Barium in PDB 6cc1: Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium

The structure of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium, PDB code: 6cc1 was solved by S.T.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)	42.98 / 2.54
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	73.089, 73.089, 117.082, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 28.1

The structure of Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium also contains other interesting chemical elements:

Cadmium	(Cd)	23 atoms
Magnesium	(Mg)	1 atom

The binding sites of Barium atom in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium (pdb code 6cc1). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 8 binding sites of Barium where determined in the Crystal Structure of Ykoy-Alx Riboswitch Chimera Bound to Cadmium, PDB code: 6cc1:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Barium binding site 1 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba209 b:68.5 occ:1.00 O A:HOH304 2.5 54.1 1.0 O6 A:G62 3.0 61.3 1.0 O6 A:G61 3.1 61.5 1.0 O6 A:G35 3.6 63.7 1.0 C6 A:G61 3.9 58.8 1.0 O4 A:U36 4.0 67.2 1.0 C6 A:G62 4.1 60.9 1.0 N6 A:A34 4.3 62.0 1.0 C5 A:G61 4.5 59.6 1.0 N7 A:G61 4.5 66.7 1.0 N7 A:G62 4.7 66.9 1.0 C6 A:G35 4.7 62.0 1.0 N4 A:C63 4.7 62.9 1.0 C5 A:G62 4.8 61.3 1.0 N1 A:G61 4.8 59.1 1.0

Barium binding site 2 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba210 b:0.0 occ:1.00 O A:HOH333 2.7 60.1 1.0 O6 A:G8 2.9 61.2 1.0 O A:HOH319 3.3 63.7 1.0 C6 A:G8 4.0 61.2 1.0 O A:HOH314 4.5 63.0 1.0 OP2 A:G94 4.5 64.6 1.0 O5' A:A93 4.5 67.4 1.0 N7 A:G6 4.6 63.2 1.0 N1 A:G8 4.8 62.8 1.0 OP1 A:G94 4.9 66.0 1.0 C5 A:G8 4.9 61.4 1.0 O6 A:G6 4.9 60.7 1.0

Barium binding site 3 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba211 b:98.9 occ:1.00 O4 A:U69 3.4 60.7 1.0 O6 A:G70 3.7 61.3 1.0 O4 A:U87 3.7 73.8 1.0 O4 A:U86 3.7 69.5 1.0 O A:HOH334 3.9 57.3 1.0 O A:HOH328 4.0 54.6 1.0 N3 A:U87 4.0 64.5 1.0 C4 A:U69 4.3 58.3 1.0 C4 A:U87 4.3 69.7 1.0 C5 A:U69 4.5 60.2 1.0 C4 A:U86 4.7 58.0 1.0 C6 A:G70 4.8 60.8 1.0

Barium binding site 4 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba212 b:87.7 occ:1.00 O6 A:G46 2.7 69.1 1.0 N7 A:G46 2.9 64.6 1.0 C6 A:G46 3.4 63.5 1.0 C5 A:G46 3.5 66.0 1.0 O A:HOH335 3.6 55.1 1.0 O6 A:G38 4.1 64.0 1.0 C8 A:G46 4.1 67.3 1.0 O4 A:U47 4.2 58.9 1.0 N7 A:G38 4.5 63.9 1.0 C6 A:G38 4.7 63.8 1.0 N1 A:G46 4.8 58.7 1.0 C4 A:G46 4.9 68.9 1.0 C5 A:G38 4.9 67.4 1.0

Barium binding site 5 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba217 b:64.9 occ:1.00 O6 B:G35 2.6 55.7 1.0 O6 B:G61 2.7 65.1 1.0 O4 B:U36 2.9 68.1 1.0 O6 B:G62 2.9 62.3 1.0 C6 B:G61 3.2 67.3 1.0 N1 B:G61 3.2 69.4 1.0 C6 B:G35 3.5 58.4 1.0 N4 B:C63 4.1 61.6 1.0 C4 B:U36 4.1 63.8 1.0 C6 B:G62 4.1 62.2 1.0 C5 B:G35 4.2 65.2 1.0 N1 B:G35 4.3 57.8 1.0 C2 B:G61 4.4 65.0 1.0 C5 B:G61 4.4 61.5 1.0 N7 B:G35 4.4 69.5 1.0 N4 B:C37 4.8 63.2 1.0 N2 B:G61 4.9 63.8 1.0 N3 B:U36 5.0 65.6 1.0 C5 B:G62 5.0 63.7 1.0

Barium binding site 6 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba218 b:83.5 occ:1.00 O B:HOH346 2.8 54.7 1.0 O6 B:G85 2.9 65.7 1.0 O4 B:U84 3.3 60.0 1.0 C4 B:U84 3.9 62.3 1.0 C6 B:G85 4.0 58.4 1.0 C5 B:U84 4.0 63.3 1.0 N7 B:G85 4.6 56.0 1.0 C5 B:G85 4.7 56.9 1.0 O B:HOH334 4.8 50.5 1.0

Barium binding site 7 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba219 b:78.9 occ:1.00 O B:HOH301 2.6 54.6 1.0 CD B:CD216 2.9 0.4 1.0 O B:HOH335 3.1 56.6 1.0 OP1 B:U88 3.4 59.4 1.0 C2' B:U87 3.8 59.1 1.0 N7 B:A29 3.9 52.2 1.0 P B:U88 4.2 60.1 1.0 C3' B:U87 4.2 58.2 1.0 OP2 B:U88 4.2 60.2 1.0 OP2 B:A29 4.3 54.0 1.0 C2 B:U87 4.3 56.7 1.0 N1 B:U87 4.4 57.0 1.0 O2 B:U87 4.5 55.9 1.0 O3' B:U87 4.6 57.5 1.0 O2' B:U87 4.6 57.7 1.0 C8 B:A29 4.7 52.3 1.0 N3 B:U87 4.7 56.9 1.0 O2' B:A28 4.7 59.8 1.0 C1' B:U87 4.7 57.3 1.0 N6 B:A29 4.8 51.9 1.0 C6 B:U87 4.8 59.1 1.0 O3' B:A28 4.9 56.8 1.0 C5 B:A29 5.0 52.0 1.0

Barium binding site 8 out of 8 in the Crystal Structure of Ykoy-Alx Riboswitch Chimera 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 Ykoy-Alx Riboswitch Chimera Bound to Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba220 b:0.3 occ:1.00 O2 B:C40 2.6 75.0 1.0 O4 B:U39 2.9 69.7 1.0 C2 B:C40 3.3 67.8 1.0 N3 B:C40 3.4 68.4 1.0 C4 B:U39 4.0 64.1 1.0 N1 B:C40 4.6 63.2 1.0 C4 B:C40 4.6 69.0 1.0 N3 B:U39 4.7 67.0 1.0 C5 B:U39 4.9 62.2 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