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Barium in PDB 3iqr: Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam

Protein crystallography data

The structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam, PDB code: 3iqr 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) 19.93 / 2.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.804, 61.804, 157.568, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 29.3

Barium Binding Sites:

The binding sites of Barium atom in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam (pdb code 3iqr). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam, PDB code: 3iqr:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 3iqr

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Barium binding site 1 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba201

b:95.9
occ:1.00
N7 A:G50 2.9 61.3 1.0
O6 A:G50 3.1 62.0 1.0
O A:HOH440 3.5 37.5 1.0
C5 A:G50 3.5 60.9 1.0
C6 A:G50 3.6 61.5 1.0
C8 A:G50 4.0 62.1 1.0
OP1 A:A52 4.1 86.1 1.0
OP2 A:A52 4.2 85.8 1.0
N7 A:A49 4.6 51.1 1.0
P A:A52 4.6 86.4 1.0
C4 A:G50 4.8 61.2 1.0
N1 A:G50 4.9 61.6 1.0
N9 A:G50 5.0 62.7 1.0

Barium binding site 2 out of 9 in 3iqr

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Barium binding site 2 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba202

b:0.4
occ:1.00
O6 A:G18 2.7 65.9 1.0
C6 A:G18 3.8 62.4 1.0
C5 A:G18 4.5 62.3 1.0
N7 A:G18 4.5 61.8 1.0
OP2 A:U17 4.7 81.4 1.0
O4 A:U17 4.8 72.3 1.0
N1 A:G18 4.8 60.6 1.0
O6 A:G19 4.8 60.5 1.0
C5 A:U17 4.9 74.0 1.0
OP2 A:G16 5.0 77.8 1.0

Barium binding site 3 out of 9 in 3iqr

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Barium binding site 3 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba203

b:83.9
occ:1.00
O6 A:G74 2.7 50.4 1.0
N7 A:G74 3.1 50.0 1.0
C6 A:G74 3.4 47.9 1.0
C5 A:G74 3.5 47.9 1.0
O A:HOH405 4.2 29.2 1.0
C8 A:G74 4.3 50.2 1.0
OP1 A:A76 4.3 50.7 1.0
N1 A:G74 4.6 46.4 1.0
C4 A:G74 4.8 48.0 1.0
OP2 A:A76 4.8 50.5 1.0
N7 A:G73 4.9 59.9 1.0

Barium binding site 4 out of 9 in 3iqr

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Barium binding site 4 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba204

b:57.7
occ:1.00
O2' A:U64 2.9 59.9 1.0
O4 A:U67 3.0 43.5 1.0
O2 A:U64 3.1 51.3 1.0
C2' A:U64 3.7 54.8 1.0
C4 A:U67 4.0 40.0 1.0
C2 A:U64 4.1 52.0 1.0
C5 A:U67 4.3 39.4 1.0
C1' A:U64 4.3 54.4 1.0
OP2 A:C66 4.3 43.9 1.0
N4 A:C25 4.6 41.6 1.0
O6 A:G68 4.7 55.7 1.0
N1 A:U64 4.7 53.2 1.0
O A:HOH419 4.7 30.5 1.0

Barium binding site 5 out of 9 in 3iqr

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Barium binding site 5 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba205

b:0.8
occ:1.00
N7 A:G32 3.9 60.1 1.0
C8 A:G32 4.6 59.5 1.0
OP2 A:G32 4.6 48.9 1.0
C5 A:G32 4.7 59.3 1.0
O6 A:G32 4.7 59.4 1.0
OP2 A:C31 4.7 51.6 1.0

Barium binding site 6 out of 9 in 3iqr

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Barium binding site 6 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba206

b:0.3
occ:1.00
OP2 A:A10 2.9 59.8 1.0
OP2 A:U64 3.2 46.0 1.0
O3' A:U63 3.4 47.6 1.0
O3' A:A9 3.6 64.4 1.0
P A:A10 3.8 60.2 1.0
P A:U64 3.8 45.2 1.0
OP1 A:A62 3.9 42.9 1.0
N7 A:G11 4.0 46.7 1.0
C4' A:U63 4.1 46.6 1.0
O5' A:A10 4.2 58.6 1.0
C3' A:U63 4.3 47.2 1.0
O6 A:G11 4.3 47.5 1.0
OP1 A:U64 4.4 46.4 1.0
N7 A:A10 4.6 48.9 1.0
C5' A:U63 4.7 47.2 1.0
OP2 A:G11 4.7 49.1 1.0
C8 A:A10 4.8 48.4 1.0
C5 A:G11 4.9 47.8 1.0
C3' A:A9 4.9 66.9 1.0
C6 A:G11 5.0 48.0 1.0
C8 A:G11 5.0 45.8 1.0

Barium binding site 7 out of 9 in 3iqr

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Barium binding site 7 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba207

b:0.9
occ:1.00
N7 A:G86 3.1 51.7 1.0
O6 A:G86 3.3 50.5 1.0
C5 A:G86 3.8 50.1 1.0
C6 A:G86 3.9 50.9 1.0
N7 A:A85 4.0 56.9 1.0
C8 A:G86 4.2 50.7 1.0
N6 A:A85 4.4 57.7 1.0
C5 A:A85 4.5 58.1 1.0
C8 A:A85 4.7 56.7 1.0
C6 A:A85 4.7 57.8 1.0
N6 A:A87 4.7 46.2 1.0
OP2 A:A85 4.9 59.8 1.0

Barium binding site 8 out of 9 in 3iqr

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Barium binding site 8 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba208

b:0.2
occ:1.00
N1 A:A46 3.1 48.0 1.0
N7 A:G55 3.3 59.8 1.0
C2 A:A46 3.4 47.7 1.0
O6 A:G55 3.8 60.9 1.0
C5 A:G55 4.0 60.3 1.0
C6 A:G55 4.2 60.1 1.0
C8 A:G55 4.2 60.7 1.0
N1 A:A45 4.3 46.3 1.0
C6 A:A46 4.4 46.5 1.0
N6 A:A45 4.6 42.6 1.0
N3 A:A46 4.6 47.7 1.0
N6 A:A46 4.8 48.1 1.0
OP2 A:G55 4.8 75.1 1.0
C6 A:A45 4.9 46.1 1.0
O6 A:G56 5.0 51.5 1.0

Barium binding site 9 out of 9 in 3iqr

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Barium binding site 9 out of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba209

b:0.5
occ:1.00
N7 A:G1 2.9 53.7 1.0
O6 A:G1 3.5 57.9 1.0
C5 A:G1 3.8 54.5 1.0
C8 A:G1 4.0 54.7 1.0
C6 A:G1 4.0 55.2 1.0
O A:HOH403 4.2 24.2 1.0
OP3 A:G1 4.5 64.2 1.0
O A:HOH402 4.9 23.4 1.0
O6 A:G2 5.0 45.3 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 01:55:48 2020

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