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Barium in PDB 3iqp: Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form

Protein crystallography data

The structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form, PDB code: 3iqp 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) 19.91 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.702, 62.702, 159.260, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 27.1

Barium Binding Sites:

The binding sites of Barium atom in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form (pdb code 3iqp). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 10 binding sites of Barium where determined in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form, PDB code: 3iqp:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 10 in 3iqp

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Barium binding site 1 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba301

b:82.0
occ:1.00
 O6 A:G11 2.7 65.5 1.0
O A:HOH464 2.9 56.8 1.0
C6 A:G11 3.8 64.6 1.0
N6 A:A10 4.0 70.8 1.0
N1 A:G11 4.4 64.4 1.0
N6 A:A12 4.8 68.8 1.0
O2' A:C59 4.9 48.4 1.0
OP2 A:U64 5.0 47.0 1.0

Barium binding site 2 out of 10 in 3iqp

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Barium binding site 2 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba302

b:96.8
occ:1.00
 O A:HOH474 2.7 69.2 1.0
OP1 A:A62 2.8 45.0 1.0
OP2 A:A10 3.0 75.8 1.0
OP2 A:G11 3.4 69.6 1.0
P A:A62 4.3 45.0 1.0
P A:A10 4.4 75.1 1.0
O5' A:A62 4.7 44.2 1.0
N7 A:G11 4.7 64.3 1.0
O3' A:A9 4.8 75.3 1.0
P A:G11 4.9 71.6 1.0

Barium binding site 3 out of 10 in 3iqp

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Barium binding site 3 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba303

b:93.4
occ:1.00
 O A:HOH462 2.6 36.0 1.0
N7 A:G86 2.9 42.2 1.0
O6 A:G86 3.1 46.0 1.0
N7 A:A85 3.4 51.8 1.0
O A:HOH480 3.5 54.9 1.0
C5 A:G86 3.6 42.0 1.0
C6 A:G86 3.6 42.9 1.0
C8 A:G86 4.0 42.8 1.0
C5 A:A85 4.1 51.5 1.0
N6 A:A85 4.1 51.7 1.0
C8 A:A85 4.1 53.0 1.0
C6 A:A85 4.4 51.9 1.0
OP2 A:A85 4.6 55.7 1.0
N6 A:A87 4.7 41.3 1.0
C4 A:G86 4.9 42.8 1.0
N4 A:C8 4.9 45.9 1.0

Barium binding site 4 out of 10 in 3iqp

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Barium binding site 4 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba304

b:0.9
occ:1.00
 N7 A:G1 2.8 42.2 1.0
O6 A:G1 2.9 41.4 1.0
C5 A:G1 3.5 40.6 1.0
C6 A:G1 3.5 40.0 1.0
O A:HOH401 3.9 27.4 1.0
C8 A:G1 3.9 43.0 1.0
OP3 A:G1 4.5 63.7 1.0
O6 A:G2 4.7 42.0 1.0
C4 A:G1 4.8 42.3 1.0
N1 A:G1 4.9 39.2 1.0

Barium binding site 5 out of 10 in 3iqp

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Barium binding site 5 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba305

b:93.0
occ:1.00
 O4 A:U67 2.9 42.6 1.0
O A:HOH457 3.0 51.1 1.0
O2' A:U64 3.0 47.0 1.0
O2 A:U64 3.2 38.8 1.0
C2' A:U64 3.7 44.1 1.0
C4 A:U67 4.0 41.2 1.0
N4 A:C25 4.2 55.4 1.0
C2 A:U64 4.2 41.5 1.0
N7 A:A24 4.3 51.5 1.0
N6 A:A24 4.4 50.6 1.0
OP2 A:C66 4.5 33.5 1.0
C5 A:U67 4.5 41.8 1.0
C1' A:U64 4.6 43.6 1.0
O6 A:G68 4.7 65.5 1.0
C2 A:A85 4.7 53.3 1.0
N1 A:U64 4.9 42.6 1.0
O3' A:U64 4.9 41.9 1.0
OP2 A:A24 4.9 50.3 1.0

Barium binding site 6 out of 10 in 3iqp

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Barium binding site 6 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba306

b:84.8
occ:1.00
 O6 A:G27 2.8 58.9 1.0
N7 A:G27 3.3 63.1 1.0
O6 A:G28 3.3 61.5 1.0
C6 A:G27 3.5 59.6 1.0
C5 A:G27 3.7 61.2 1.0
O A:HOH469 3.7 62.5 1.0
N7 A:G28 4.0 59.3 1.0
C6 A:G28 4.1 58.9 1.0
C5 A:U26 4.3 62.8 1.0
C5 A:G28 4.3 58.6 1.0
N4 A:C65 4.4 39.4 1.0
C8 A:G27 4.4 64.4 1.0
OP2 A:U26 4.5 60.7 1.0
C4 A:U26 4.6 62.5 1.0
O4 A:U26 4.8 62.5 1.0
C6 A:U26 4.8 63.8 1.0
N1 A:G27 4.8 58.4 1.0
O6 A:G23 4.9 55.6 1.0

Barium binding site 7 out of 10 in 3iqp

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Barium binding site 7 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba307

b:75.9
occ:1.00
 O A:HOH486 2.2 40.8 1.0
O A:HOH431 2.9 38.4 1.0
O6 A:G18 2.9 67.7 1.0
O A:HOH420 3.0 28.0 1.0
C6 A:G18 4.1 68.5 1.0
N7 A:G18 4.7 70.4 1.0
C5 A:G18 4.8 69.2 1.0
O4 A:U17 4.9 69.1 1.0
OP2 A:U17 5.0 66.8 1.0
OP2 A:G16 5.0 62.9 1.0

Barium binding site 8 out of 10 in 3iqp

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Barium binding site 8 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba308

b:0.3
occ:1.00
 N1 A:G74 2.4 36.7 1.0
C6 A:G74 3.1 26.5 1.0
C2 A:G74 3.3 42.5 1.0
N2 A:G74 3.3 43.3 1.0
O6 A:G74 3.4 15.9 1.0
O A:HOH418 3.5 33.5 1.0
C5 A:G74 4.2 35.7 1.0
OP1 A:A76 4.3 49.1 1.0
N3 A:G74 4.5 43.2 1.0
C4 A:G74 4.8 45.2 1.0

Barium binding site 9 out of 10 in 3iqp

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Barium binding site 9 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba309

b:88.3
occ:1.00
 N7 A:G50 2.8 73.2 1.0
O6 A:G50 3.6 71.9 1.0
C5 A:G50 3.8 72.5 1.0
C8 A:G50 3.8 74.5 1.0
OP1 A:A52 3.8 86.4 1.0
O A:HOH409 3.9 38.3 1.0
C6 A:G50 4.0 72.2 1.0
N7 A:A49 4.4 73.0 1.0
C8 A:A49 4.8 73.8 1.0
C4 A:G50 4.9 73.4 1.0

Barium binding site 10 out of 10 in 3iqp

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Barium binding site 10 out of 10 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Sam-I Riboswitch From T. Tencongensis Variant A94G Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba310

b:0.2
occ:1.00
 O A:HOH439 3.5 41.2 1.0
N7 A:G32 4.2 52.7 1.0
C8 A:G32 4.8 51.5 1.0
OP2 A:G32 4.9 36.8 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: Wed Jul 10 15:13:41 2024

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