Cobalt in PDB 8sa5: Adenosylcobalamin-Bound Riboswitch Dimer, Form 4

The binding sites of Cobalt atom in the Adenosylcobalamin-Bound Riboswitch Dimer, Form 4 (pdb code 8sa5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Adenosylcobalamin-Bound Riboswitch Dimer, Form 4, PDB code: 8sa5:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Adenosylcobalamin-Bound Riboswitch Dimer, Form 4


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Adenosylcobalamin-Bound Riboswitch Dimer, Form 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:130.0 occ:1.00 CO A:B1Z301 0.0 130.0 1.0 N24 A:B1Z301 1.8 130.0 1.0 N21 A:B1Z301 1.8 130.0 1.0 N22 A:B1Z301 1.9 130.0 1.0 N23 A:B1Z301 1.9 130.0 1.0 N3B A:B1Z301 2.3 130.0 1.0 C9 A:B1Z301 2.7 130.0 1.0 C14 A:B1Z301 2.8 130.0 1.0 C11 A:B1Z301 2.8 130.0 1.0 C19 A:B1Z301 2.8 130.0 1.0 C4 A:B1Z301 2.8 130.0 1.0 C5A A:B1Z301 2.8 130.0 1.0 C6 A:B1Z301 2.8 130.0 1.0 C16 A:B1Z301 2.8 130.0 1.0 C1 A:B1Z301 2.9 130.0 1.0 C10 A:B1Z301 3.1 130.0 1.0 C2B A:B1Z301 3.2 130.0 1.0 C15 A:B1Z301 3.2 130.0 1.0 C5 A:B1Z301 3.2 130.0 1.0 C9B A:B1Z301 3.3 130.0 1.0 C20 A:B1Z301 3.6 130.0 1.0 C4A A:B1Z301 3.7 130.0 1.0 C4B A:B1Z301 3.8 130.0 1.0 C18 A:B1Z301 4.0 130.0 1.0 C8 A:B1Z301 4.0 130.0 1.0 O6A A:B1Z301 4.1 130.0 1.0 C3 A:B1Z301 4.1 130.0 1.0 C13 A:B1Z301 4.1 130.0 1.0 C17 A:B1Z301 4.1 130.0 1.0 C12 A:B1Z301 4.1 130.0 1.0 C7 A:B1Z301 4.1 130.0 1.0 C2 A:B1Z301 4.1 130.0 1.0 N1B A:B1Z301 4.4 130.0 1.0 C35 A:B1Z301 4.4 130.0 1.0 C8B A:B1Z301 4.5 130.0 1.0 C53 A:B1Z301 4.5 130.0 1.0 C26 A:B1Z301 4.7 130.0 1.0 C37 A:B1Z301 4.7 130.0 1.0 C41 A:B1Z301 4.7 130.0 1.0 C47 A:B1Z301 4.9 130.0 1.0 C54 A:B1Z301 5.0 130.0 1.0

Cobalt binding site 2 out of 2 in the Adenosylcobalamin-Bound Riboswitch Dimer, Form 4


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Adenosylcobalamin-Bound Riboswitch Dimer, Form 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:464.5 occ:1.00 CO B:B1Z301 0.0 464.5 1.0 N24 B:B1Z301 1.8 464.5 1.0 N21 B:B1Z301 1.8 464.5 1.0 N23 B:B1Z301 1.8 464.5 1.0 N22 B:B1Z301 1.8 464.5 1.0 N3B B:B1Z301 2.3 464.5 1.0 C9 B:B1Z301 2.7 464.5 1.0 C14 B:B1Z301 2.7 464.5 1.0 C11 B:B1Z301 2.8 464.5 1.0 C4 B:B1Z301 2.8 464.5 1.0 C19 B:B1Z301 2.8 464.5 1.0 C6 B:B1Z301 2.8 464.5 1.0 C5A B:B1Z301 2.8 464.5 1.0 C16 B:B1Z301 2.8 464.5 1.0 C1 B:B1Z301 2.9 464.5 1.0 C10 B:B1Z301 3.1 464.5 1.0 C5 B:B1Z301 3.2 464.5 1.0 C15 B:B1Z301 3.2 464.5 1.0 C2B B:B1Z301 3.2 464.5 1.0 C9B B:B1Z301 3.3 464.5 1.0 C20 B:B1Z301 3.5 464.5 1.0 C4A B:B1Z301 3.7 464.5 1.0 C4B B:B1Z301 3.8 464.5 1.0 C18 B:B1Z301 4.0 464.5 1.0 C8 B:B1Z301 4.0 464.5 1.0 C12 B:B1Z301 4.1 464.5 1.0 C13 B:B1Z301 4.1 464.5 1.0 C3 B:B1Z301 4.1 464.5 1.0 C7 B:B1Z301 4.1 464.5 1.0 C17 B:B1Z301 4.1 464.5 1.0 C2 B:B1Z301 4.2 464.5 1.0 N1B B:B1Z301 4.4 464.5 1.0 C35 B:B1Z301 4.4 464.5 1.0 C8B B:B1Z301 4.5 464.5 1.0 C53 B:B1Z301 4.5 464.5 1.0 C47 B:B1Z301 4.6 464.5 1.0 O6A B:B1Z301 4.7 464.5 1.0 C26 B:B1Z301 4.8 464.5 1.0 C3A B:B1Z301 4.9 464.5 1.0 C37 B:B1Z301 4.9 464.5 1.0 C48 B:B1Z301 4.9 464.5 1.0 C41 B:B1Z301 4.9 464.5 1.0 C55 B:B1Z301 5.0 464.5 1.0 O8A B:B1Z301 5.0 464.5 1.0 C30 B:B1Z301 5.0 464.5 1.0

J.Ding, J.C.Deme, J.R.Stagno, P.Yu, S.M.Lea, Y.X.Wang. Capturing Heterogeneous Conformers of Cobalamin Riboswitch By Cryo-Em Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962