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Barium in PDB 2ydh: Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam

Protein crystallography data

The structure of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam, PDB code: 2ydh was solved by K.T.Schroeder, P.Daldrop, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.62 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.899, 61.899, 157.628, 90.00, 90.00, 90.00
R / Rfree (%) 26.892 / 32.145

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam (pdb code 2ydh). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 5 binding sites of Barium where determined in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam, PDB code: 2ydh:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in 2ydh

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Barium binding site 1 out of 5 in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1095

b:0.7
occ:1.00
O6 A:G27 2.8 1.0 1.0
N7 A:G27 3.3 0.6 1.0
O6 A:G28 3.6 96.2 1.0
C6 A:G27 3.6 0.1 1.0
C5 A:G27 3.8 0.8 1.0
C5 A:U26 3.9 0.6 1.0
N7 A:G28 4.0 97.8 1.0
O4 A:U26 4.1 0.5 1.0
OP2 A:U26 4.1 0.0 1.0
C4 A:U26 4.1 0.8 1.0
C6 A:G28 4.2 96.9 1.0
C5 A:G28 4.4 97.4 1.0
C8 A:G27 4.5 0.2 1.0
C6 A:U26 4.6 1.0 1.0
O6 A:G23 4.7 0.6 1.0
C6 A:G23 4.9 0.2 1.0
N1 A:G27 4.9 0.1 1.0
N4 A:C66 5.0 89.9 1.0
C8 A:G28 5.0 98.8 1.0

Barium binding site 2 out of 5 in 2ydh

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Barium binding site 2 out of 5 in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1096

b:1.0
occ:1.00
O2' A:U64 2.9 74.4 1.0
O2 A:U64 3.4 74.4 1.0
O4 A:U67 3.4 99.6 1.0
C2' A:U64 4.0 74.5 1.0
OP2 A:C66 4.1 84.2 1.0
O3' A:U64 4.1 72.3 1.0
C1' A:U64 4.2 73.4 1.0
C2 A:U64 4.3 72.0 1.0
C4 A:U67 4.3 97.1 1.0
C5 A:C66 4.5 89.3 1.0
N4 A:C25 4.6 0.4 1.0
C5 A:U67 4.6 96.7 1.0
N1 A:U64 4.7 71.6 1.0
C3' A:U64 4.7 73.4 1.0
N7 A:A24 4.8 92.5 1.0
N4 A:C66 5.0 89.9 1.0

Barium binding site 3 out of 5 in 2ydh

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Barium binding site 3 out of 5 in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1097

b:0.6
occ:1.00
OP2 A:U64 2.5 76.0 1.0
OP2 A:A10 2.9 94.0 1.0
P A:U64 3.4 78.8 1.0
O3' A:A9 3.5 98.1 1.0
P A:A10 3.7 94.5 1.0
OP1 A:U64 3.7 81.8 1.0
O3' A:U63 3.9 78.4 1.0
OP1 A:A62 3.9 79.7 1.0
O6 A:G11 4.0 0.2 1.0
O5' A:A10 4.0 95.4 1.0
N7 A:G11 4.1 0.3 1.0
N7 A:A10 4.4 0.5 1.0
C3' A:U63 4.4 79.4 1.0
C4' A:U63 4.5 79.8 1.0
C8 A:A10 4.6 1.0 1.0
C3' A:A9 4.6 99.1 1.0
C6 A:G11 4.7 0.5 1.0
C5 A:G11 4.8 0.7 1.0
O5' A:U64 4.8 76.8 1.0
C5' A:U63 4.9 79.8 1.0

Barium binding site 4 out of 5 in 2ydh

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Barium binding site 4 out of 5 in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1098

b:0.5
occ:0.50
N7 A:G32 4.7 98.3 1.0
C8 A:G32 4.7 99.3 1.0

Barium binding site 5 out of 5 in 2ydh

Go back to Barium Binding Sites List in 2ydh
Barium binding site 5 out of 5 in the Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of the Sam-I Riboswitch A94G U34 G18U G19U Variant in Complex with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1099

b:0.5
occ:1.00
N7 A:G55 3.8 72.1 1.0
N1 A:A46 4.1 83.8 1.0
C2 A:A46 4.3 84.0 1.0
N1 A:A45 4.3 97.2 1.0
C8 A:G55 4.4 73.2 1.0
N7 A:G56 4.4 74.4 1.0
C5 A:G55 4.6 70.6 1.0
O6 A:G56 4.7 72.9 1.0
O6 A:G55 4.8 67.1 1.0
N6 A:A45 4.8 96.5 1.0
OP2 A:G55 4.9 98.3 1.0
C6 A:A45 5.0 97.2 1.0

Reference:

K.T.Schroeder, P.Daldrop, D.M.J.Lilley. Rna Tertiary Interactions in A Riboswitch Stabilize the Structure of A Kink Turn. Structure V. 19 1233 2011.
ISSN: ISSN 0969-2126
PubMed: 21893284
DOI: 10.1016/J.STR.2011.07.003
Page generated: Sat Dec 12 01:55:38 2020

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