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Barium 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:

Potassium (K) 6 atoms

Barium Binding Sites:

The binding sites of Barium 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 Barium atom.
In total 5 binding sites of Barium where determined in the Free-State Structural Transitions of the Sam-I Riboswitch, PDB code: 3iqn:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in 3iqn

Go back to Barium Binding Sites List in 3iqn
Barium binding site 1 out of 5 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba201

b:0.9
occ:1.00
N7 A:G50 3.3 69.1 1.0
O6 A:G50 3.6 69.6 1.0
C5 A:G50 4.0 68.7 1.0
C6 A:G50 4.2 68.6 1.0
C8 A:G50 4.3 68.7 1.0
OP2 A:A52 4.3 76.1 1.0
O A:HOH403 4.6 22.8 1.0
N7 A:A49 4.6 42.0 1.0

Barium binding site 2 out of 5 in 3iqn

Go back to Barium Binding Sites List in 3iqn
Barium binding site 2 out of 5 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba203

b:0.1
occ:1.00
OP2 A:A10 2.5 51.8 1.0
OP2 A:U64 3.0 41.9 1.0
P A:A10 3.7 51.9 1.0
P A:U64 3.8 40.2 1.0
OP1 A:A62 4.0 38.4 1.0
OP1 A:U64 4.0 39.7 1.0
N7 A:G11 4.0 39.4 1.0
O5' A:A10 4.1 50.4 1.0
O3' A:U63 4.1 38.2 1.0
O6 A:G11 4.4 40.1 1.0
C4' A:U63 4.4 37.0 1.0
N7 A:A10 4.4 43.2 1.0
C3' A:U63 4.4 37.0 1.0
OP1 A:A10 4.5 51.4 1.0
C8 A:A10 4.5 43.3 1.0
OP2 A:G11 4.6 42.6 1.0
O A:HOH431 4.8 13.3 1.0
C5' A:U63 4.8 37.7 1.0
C5 A:G11 4.9 40.1 1.0
O3' A:A9 5.0 56.5 1.0
C8 A:G11 5.0 38.8 1.0

Barium binding site 3 out of 5 in 3iqn

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


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba204

b:0.2
occ:1.00
OP2 A:G32 4.7 45.9 1.0
OP2 A:A33 4.8 48.0 1.0

Barium binding site 4 out of 5 in 3iqn

Go back to Barium Binding Sites List in 3iqn
Barium binding site 4 out of 5 in the Free-State Structural Transitions of the Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba205

b:93.1
occ:1.00
O6 A:G74 2.8 63.4 1.0
N7 A:G74 3.3 60.1 1.0
C6 A:G74 3.4 61.7 1.0
C5 A:G74 3.6 60.4 1.0
O A:HOH404 3.7 46.0 1.0
OP1 A:A76 4.2 58.0 1.0
C8 A:G74 4.4 59.8 1.0
N1 A:G74 4.6 61.2 1.0
C4 A:G74 4.8 60.0 1.0
N7 A:G73 4.8 59.6 1.0
K A:K504 5.0 85.1 1.0

Barium binding site 5 out of 5 in 3iqn

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


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba 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:Ba206

b:0.2
occ:1.00
N4 A:C72 3.0 72.7 1.0
O6 A:G79 3.0 42.7 1.0
O4 A:U80 3.2 40.5 1.0
N6 A:A70 3.5 70.6 1.0
C4 A:U80 4.1 40.0 1.0
C6 A:G79 4.2 41.0 1.0
C4 A:C72 4.2 72.5 1.0
C6 A:A70 4.3 71.3 1.0
N3 A:U80 4.3 39.8 1.0
N3 A:C72 4.7 73.4 1.0
C5 A:A70 4.8 71.5 1.0
N7 A:A70 4.9 71.5 1.0
O6 A:G71 5.0 65.2 1.0
O4 A:U81 5.0 53.4 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: Sat Dec 12 01:55:47 2020

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