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Potassium in PDB 3iqn: Free-State Structural Transitions of the Sam-I Riboswitch

Protein crystallography data

The structure of Free-State Structural Transitions of the Sam-I Riboswitch, PDB code: 3iqn was solved by R.K.Montange, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.980, 61.980, 159.070, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 29.9

Other elements in 3iqn:

The structure of Free-State Structural Transitions of the Sam-I Riboswitch also contains other interesting chemical elements:

Barium (Ba) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Free-State Structural Transitions of the Sam-I Riboswitch (pdb code 3iqn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Free-State Structural Transitions of the Sam-I Riboswitch, PDB code: 3iqn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 1 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:74.7
occ:1.00
N7 A:G86 3.1 36.0 1.0
O6 A:G86 3.3 40.3 1.0
C5 A:G86 3.8 36.7 1.0
C6 A:G86 3.9 37.5 1.0
N7 A:A85 4.1 44.7 1.0
C8 A:G86 4.2 36.9 1.0
N6 A:A85 4.4 40.5 1.0
C5 A:A85 4.6 42.8 1.0
C6 A:A85 4.7 41.1 1.0
OP2 A:A85 4.8 54.5 1.0
N6 A:A87 4.8 37.1 1.0
C8 A:A85 4.9 45.4 1.0
OP2 A:A84 4.9 54.1 1.0

Potassium binding site 2 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 2 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:61.7
occ:1.00
O6 A:G18 2.7 55.8 1.0
C6 A:G18 3.8 53.1 1.0
N7 A:G18 4.5 55.2 1.0
C5 A:G18 4.6 53.8 1.0
O6 A:G19 4.6 59.3 1.0
OP2 A:U17 4.8 63.1 1.0
OP2 A:G16 4.9 68.4 1.0
N1 A:G18 4.9 51.0 1.0
O4 A:U17 5.0 50.6 1.0

Potassium binding site 3 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 3 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:71.2
occ:1.00
O4 A:U88 3.0 32.2 1.0
O6 A:G89 3.0 33.2 1.0
O4 A:U5 3.2 40.1 1.0
O4 A:U4 3.4 41.1 1.0
C4 A:U88 4.0 28.6 1.0
C4 A:U5 4.2 38.4 1.0
N6 A:A90 4.2 35.7 1.0
C6 A:G89 4.2 31.7 1.0
N3 A:U5 4.3 37.5 1.0
N6 A:A6 4.3 31.2 1.0
C4 A:U4 4.4 40.4 1.0
C5 A:U88 4.6 28.5 1.0
N3 A:U88 4.9 25.8 1.0

Potassium binding site 4 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 4 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:85.1
occ:1.00
OP2 A:A75 2.6 64.1 1.0
OP2 A:G74 2.6 68.5 1.0
O5' A:G74 3.0 68.2 1.0
C8 A:G74 3.2 59.8 1.0
C3' A:G74 3.3 62.6 1.0
P A:G74 3.4 68.8 1.0
N7 A:G74 3.8 60.1 1.0
P A:A75 3.8 62.5 1.0
C5' A:G74 3.8 65.4 1.0
O3' A:G74 3.9 62.8 1.0
C4' A:G74 3.9 63.0 1.0
N9 A:G74 4.0 59.9 1.0
O4' A:G74 4.2 61.4 1.0
C2' A:G74 4.2 62.1 1.0
C1' A:G74 4.4 60.8 1.0
OP1 A:G74 4.5 67.3 1.0
C5' A:A75 4.5 56.9 1.0
O3' A:G73 4.5 67.6 1.0
C3' A:G73 4.6 66.8 1.0
O5' A:A75 4.7 59.2 1.0
OP1 A:A75 4.8 62.8 1.0
C5 A:G74 4.8 60.4 1.0
C4 A:G74 5.0 60.0 1.0
C2' A:G73 5.0 65.8 1.0
OP2 A:A76 5.0 58.1 1.0
BA A:BA205 5.0 93.1 1.0

Potassium binding site 5 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 5 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:57.9
occ:1.00
O3' A:G27 2.3 59.1 1.0
O5' A:G28 2.8 56.5 1.0
P A:G28 2.8 57.8 1.0
OP1 A:G28 2.9 57.1 1.0
O2' A:G27 2.9 54.5 1.0
C3' A:G27 3.4 58.5 1.0
C2' A:G27 3.6 57.1 1.0
C4' A:G27 4.0 58.8 1.0
C5' A:G28 4.2 53.5 1.0
OP2 A:G28 4.3 57.1 1.0
C4' A:G28 4.8 51.8 1.0
C1' A:G27 4.9 57.0 1.0
O4' A:G27 4.9 57.6 1.0
C5' A:G27 5.0 59.6 1.0

Potassium binding site 6 out of 6 in 3iqn

Go back to Potassium Binding Sites List in 3iqn
Potassium binding site 6 out of 6 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Free-State Structural Transitions of the Sam-I Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K420

b:79.2
occ:1.00
C1' A:G15 3.2 67.3 1.0
O4' A:G15 3.7 68.6 1.0
N2 A:G13 3.9 77.5 1.0
N9 A:G15 3.9 66.4 1.0
O2' A:G15 4.2 65.5 1.0
C2' A:G15 4.3 67.0 1.0
C8 A:G15 4.5 66.2 1.0
C4 A:G15 4.6 65.6 1.0
N3 A:G13 4.7 77.5 1.0
C2 A:G13 4.8 77.9 1.0
C4' A:G15 4.9 68.8 1.0
N3 A:G15 4.9 64.4 1.0

Reference:

C.D.Stoddard, R.K.Montange, S.P.Hennelly, R.P.Rambo, K.Y.Sanbonmatsu, R.T.Batey. Free State Conformational Sampling of the Sam-I Riboswitch Aptamer Domain. Structure V. 18 787 2010.
ISSN: ISSN 0969-2126
PubMed: 20637415
DOI: 10.1016/J.STR.2010.04.006
Page generated: Sun Dec 13 23:19:54 2020

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