Cobalt in PDB 1ddy: Molecular Recognition By the Vitamin B12 Rna Aptamer

The structure of Molecular Recognition By the Vitamin B12 Rna Aptamer, PDB code: 1ddy was solved by D.Sussman, J.C.Nix, C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.330, 161.880, 100.960, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.6

The binding sites of Cobalt atom in the Molecular Recognition By the Vitamin B12 Rna Aptamer (pdb code 1ddy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Molecular Recognition By the Vitamin B12 Rna Aptamer, PDB code: 1ddy:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Molecular Recognition By the Vitamin B12 Rna Aptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Molecular Recognition By the Vitamin B12 Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:33.9 occ:1.00 CO A:B12101 0.0 33.9 1.0 C A:NME102 1.8 33.0 1.0 N24 A:B12101 1.9 29.9 1.0 N21 A:B12101 1.9 30.4 1.0 N22 A:B12101 1.9 30.4 1.0 N23 A:B12101 2.0 30.9 1.0 N3B A:B12101 2.1 32.5 1.0 C19 A:B12101 2.9 29.2 1.0 C9 A:B12101 2.9 31.6 1.0 C11 A:B12101 2.9 32.3 1.0 C1 A:B12101 2.9 29.9 1.0 C4 A:B12101 3.0 29.8 1.0 C16 A:B12101 3.0 31.2 1.0 N A:NME102 3.0 36.7 1.0 C6 A:B12101 3.0 30.4 1.0 C14 A:B12101 3.0 31.4 1.0 C2B A:B12101 3.0 30.9 1.0 C10 A:B12101 3.2 30.5 1.0 C9B A:B12101 3.3 32.2 1.0 C5 A:B12101 3.4 27.4 1.0 C15 A:B12101 3.4 30.7 1.0 C20 A:B12101 3.6 27.2 1.0 C4B A:B12101 3.9 33.1 1.0 C18 A:B12101 4.1 31.2 1.0 C8 A:B12101 4.2 35.6 1.0 N1B A:B12101 4.2 28.1 1.0 C17 A:B12101 4.2 31.9 1.0 C2 A:B12101 4.3 31.4 1.0 C12 A:B12101 4.3 33.8 1.0 C3 A:B12101 4.3 30.9 1.0 C7 A:B12101 4.3 34.0 1.0 C13 A:B12101 4.3 34.0 1.0 C8B A:B12101 4.4 30.9 1.0 C26 A:B12101 4.7 36.2 1.0 C46 A:B12101 4.8 34.2 1.0 C37 A:B12101 4.9 37.4 1.0 C35 A:B12101 4.9 31.4 1.0 C41 A:B12101 4.9 39.9 1.0 C53 A:B12101 4.9 32.3 1.0 C54 A:B12101 4.9 32.6 1.0 C48 A:B12101 5.0 42.7 1.0

Cobalt binding site 2 out of 4 in the Molecular Recognition By the Vitamin B12 Rna Aptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Molecular Recognition By the Vitamin B12 Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:27.7 occ:1.00 CO C:B12301 0.0 27.7 1.0 C C:NME302 1.8 27.6 1.0 N24 C:B12301 1.9 22.5 1.0 N21 C:B12301 1.9 22.2 1.0 N22 C:B12301 1.9 26.3 1.0 N23 C:B12301 2.0 23.9 1.0 N3B C:B12301 2.0 28.5 1.0 C19 C:B12301 2.8 21.5 1.0 C9 C:B12301 2.9 27.2 1.0 C1 C:B12301 2.9 22.3 1.0 C11 C:B12301 2.9 25.2 1.0 C2B C:B12301 2.9 29.6 1.0 C4 C:B12301 2.9 21.5 1.0 C16 C:B12301 3.0 23.0 1.0 C6 C:B12301 3.0 25.8 1.0 N C:NME302 3.0 32.6 1.0 C14 C:B12301 3.0 24.2 1.0 C9B C:B12301 3.2 31.0 1.0 C10 C:B12301 3.3 27.3 1.0 C5 C:B12301 3.4 22.4 1.0 C15 C:B12301 3.4 25.5 1.0 C20 C:B12301 3.6 25.8 1.0 C4B C:B12301 3.8 33.3 1.0 C18 C:B12301 4.1 20.9 1.0 N1B C:B12301 4.1 32.3 1.0 C2 C:B12301 4.2 22.4 1.0 C8 C:B12301 4.2 29.6 1.0 C3 C:B12301 4.2 22.2 1.0 C17 C:B12301 4.2 21.1 1.0 C7 C:B12301 4.3 27.5 1.0 C12 C:B12301 4.3 24.0 1.0 C8B C:B12301 4.3 33.3 1.0 C13 C:B12301 4.3 24.6 1.0 C26 C:B12301 4.6 23.9 1.0 C37 C:B12301 4.7 29.6 1.0 C46 C:B12301 4.8 20.9 1.0 C48 C:B12301 4.9 26.8 1.0 C41 C:B12301 4.9 34.2 1.0 C35 C:B12301 4.9 23.7 1.0 C53 C:B12301 5.0 21.5 1.0 C54 C:B12301 5.0 20.0 1.0

Cobalt binding site 3 out of 4 in the Molecular Recognition By the Vitamin B12 Rna Aptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Molecular Recognition By the Vitamin B12 Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Co501 b:26.2 occ:1.00 CO E:B12501 0.0 26.2 1.0 C E:NME502 1.9 23.1 1.0 N24 E:B12501 1.9 19.0 1.0 N21 E:B12501 1.9 18.3 1.0 N22 E:B12501 1.9 20.2 1.0 N23 E:B12501 2.0 22.3 1.0 N3B E:B12501 2.0 21.5 1.0 C19 E:B12501 2.8 17.3 1.0 C9 E:B12501 2.9 22.5 1.0 C1 E:B12501 2.9 17.6 1.0 C11 E:B12501 2.9 24.1 1.0 C4 E:B12501 2.9 17.8 1.0 C2B E:B12501 3.0 22.4 1.0 C16 E:B12501 3.0 19.2 1.0 C6 E:B12501 3.0 20.8 1.0 N E:NME502 3.0 26.6 1.0 C14 E:B12501 3.0 21.2 1.0 C9B E:B12501 3.2 23.5 1.0 C10 E:B12501 3.2 24.6 1.0 C5 E:B12501 3.4 17.7 1.0 C15 E:B12501 3.4 20.3 1.0 C20 E:B12501 3.6 16.2 1.0 C4B E:B12501 3.8 25.1 1.0 C18 E:B12501 4.1 17.8 1.0 N1B E:B12501 4.2 21.8 1.0 C2 E:B12501 4.2 16.7 1.0 C8 E:B12501 4.2 23.0 1.0 C3 E:B12501 4.2 18.3 1.0 C17 E:B12501 4.2 19.8 1.0 C12 E:B12501 4.3 23.9 1.0 C7 E:B12501 4.3 22.2 1.0 C8B E:B12501 4.3 24.4 1.0 C13 E:B12501 4.3 23.2 1.0 C26 E:B12501 4.6 15.6 1.0 C46 E:B12501 4.8 24.6 1.0 C37 E:B12501 4.8 26.7 1.0 C35 E:B12501 4.9 16.3 1.0 C41 E:B12501 4.9 27.9 1.0 C54 E:B12501 4.9 22.7 1.0 C53 E:B12501 5.0 21.4 1.0

Cobalt binding site 4 out of 4 in the Molecular Recognition By the Vitamin B12 Rna Aptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Molecular Recognition By the Vitamin B12 Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ G:Co701 b:23.3 occ:1.00 CO G:B12701 0.0 23.3 1.0 C G:NME702 1.8 22.8 1.0 N21 G:B12701 1.9 16.5 1.0 N24 G:B12701 1.9 17.9 1.0 N22 G:B12701 1.9 19.4 1.0 N23 G:B12701 2.0 18.0 1.0 N3B G:B12701 2.0 20.5 1.0 C19 G:B12701 2.9 17.2 1.0 C9 G:B12701 2.9 20.3 1.0 C1 G:B12701 2.9 16.1 1.0 C11 G:B12701 2.9 18.8 1.0 C4 G:B12701 2.9 15.8 1.0 C2B G:B12701 3.0 22.3 1.0 C6 G:B12701 3.0 18.6 1.0 C16 G:B12701 3.0 17.9 1.0 N G:NME702 3.0 30.6 1.0 C14 G:B12701 3.0 18.2 1.0 C9B G:B12701 3.2 21.1 1.0 C10 G:B12701 3.2 18.6 1.0 C5 G:B12701 3.4 17.4 1.0 C15 G:B12701 3.4 16.8 1.0 C20 G:B12701 3.5 18.2 1.0 C4B G:B12701 3.9 20.7 1.0 C18 G:B12701 4.1 18.8 1.0 N1B G:B12701 4.2 21.1 1.0 C2 G:B12701 4.2 15.7 1.0 C8 G:B12701 4.2 20.1 1.0 C3 G:B12701 4.2 15.8 1.0 C12 G:B12701 4.3 21.5 1.0 C7 G:B12701 4.3 19.1 1.0 C17 G:B12701 4.3 19.6 1.0 C13 G:B12701 4.3 22.6 1.0 C8B G:B12701 4.3 22.6 1.0 C26 G:B12701 4.6 17.6 1.0 C46 G:B12701 4.8 24.5 1.0 C37 G:B12701 4.8 21.7 1.0 C41 G:B12701 4.9 23.1 1.0 C35 G:B12701 4.9 18.1 1.0 C48 G:B12701 5.0 29.3 1.0 C53 G:B12701 5.0 15.4 1.0 C54 G:B12701 5.0 19.1 1.0

D.Sussman, J.C.Nix, C.Wilson. The Structural Basis For Molecular Recognition By the Vitamin B 12 Rna Aptamer. Nat.Struct.Biol. V. 7 53 2000.
ISSN: ISSN 1072-8368
PubMed: 10625428
DOI: 10.1038/71253