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

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

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

Magnesium	(Mg)	6 atoms
Barium	(Ba)	13 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 38 binding sites of Cadmium where determined in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium, PDB code: 6cb3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd201 b:49.6 occ:1.00 N7 A:G51 2.4 28.2 1.0 O A:HOH358 2.4 40.3 1.0 CD A:CD217 2.6 0.0 1.0 O A:HOH371 2.6 46.0 1.0 O B:HOH389 2.6 36.5 1.0 O A:HOH317 2.6 35.9 1.0 C8 A:G51 3.3 29.8 1.0 C5 A:G51 3.4 27.4 1.0 O6 A:G51 3.7 39.3 1.0 O A:HOH384 3.8 36.1 1.0 N7 A:G50 3.9 22.4 1.0 C6 A:G51 3.9 29.6 1.0 OP2 A:A53 4.0 41.6 1.0 O1G B:GTP221 4.1 67.6 1.0 C8 A:G50 4.4 23.5 1.0 N9 A:G51 4.5 25.1 1.0 C4 A:G51 4.5 27.1 1.0 O2G B:GTP221 4.6 64.7 1.0 C5 A:G50 4.6 22.5 1.0 OP2 A:G51 4.7 32.8 1.0 OP2 A:G50 4.8 40.2 1.0 PG B:GTP221 4.8 64.7 1.0 OP1 A:A53 4.9 42.9 1.0 O6 A:G50 4.9 26.1 1.0

Cadmium binding site 2 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd202 b:28.9 occ:1.00 OP1 A:A10 2.5 37.4 1.0 OP1 A:G8 2.5 47.1 1.0 OP2 A:G9 2.6 44.4 1.0 O A:HOH374 2.6 38.0 1.0 OP1 A:U39 2.7 30.4 1.0 O A:HOH343 2.8 30.6 1.0 O2 A:U44 2.9 47.0 1.0 O A:HOH359 2.9 32.9 1.0 P A:G8 3.8 34.3 1.0 P A:U39 3.9 23.2 1.0 P A:A10 3.9 34.8 1.0 C2 A:U44 3.9 26.1 1.0 P A:G9 3.9 34.3 1.0 C5' A:G8 4.0 28.8 1.0 O A:HOH396 4.0 57.3 1.0 OP2 A:U39 4.2 20.4 1.0 O2' A:U44 4.2 28.9 1.0 C5' A:G38 4.2 31.9 1.0 O5' A:G8 4.3 31.5 1.0 OP1 A:G9 4.5 39.8 1.0 C3' A:G9 4.6 27.0 1.0 C4' A:G38 4.6 25.8 1.0 C3' A:G38 4.6 28.1 1.0 N3 A:U44 4.7 28.2 1.0 OP2 A:A10 4.7 31.3 1.0 OP2 A:G8 4.7 39.8 1.0 CD A:CD206 4.7 29.0 1.0 O5' A:G9 4.8 32.1 1.0 C5' A:A10 4.8 35.4 1.0 O3' A:G9 4.8 32.1 1.0 N1 A:U44 4.8 26.0 1.0 O5' A:A10 4.8 39.4 1.0 O3' A:G38 4.8 25.4 1.0 C1' A:U44 4.8 35.9 1.0 O3' A:G7 4.9 36.9 1.0 OP1 A:G38 4.9 44.4 1.0 O A:HOH391 5.0 33.7 1.0

Cadmium binding site 3 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd203 b:32.9 occ:1.00 OP1 A:A78 2.2 28.1 1.0 N7 A:A78 2.5 30.9 1.0 C8 A:A78 3.0 34.9 1.0 P A:A78 3.4 34.2 1.0 O3' A:G77 3.6 36.0 1.0 C5 A:A78 3.8 33.5 1.0 O5' A:A78 4.2 40.8 1.0 N6 A:A78 4.3 38.8 1.0 N9 A:A78 4.3 31.7 1.0 C6 A:A78 4.5 35.7 1.0 OP2 A:A78 4.6 28.8 1.0 C4 A:A78 4.7 30.5 1.0 O2' A:G77 4.9 32.7 1.0 N6 A:A79 4.9 41.1 1.0

Cadmium binding site 4 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd204 b:37.3 occ:1.00 N7 A:A42 2.4 32.3 1.0 OP1 B:U43 2.4 36.3 1.0 O B:HOH326 2.4 50.8 1.0 O B:HOH363 2.4 46.2 1.0 O A:HOH403 2.5 27.5 1.0 O A:HOH382 2.6 24.9 1.0 C8 A:A42 3.2 34.2 1.0 C5 A:A42 3.5 30.5 1.0 O4 A:U43 3.5 46.8 1.0 N6 A:A42 3.6 44.0 1.0 P B:U43 3.6 37.0 1.0 C6 A:A42 4.0 33.7 1.0 OP2 B:U43 4.0 33.7 1.0 O B:HOH337 4.4 36.7 1.0 C4 A:U43 4.4 35.9 1.0 O3' B:A42 4.4 39.2 1.0 N9 A:A42 4.4 33.1 1.0 O B:HOH446 4.5 28.7 1.0 C4 A:A42 4.6 32.8 1.0 O5' B:U43 4.6 40.1 1.0 C6 B:U43 4.7 33.5 1.0 C5 A:U43 4.7 32.1 1.0 OP1 A:A42 4.8 31.5 1.0 C5 B:U43 4.8 42.0 1.0 O A:HOH355 4.8 41.2 1.0 O2' B:A42 4.8 41.9 1.0 C5 B:U44 4.8 30.1 1.0 C2' B:A42 4.9 38.1 1.0 C3' B:A42 5.0 38.2 1.0

Cadmium binding site 5 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd205 b:45.1 occ:1.00 O A:HOH383 2.4 47.0 1.0 O A:HOH424 2.4 27.5 1.0 N7 A:A29 2.5 32.3 1.0 O A:HOH433 2.6 21.8 1.0 C8 A:A29 3.3 32.6 1.0 C5 A:A29 3.5 32.2 1.0 O A:HOH393 3.7 26.9 1.0 N6 A:A29 3.7 32.1 1.0 OP2 A:A29 3.9 38.9 1.0 C6 A:A29 4.0 30.5 1.0 O A:HOH313 4.0 41.0 1.0 OP2 A:U88 4.4 45.2 1.0 N9 A:A29 4.5 33.0 1.0 C4 A:A29 4.6 32.4 1.0 C2' A:U87 4.7 41.2 1.0 O2' A:U87 4.9 42.4 1.0 O3' A:A28 4.9 33.2 1.0 P A:A29 4.9 35.1 1.0

Cadmium binding site 6 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd206 b:29.0 occ:1.00 OP1 A:G9 2.1 39.8 1.0 OP2 A:C40 2.2 36.5 1.0 N3 A:U44 2.2 28.2 1.0 OP2 A:U39 2.3 20.4 1.0 N7 A:A41 2.3 29.7 1.0 O4 A:U44 3.0 29.6 1.0 C2 A:U44 3.0 26.1 1.0 C4 A:U44 3.0 24.0 1.0 O2 A:U44 3.1 47.0 1.0 C8 A:A41 3.1 35.4 1.0 P A:G9 3.2 34.3 1.0 P A:U39 3.3 23.2 1.0 C5 A:A41 3.3 31.1 1.0 P A:C40 3.5 35.3 1.0 O5' A:U39 3.6 30.8 1.0 OP2 A:G9 3.7 44.4 1.0 N6 A:A41 3.8 31.3 1.0 OP1 A:U39 3.8 30.4 1.0 O3' A:G8 3.8 36.9 1.0 C6 A:A41 4.0 27.4 1.0 O3' A:U39 4.1 40.8 1.0 OP1 A:C40 4.1 34.3 1.0 C5' A:U39 4.2 28.5 1.0 N1 A:U44 4.3 26.0 1.0 O A:HOH349 4.3 46.1 1.0 C5 A:U44 4.3 21.7 1.0 O5' A:G9 4.3 32.1 1.0 N9 A:A41 4.3 33.5 1.0 C3' A:U39 4.4 25.8 1.0 C4 A:A41 4.4 33.1 1.0 C5 A:C40 4.5 30.2 1.0 O3' A:G38 4.5 25.4 1.0 O5' A:C40 4.6 31.9 1.0 CD A:CD202 4.7 28.9 1.0 C6 A:U44 4.8 27.8 1.0 O A:HOH343 4.8 30.6 1.0 C4' A:U39 4.9 21.3 1.0 C6 A:C40 5.0 33.8 1.0 O A:HOH360 5.0 39.6 1.0

Cadmium binding site 7 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd207 b:27.3 occ:1.00 O A:HOH443 2.4 56.3 1.0 O A:HOH347 2.6 41.5 1.0 OP1 A:U43 2.6 32.4 1.0 O A:HOH360 2.7 39.6 1.0 O A:HOH349 2.7 46.1 1.0 O4 A:U44 2.8 29.6 1.0 O2' A:A41 2.9 35.2 1.0 C4 A:U44 3.8 24.0 1.0 P A:U43 3.8 30.1 1.0 C2' A:A41 3.8 24.5 1.0 C5 A:U44 4.1 21.7 1.0 O A:HOH377 4.3 49.5 1.0 OP2 A:U43 4.3 25.8 1.0 O2' A:G8 4.4 27.0 1.0 O3' A:A42 4.5 34.4 1.0 O A:HOH361 4.6 40.0 1.0 C8 A:A41 4.6 35.4 1.0 OP1 A:C40 4.6 34.3 1.0 C3' A:A41 4.8 24.7 1.0 N1 A:A95 4.9 33.8 1.0 OP2 A:A41 4.9 31.6 1.0

Cadmium binding site 8 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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 A:Cd208 b:45.2 occ:1.00 N7 A:A3 2.4 44.1 1.0 O A:HOH324 2.5 38.9 1.0 O A:HOH419 2.6 29.1 1.0 O A:HOH422 2.6 47.7 1.0 O A:HOH357 2.8 40.9 1.0 C8 A:A3 3.3 45.1 1.0 C5 A:A3 3.4 39.3 1.0 O1B A:GTP219 3.4 63.5 1.0 OP1 A:A3 3.6 52.3 1.0 N6 A:A3 3.7 32.4 1.0 C6 A:A3 3.9 32.9 1.0 O A:HOH441 4.1 52.4 1.0 N9 A:A3 4.5 41.1 1.0 N7 A:GTP219 4.5 33.1 1.0 C4 A:A3 4.5 43.0 1.0 C5 A:GTP219 4.6 30.4 1.0 P A:A3 4.7 58.4 1.0 PB A:GTP219 4.8 57.5 1.0 C6 A:GTP219 4.8 33.9 1.0 O6 A:GTP219 4.8 39.4 1.0 O5' A:A3 4.9 53.4 1.0 CD B:CD206 4.9 47.7 1.0

Cadmium binding site 9 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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 A:Cd209 b:48.8 occ:1.00 O A:HOH320 2.3 27.4 1.0 N7 B:GTP221 2.3 32.5 1.0 O3B B:GTP221 2.4 65.1 1.0 O B:HOH361 2.6 31.0 1.0 O1G B:GTP221 2.7 67.6 1.0 PG B:GTP221 2.7 64.7 1.0 O2G B:GTP221 2.7 64.7 1.0 OP1 A:A53 2.9 42.9 1.0 C8 B:GTP221 3.1 31.5 1.0 C5 B:GTP221 3.4 29.1 1.0 O3A B:GTP221 3.4 62.5 1.0 PB B:GTP221 3.4 66.8 1.0 O6 B:GTP221 3.5 38.5 1.0 O A:HOH371 3.9 46.0 1.0 C6 B:GTP221 3.9 29.2 1.0 O3' A:A52 3.9 31.3 1.0 P A:A53 4.0 33.3 1.0 O3G B:GTP221 4.2 63.1 1.0 O2B B:GTP221 4.2 70.1 1.0 N9 B:GTP221 4.3 32.2 1.0 C4 B:GTP221 4.4 28.8 1.0 O1B B:GTP221 4.5 65.5 1.0 O A:HOH317 4.7 35.9 1.0 PA B:GTP221 4.7 57.7 1.0 OP2 A:A53 4.7 41.6 1.0 CD B:CD211 4.9 54.1 1.0 O1A B:GTP221 5.0 50.0 1.0

Cadmium binding site 10 out of 38 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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 A:Cd210 b:41.2 occ:1.00 O A:HOH446 2.4 46.6 1.0 O A:HOH461 2.4 48.5 1.0 O A:HOH421 2.4 51.8 1.0 O A:HOH397 2.4 37.5 1.0 N7 A:G21 2.5 43.4 1.0 O6 A:G21 2.5 52.8 1.0 O A:HOH341 2.6 51.8 1.0 C5 A:G21 3.0 46.7 1.0 O A:HOH311 3.0 31.4 1.0 C6 A:G21 3.0 49.0 1.0 C8 A:G21 3.6 50.5 1.0 O A:HOH466 3.9 48.5 1.0 N7 A:G20 4.0 54.7 1.0 C4 A:G21 4.3 43.6 1.0 OP2 A:A23 4.3 46.2 1.0 N1 A:G21 4.3 47.9 1.0 CD A:CD211 4.4 43.8 1.0 C8 A:G20 4.6 42.9 1.0 N9 A:G21 4.6 49.9 1.0 C5 A:G20 4.6 39.9 1.0 OP1 A:A23 4.7 56.0 1.0 OP2 A:G20 4.9 45.1 1.0 OP2 A:G21 4.9 46.2 1.0 O6 A:G20 4.9 50.1 1.0 P A:A23 5.0 46.8 1.0

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