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Potassium in PDB 4aob: Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine

Protein crystallography data

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob was solved by K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50 / 2.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.300, 61.300, 157.538, 90.00, 90.00, 90.00
R / Rfree (%) 18.906 / 23.943

Other elements in 4aob:

The structure of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine also contains other interesting chemical elements:

Barium (Ba) 15 atoms
Sodium (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine (pdb code 4aob). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine, PDB code: 4aob:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4aob

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Potassium binding site 1 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1108

b:57.4
occ:1.00
 OP1 A:G1 2.5 0.6 1.0
P A:G1 3.7 83.0 1.0
OP2 A:G1 3.9 70.2 1.0
O5' A:G1 4.5 76.4 1.0
OP3 A:G1 4.7 82.1 1.0
BA A:BA1101 5.0 0.5 1.0

Potassium binding site 2 out of 8 in 4aob

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Potassium binding site 2 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1109

b:77.1
occ:1.00
 O4 A:U80 3.0 69.5 1.0
O6 A:G79 3.2 62.0 1.0
O6 A:G71 3.3 74.4 1.0
N6 A:A70 3.5 61.4 1.0
N6 A:A72 3.7 80.4 1.0
C4 A:U80 4.0 70.6 1.0
C6 A:A70 4.3 71.6 1.0
O A:HOH2007 4.3 31.2 1.0
N3 A:U80 4.4 68.8 1.0
C6 A:G71 4.4 74.0 1.0
C6 A:G79 4.4 64.3 1.0
C6 A:A72 4.6 84.5 1.0
N1 A:A72 4.7 96.0 1.0
N7 A:G71 4.8 74.2 1.0
C5 A:A70 4.9 75.1 1.0
N1 A:A70 5.0 67.7 1.0
C5 A:G71 5.0 71.8 1.0

Potassium binding site 3 out of 8 in 4aob

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Potassium binding site 3 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1110

b:78.8
occ:1.00
 N7 A:G42 3.3 86.6 1.0
OP2 A:C41 3.4 94.6 1.0
O6 A:G42 3.5 77.8 1.0
C5 A:G42 4.1 87.4 1.0
C6 A:G42 4.2 87.7 1.0
O6 A:G43 4.2 78.2 1.0
C8 A:G42 4.4 99.3 1.0
C5 A:C41 4.5 0.7 1.0
P A:C41 4.6 94.9 1.0
O5' A:C41 4.9 92.6 1.0
OP1 A:C41 5.0 0.7 1.0
N7 A:G43 5.0 91.5 1.0

Potassium binding site 4 out of 8 in 4aob

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Potassium binding site 4 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1111

b:0.2
occ:1.00
 NA A:NA1138 3.3 63.2 1.0
OP1 A:C3 3.4 64.6 1.0
OP1 A:A85 4.0 81.4 1.0
OP2 A:C3 4.0 56.9 1.0
P A:C3 4.2 67.8 1.0
OP2 A:A85 4.6 69.8 1.0
OP2 A:U4 4.6 59.5 1.0
P A:A85 4.7 76.9 1.0

Potassium binding site 5 out of 8 in 4aob

Go back to Potassium Binding Sites List in 4aob
Potassium binding site 5 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1112

b:89.0
occ:1.00
 OP2 A:A10 2.8 87.2 1.0
OP2 A:U64 3.0 65.5 1.0
N7 A:G11 3.6 91.9 1.0
P A:A10 3.6 69.9 1.0
OP1 A:A10 3.7 60.5 1.0
BA A:BA1107 3.7 0.8 1.0
OP1 A:U64 3.9 56.3 1.0
N7 A:A10 3.9 82.2 1.0
P A:U64 3.9 65.1 1.0
K A:K1115 4.0 73.0 1.0
O5' A:A10 4.0 76.7 1.0
O6 A:G11 4.0 78.2 1.0
C8 A:A10 4.0 82.9 1.0
OP1 A:A62 4.3 81.7 1.0
C5 A:G11 4.4 86.6 1.0
C8 A:G11 4.5 87.1 1.0
C6 A:G11 4.6 78.9 1.0
OP2 A:G11 4.6 66.5 1.0
C5 A:A10 5.0 79.5 1.0

Potassium binding site 6 out of 8 in 4aob

Go back to Potassium Binding Sites List in 4aob
Potassium binding site 6 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1115

b:73.0
occ:1.00
 OP2 A:G11 2.5 66.5 1.0
O A:HOH2005 2.8 51.9 1.0
OP1 A:A62 3.0 81.7 1.0
P A:G11 3.8 77.0 1.0
K A:K1112 4.0 89.0 1.0
O5' A:G11 4.3 72.3 1.0
P A:A62 4.5 76.8 1.0
OP1 A:G11 4.5 81.0 1.0
O5' A:A10 4.5 76.7 1.0
N7 A:G11 4.5 91.9 1.0
C8 A:G11 4.5 87.1 1.0
C5' A:A62 4.6 72.7 1.0
OP1 A:A10 4.7 60.5 1.0
O5' A:A62 5.0 75.7 1.0
O3' A:A61 5.0 68.6 1.0

Potassium binding site 7 out of 8 in 4aob

Go back to Potassium Binding Sites List in 4aob
Potassium binding site 7 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


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 Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1131

b:82.4
occ:1.00
 O4 A:U88 3.2 67.4 1.0
O4 A:U5 4.0 58.5 1.0
O4 A:U4 4.2 66.5 1.0
C4 A:U88 4.2 60.7 1.0
O6 A:G89 4.3 61.3 1.0
C5 A:U88 4.8 54.0 1.0
N6 A:A6 4.9 60.4 1.0

Potassium binding site 8 out of 8 in 4aob

Go back to Potassium Binding Sites List in 4aob
Potassium binding site 8 out of 8 in the Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Sam-I Riboswitch Containing the T. Solenopsae Kt-23 in Complex with S-Adenosyl Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1136

b:92.2
occ:1.00
 OP2 A:U57 4.5 88.5 1.0
OP1 A:G56 4.7 83.7 1.0
O6 A:G58 4.8 61.9 1.0
N7 A:G58 5.0 62.9 1.0

Reference:

K.T.Schroeder, P.Daldrop, S.A.Mcphee, D.M.J.Lilley. Structure and Folding of A Rare, Natural Kink Turn in Rna with An A*A Pair at the 2B*2N Position. Rna V. 18 1257 2012.
ISSN: ISSN 1355-8382
PubMed: 22539525
DOI: 10.1261/RNA.032409.112
Page generated: Mon Aug 12 10:02:22 2024

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