding site 3 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1100

b:38.9
occ:1.00
O6 A:G82 3.0 27.2 1.0
O4 A:U81 3.6 24.5 1.0
OP1 A:U67 3.9 26.0 1.0
C6 A:G82 4.0 26.0 1.0
C4 A:U81 4.2 25.6 1.0
N6 A:A83 4.3 28.6 1.0
N4 A:C69 4.3 24.8 1.0
N7 A:G82 4.3 25.4 1.0
C5 A:G82 4.6 25.4 1.0
C5 A:U81 4.6 26.0 1.0
OP2 A:G68 4.7 27.6 1.0
P A:U67 4.9 25.6 1.0

Potassium binding site 4 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1102

b:37.0
occ:1.00
O6 A:G79 2.7 33.1 1.0
O4 A:U80 3.2 33.8 1.0
O6 A:G71 3.2 32.6 1.0
N6 A:A70 3.5 25.6 1.0
C6 A:G79 3.8 33.3 1.0
N4 A:C72 4.1 25.2 1.0
C4 A:U80 4.1 33.6 1.0
N3 A:U80 4.2 33.4 1.0
C6 A:G71 4.4 31.5 1.0
C6 A:A70 4.5 26.3 1.0
N7 A:G79 4.5 32.2 1.0
C5 A:G79 4.5 31.8 1.0
N7 A:A70 4.8 26.6 1.0
N1 A:G79 4.9 33.9 1.0
OP1 A:G68 4.9 28.6 1.0
C5 A:A70 4.9 26.8 1.0
N7 A:G71 5.0 31.1 1.0

Potassium binding site 5 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1103

b:26.3
occ:1.00
O6 A:G86 3.4 30.2 1.0
N7 A:G86 3.5 28.8 1.0
N7 A:A85 3.5 29.5 1.0
C6 A:G86 4.1 28.0 1.0
C5 A:G86 4.1 28.1 1.0
C8 A:A85 4.2 29.6 1.0
OP2 A:A85 4.3 30.0 1.0
C5 A:A85 4.5 29.2 1.0
N6 A:A85 4.6 30.2 1.0
C8 A:G86 4.6 27.8 1.0
N6 A:A87 4.6 28.1 1.0
OP2 A:A84 4.9 29.6 1.0
C6 A:A85 4.9 30.5 1.0

Potassium binding site 6 out of 7 in 4b5r

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Potassium binding site 6 out of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1113

b:42.2
occ:1.00
N7 A:G56 3.3 72.4 1.0
O6 A:G56 3.5 69.0 1.0
N1 A:A45 3.7 38.9 1.0
C5 A:G56 4.1 71.2 1.0
N6 A:A45 4.1 38.1 1.0
C6 A:G56 4.2 68.2 1.0
C8 A:G56 4.4 71.9 1.0
C6 A:A45 4.4 38.4 1.0
OP2 A:G56 4.4 70.8 1.0
C2 A:A45 4.7 38.9 1.0
OP2 A:G55 4.8 56.9 1.0
N4 A:C44 4.9 32.5 1.0
N7 A:G55 4.9 70.5 1.0

Potassium binding site 7 out of 7 in 4b5r

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1114

b:37.0
occ:1.00
N7 A:G13 3.0 44.2 1.0
C8 A:G13 3.6 45.9 1.0
OP2 A:A61 3.9 25.7 1.0
C5 A:G13 4.2 45.5 1.0
C2' A:C60 4.4 25.1 1.0
O2 A:C60 4.6 23.8 1.0
O6 A:G13 4.7 44.6 1.0
C2 A:C60 4.9 24.5 1.0
C6 A:G13 4.9 45.2 1.0
O2' A:C60 4.9 26.2 1.0
N9 A:G13 4.9 47.5 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: Sun Dec 13 23:26:40 2020

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