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Barium in PDB 6cb3: Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium

Protein crystallography data

The structure of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium, PDB code: 6cb3 was solved by S.Bachas, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.10 / 1.89
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 73.141, 73.141, 117.610, 90.00, 90.00, 120.00
R / Rfree (%) 14 / 17.4

Other elements in 6cb3:

The structure of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium also contains other interesting chemical elements:

Cadmium (Cd) 38 atoms
Magnesium (Mg) 6 atoms

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium (pdb code 6cb3). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 13 binding sites of Barium where determined in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium, PDB code: 6cb3:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 13 in 6cb3

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Barium binding site 1 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


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 L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba220

b:58.0
occ:1.00
O4 A:U87 2.7 42.0 1.0
O6 A:G70 2.9 29.5 1.0
O4 A:U69 3.0 31.2 1.0
N3 A:U87 3.3 44.4 1.0
C4 A:U87 3.4 43.4 1.0
C4 A:U69 3.9 31.6 1.0
C6 A:G70 3.9 29.7 1.0
O4 A:U86 3.9 42.7 1.0
C5 A:U69 4.2 32.0 1.0
O A:HOH444 4.3 45.2 1.0
N7 A:G70 4.4 38.0 1.0
C5 A:G70 4.5 35.4 1.0
C2 A:U87 4.6 47.4 1.0
N6 A:A71 4.6 36.5 1.0
N6 A:A29 4.7 32.1 1.0
O2 A:U87 4.9 49.3 1.0
C5 A:U87 4.9 36.2 1.0
C4 A:U86 4.9 35.0 1.0
O4 A:U68 4.9 41.1 1.0

Barium binding site 2 out of 13 in 6cb3

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Barium binding site 2 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


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 L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba221

b:0.8
occ:1.00
O2 A:C40 2.8 35.6 1.0
O A:HOH400 3.1 26.9 1.0
O A:HOH467 3.1 64.4 1.0
C2 A:C40 4.0 26.8 1.0
O A:HOH434 4.3 54.0 1.0
N3 A:C40 4.6 26.7 1.0
O4 A:U39 5.0 37.3 1.0

Barium binding site 3 out of 13 in 6cb3

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Barium binding site 3 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


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 L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba222

b:77.0
occ:1.00
O6 A:G8 2.5 26.5 1.0
O A:HOH399 2.7 30.1 1.0
CD A:CD218 2.9 63.0 1.0
C6 A:G8 3.7 29.3 1.0
O A:HOH445 3.8 45.4 1.0
OP2 A:G7 4.3 47.3 1.0
OP1 A:A93 4.4 40.4 1.0
C5 A:G8 4.5 24.1 1.0
N7 A:G8 4.5 23.6 1.0
N1 A:G8 4.7 25.9 1.0
C5' A:A93 4.8 34.2 1.0
OP2 A:G94 5.0 42.0 1.0

Barium binding site 4 out of 13 in 6cb3

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Barium binding site 4 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


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 L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba223

b:74.8
occ:1.00
OP1 A:G77 2.5 32.4 1.0
O A:HOH425 2.5 26.1 1.0
P A:G77 3.6 31.0 1.0
OP2 A:G77 4.0 27.1 1.0
O3' A:C76 4.4 30.8 1.0
O5' A:G77 4.7 28.7 1.0
OP2 A:A78 4.9 28.8 1.0

Barium binding site 5 out of 13 in 6cb3

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Barium binding site 5 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


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 L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba224

b:39.0
occ:1.00
O A:HOH418 2.4 63.4 1.0
N7 A:G46 2.4 26.6 1.0
O A:HOH346 2.4 31.1 1.0
O A:HOH465 2.5 39.3 1.0
O A:HOH430 2.5 25.6 1.0
C8 A:G46 3.2 22.4 1.0
C5 A:G46 3.6 26.0 1.0
O6 A:G46 3.9 20.5 1.0
N7 A:G38 4.1 21.5 1.0
C6 A:G46 4.1 22.6 1.0
O A:HOH413 4.3 47.8 1.0
O4 A:U47 4.4 30.4 1.0
N9 A:G46 4.4 19.8 1.0
C5 A:G38 4.6 23.3 1.0
OP1 A:G46 4.6 36.6 1.0
C4 A:G46 4.6 19.9 1.0
O6 A:G38 4.7 28.0 1.0
C8 A:G38 4.7 24.7 1.0
C6 A:G38 4.8 20.4 1.0
O A:HOH437 4.8 38.2 1.0

Barium binding site 6 out of 13 in 6cb3

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Barium binding site 6 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba225

b:80.1
occ:1.00
O6 A:G85 3.3 36.1 1.0
O4 A:U84 3.5 28.0 1.0
O A:HOH451 4.1 53.1 1.0
C4 A:U84 4.2 28.0 1.0
O A:HOH444 4.3 45.2 1.0
C6 A:G85 4.3 31.6 1.0
C5 A:U84 4.3 28.4 1.0
N7 A:G85 4.5 39.9 1.0
N4 A:C72 4.5 35.5 1.0
O A:HOH429 4.5 41.5 1.0
N6 A:A71 4.5 36.5 1.0
C5 A:G85 4.8 36.6 1.0
O4 A:U86 5.0 42.7 1.0

Barium binding site 7 out of 13 in 6cb3

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Barium binding site 7 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba226

b:36.8
occ:1.00
O A:HOH415 2.4 58.8 1.0
O A:HOH408 2.4 53.8 1.0
O4 A:U36 2.6 30.8 1.0
O6 A:G35 2.7 37.6 1.0
O6 A:G61 2.7 31.6 1.0
O A:HOH416 2.8 27.6 1.0
O6 A:G62 2.9 31.3 1.0
O A:HOH354 3.4 28.1 1.0
C4 A:U36 3.6 34.8 1.0
C6 A:G61 3.6 25.9 1.0
C6 A:G35 3.8 28.7 1.0
N3 A:U36 3.9 36.8 1.0
C6 A:G62 4.0 21.1 1.0
N4 A:C63 4.0 29.8 1.0
O A:HOH463 4.2 36.4 1.0
N4 A:C37 4.3 26.8 1.0
C5 A:G61 4.3 25.5 1.0
O A:HOH410 4.4 34.7 1.0
N7 A:G61 4.4 28.7 1.0
C5 A:G35 4.5 27.0 1.0
N7 A:G35 4.6 24.4 1.0
O A:HOH330 4.6 41.2 1.0
N1 A:G61 4.6 26.7 1.0
N7 A:G62 4.7 24.2 1.0
C5 A:G62 4.7 22.8 1.0
N6 A:A34 4.8 37.5 1.0
N1 A:G35 4.8 28.6 1.0
C5 A:U36 4.9 33.5 1.0
C4 A:C63 5.0 23.7 1.0

Barium binding site 8 out of 13 in 6cb3

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Barium binding site 8 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba222

b:45.8
occ:1.00
O B:HOH438 2.5 65.2 1.0
O6 B:G8 2.7 28.7 1.0
O B:HOH448 2.7 46.6 1.0
O B:HOH311 2.9 54.4 1.0
O B:HOH392 3.0 58.7 1.0
O B:HOH352 3.1 34.5 1.0
C6 B:G8 3.8 25.9 1.0
O B:HOH407 4.4 57.6 1.0
OP2 B:G7 4.7 35.2 1.0
O5' B:A93 4.7 40.9 1.0
C5 B:G8 4.7 25.5 1.0
N7 B:G8 4.8 27.4 1.0
N1 B:G8 4.8 35.0 1.0
O B:HOH445 4.9 44.6 1.0
N7 B:G7 4.9 29.3 1.0
CD B:CD217 5.0 0.4 1.0

Barium binding site 9 out of 13 in 6cb3

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Barium binding site 9 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba223

b:71.1
occ:1.00
O B:HOH379 2.6 58.2 1.0
OP2 B:A13 2.6 36.0 1.0
O B:HOH362 2.8 38.3 1.0
OP2 B:U12 3.0 38.5 1.0
O2' B:G11 3.6 44.4 1.0
O3' B:G11 3.8 33.1 1.0
O B:HOH442 3.9 56.0 1.0
P B:U12 4.0 31.7 1.0
P B:A13 4.1 35.1 1.0
O B:HOH459 4.5 65.5 1.0
O5' B:U12 4.5 32.3 1.0
C3' B:G11 4.6 29.4 1.0
C2' B:G11 4.6 29.6 1.0
O5' B:A13 4.8 37.1 1.0
O6 B:G14 4.9 26.1 1.0
OP1 B:A13 4.9 37.5 1.0
O3' B:U12 4.9 34.2 1.0

Barium binding site 10 out of 13 in 6cb3

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Barium binding site 10 out of 13 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba224

b:79.0
occ:1.00
O4 B:U87 2.6 39.9 1.0
O4 B:U69 2.9 37.1 1.0
O6 B:G70 3.3 40.2 1.0
O B:HOH423 3.7 43.3 1.0
C4 B:U87 3.7 30.3 1.0
C4 B:U69 3.7 30.1 1.0
O B:HOH385 3.9 54.5 1.0
C5 B:U69 4.0 30.8 1.0
N3 B:U87 4.1 28.5 1.0
O B:HOH432 4.1 65.2 1.0
O4 B:U86 4.2 37.5 1.0
C6 B:G70 4.3 33.1 1.0
CD B:CD213 4.4 0.3 1.0
O4 B:U68 4.5 34.5 1.0
O B:HOH404 4.7 36.3 1.0
O B:HOH376 4.8 44.3 1.0
N6 B:A29 4.8 28.4 1.0
N7 B:G70 4.9 40.5 1.0
C5 B:U68 4.9 30.6 1.0
C4 B:U68 4.9 35.0 1.0
C5 B:G70 5.0 36.6 1.0
C5 B:U87 5.0 26.5 1.0
N3 B:U69 5.0 29.8 1.0

Reference:

S.T.Bachas, A.R.Ferre-D'amare. Convergent Use of Heptacoordination For Cation Selectivity By Rna and Protein Metalloregulators. Cell Chem Biol V. 25 962 2018.
ISSN: ESSN 2451-9448
PubMed: 29805037
DOI: 10.1016/J.CHEMBIOL.2018.04.016
Page generated: Wed Jul 10 15:53:49 2024

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