Magnesium 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:

Cadmium	(Cd)	38 atoms
Barium	(Ba)	13 atoms

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

Magnesium binding site 1 out of 6 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg227 b:33.6 occ:1.00 C5 A:C45 3.2 33.6 1.0 OP1 B:U98 3.3 46.6 1.0 C4 A:U43 3.4 35.9 1.0 O4 A:U43 3.4 46.8 1.0 O A:HOH449 3.4 59.8 1.0 C5 A:U43 3.6 32.1 1.0 O3' B:C97 3.7 30.4 1.0 C6 A:C45 3.8 30.7 1.0 O A:HOH403 3.9 27.5 1.0 N3 A:U43 4.0 28.8 1.0 O A:HOH355 4.0 41.2 1.0 C4 A:C45 4.0 34.0 1.0 O B:HOH446 4.0 28.7 1.0 P B:U98 4.1 37.5 1.0 O A:HOH331 4.2 32.3 1.0 N4 A:C45 4.2 36.0 1.0 C6 A:U43 4.3 24.0 1.0 C5' B:C97 4.3 30.2 1.0 C4' B:C97 4.7 31.6 1.0 C2 A:U43 4.7 31.3 1.0 C3' B:C97 4.7 32.8 1.0 OP2 B:U98 4.8 33.7 1.0 N1 A:U43 4.8 23.8 1.0 N1 A:C45 4.9 35.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg228 b:45.8 occ:1.00 O A:HOH302 2.3 45.3 1.0 N2 A:G62 2.7 23.0 1.0 O2 A:U36 2.9 38.7 1.0 O2' A:U36 2.9 35.0 1.0 O4' A:C37 3.4 26.6 1.0 O A:HOH312 3.4 44.4 1.0 C2' A:U36 3.5 25.5 1.0 C1' A:C37 3.6 28.6 1.0 C1' A:U36 3.8 27.4 1.0 C2 A:G62 3.9 21.1 1.0 O2 A:C63 3.9 42.4 1.0 C2 A:U36 4.0 33.1 1.0 N1 A:G62 4.2 21.4 1.0 N1 A:C37 4.2 28.5 1.0 N1 A:U36 4.5 28.6 1.0 N2 A:G35 4.5 32.1 1.0 C4' A:C37 4.6 29.9 1.0 C6 A:C37 4.6 38.2 1.0 OP1 A:G11 4.6 35.7 1.0 O A:HOH405 4.7 40.5 1.0 OP2 A:G11 4.8 37.7 1.0 C2 A:C63 4.8 30.4 1.0 C2 A:C37 4.9 23.2 1.0 O2' A:C37 4.9 32.6 1.0 C2' A:C37 4.9 30.7 1.0 O4' A:U36 5.0 34.3 1.0 C3' A:U36 5.0 28.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg229 b:47.7 occ:1.00 OP2 A:U12 2.3 32.7 1.0 OP2 A:A13 2.7 39.8 1.0 O A:HOH350 3.1 46.0 1.0 O A:HOH353 3.2 30.1 1.0 P A:U12 3.5 28.9 1.0 O3' A:G11 3.9 31.0 1.0 P A:A13 4.0 35.0 1.0 O5' A:U12 4.0 33.1 1.0 O A:HOH428 4.2 51.5 1.0 O3' A:U12 4.4 33.0 1.0 C5' A:U12 4.4 29.9 1.0 OP1 A:A13 4.6 44.7 1.0 C3' A:U12 4.6 32.1 1.0 O2' A:G11 4.6 35.3 1.0 CD A:CD212 4.7 0.6 1.0 OP1 A:U12 4.8 24.0 1.0 C3' A:G11 4.9 32.1 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg230 b:52.2 occ:1.00 O6 A:G11 2.5 33.0 1.0 OP2 A:A92 2.7 39.2 1.0 CD A:CD213 3.5 0.9 1.0 C6 A:G11 3.7 25.4 1.0 P A:A92 4.0 41.1 1.0 O5' A:A92 4.4 43.7 1.0 C5 A:G11 4.6 32.3 1.0 OP1 A:A92 4.6 46.1 1.0 N1 A:G11 4.6 25.7 1.0 N7 A:A92 4.7 34.5 1.0 N7 A:G11 4.7 34.8 1.0 O A:HOH319 4.8 70.7 1.0 C8 A:A92 4.8 36.0 1.0 OP1 A:C91 5.0 44.0 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the L.Lactis Ykoy Riboswitch Bound to Cadmium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg228 b:72.8 occ:1.00 O B:HOH432 1.8 65.2 1.0 O B:HOH424 3.7 21.2 1.0 O4 B:U68 3.8 34.5 1.0 O6 B:G67 3.9 42.9 1.0 O4 B:U66 4.0 40.0 1.0 N7 B:G67 4.1 35.3 1.0 N6 B:A30 4.4 30.3 1.0 C4 B:U66 4.4 33.3 1.0 C5 B:U66 4.4 34.7 1.0 C6 B:G67 4.7 29.0 1.0 N6 B:A29 4.7 28.4 1.0 O B:HOH406 4.8 17.5 1.0 C5 B:G67 4.8 30.7 1.0 C4 B:U68 4.8 35.0 1.0 O B:HOH465 5.0 33.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg229 b:76.6 occ:1.00 O B:HOH324 1.7 74.8 1.0 OP1 B:C91 3.0 50.1 1.0 OP2 B:A92 3.1 30.8 1.0 P B:C91 3.6 42.1 1.0 OP2 B:C91 3.7 52.5 1.0 O B:HOH306 3.8 36.6 1.0 O5' B:C91 3.9 39.9 1.0 O6 B:G11 3.9 37.5 1.0 O B:HOH359 4.0 62.4 1.0 CD B:CD216 4.2 84.6 1.0 P B:A92 4.6 37.5 1.0 N7 B:A92 4.7 36.7 1.0 C5' B:C91 4.7 35.8 1.0 C6 B:G11 4.9 33.0 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