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Potassium in PDB 5fjc: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU

Protein crystallography data

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc 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) 41.134 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.398, 60.398, 152.950, 90.00, 90.00, 90.00
R / Rfree (%) 20.09 / 24.05

Other elements in 5fjc:

The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Barium (Ba) 21 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU (pdb code 5fjc). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU, PDB code: 5fjc:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5fjc

Go back to Potassium Binding Sites List in 5fjc
Potassium binding site 1 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K123

b:36.7
occ:1.00
O A:HOH2170 2.6 49.4 1.0
O4 A:U88 2.8 27.3 1.0
O6 A:G89 2.8 25.5 1.0
O A:HOH2012 2.8 42.3 1.0
O4 A:U5 2.9 33.4 1.0
O4 A:U4 3.1 37.0 1.0
O A:HOH2169 3.1 33.7 1.0
N6 A:A90 3.4 30.7 1.0
C4 A:U88 3.7 27.2 1.0
N6 A:A6 3.8 28.6 1.0
C4 A:U5 3.8 28.6 1.0
C6 A:G89 3.9 33.0 1.0
N3 A:U5 4.0 30.0 1.0
O A:HOH2005 4.0 47.7 1.0
C4 A:U4 4.1 37.0 1.0
C6 A:A90 4.3 30.2 1.0
N7 A:G89 4.4 29.8 1.0
N3 A:U88 4.5 27.9 1.0
C5 A:U88 4.5 27.3 1.0
C5 A:G89 4.5 29.4 1.0
N1 A:A90 4.6 29.1 1.0
C6 A:A6 4.6 30.5 1.0
N3 A:U4 4.7 37.0 1.0
O A:HOH2004 4.9 41.6 1.0
O A:HOH2166 4.9 51.3 1.0
N1 A:A6 4.9 34.0 1.0

Potassium binding site 2 out of 4 in 5fjc

Go back to Potassium Binding Sites List in 5fjc
Potassium binding site 2 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K124

b:49.6
occ:1.00
O A:HOH2030 2.5 50.8 1.0
O A:HOH2024 2.5 54.3 1.0
OP1 A:A62 2.6 61.6 1.0
O A:HOH2027 2.6 48.2 1.0
O A:HOH2114 2.7 54.2 1.0
OP2 A:G11 3.0 42.2 1.0
MG A:MG127 3.7 42.3 1.0
BA A:BA122 3.8 0.8 0.7
P A:A62 4.0 54.8 1.0
OP1 A:A10 4.1 57.3 1.0
P A:G11 4.4 42.5 1.0
OP2 A:A10 4.5 53.6 1.0
O5' A:A62 4.5 54.3 1.0
C5' A:A62 4.6 53.5 1.0
P A:A10 4.7 49.8 1.0
N7 A:G11 4.9 34.8 1.0
OP2 A:A62 4.9 41.5 1.0
O3' A:A61 4.9 53.1 1.0
O5' A:G11 5.0 39.0 1.0

Potassium binding site 3 out of 4 in 5fjc

Go back to Potassium Binding Sites List in 5fjc
Potassium binding site 3 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K125

b:67.8
occ:1.00
O A:HOH2005 2.3 47.7 1.0
O A:HOH2165 2.7 41.0 1.0
O A:HOH2010 2.8 41.7 1.0
O A:HOH2012 3.0 42.3 1.0
OP2 A:C3 4.2 44.7 1.0
O A:HOH2166 4.4 51.3 1.0
O A:HOH2168 4.4 53.5 1.0
OP2 A:G86 4.5 42.4 1.0
O A:HOH2170 4.5 49.4 1.0
C5 A:C3 4.8 35.5 1.0
O4 A:U5 4.8 33.4 1.0
C5 A:U4 4.9 34.2 1.0
O4 A:U4 4.9 37.0 1.0

Potassium binding site 4 out of 4 in 5fjc

Go back to Potassium Binding Sites List in 5fjc
Potassium binding site 4 out of 4 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant C-2BU


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 Kt-7 Variant C-2BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K126

b:80.3
occ:1.00
O A:HOH2043 3.2 51.4 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: Sun Dec 13 23:57:09 2020

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