Cobalt in PDB 1et4: Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A

The structure of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A, PDB code: 1et4 was solved by D.Sussman, C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.270, 98.080, 217.970, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.2

The binding sites of Cobalt atom in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A (pdb code 1et4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A, PDB code: 1et4:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Co701 b:33.9 occ:1.00 CO A:CNC701 0.0 33.9 1.0 C1A A:CNC701 1.9 33.3 1.0 N24 A:CNC701 1.9 33.0 1.0 N21 A:CNC701 1.9 33.0 1.0 N22 A:CNC701 1.9 33.6 1.0 N23 A:CNC701 2.0 33.8 1.0 N3B A:CNC701 2.1 34.1 1.0 C19 A:CNC701 2.9 32.6 1.0 C9 A:CNC701 2.9 34.2 1.0 C11 A:CNC701 2.9 34.4 1.0 C1 A:CNC701 2.9 32.3 1.0 C4 A:CNC701 2.9 32.4 1.0 C16 A:CNC701 3.0 33.5 1.0 C2B A:CNC701 3.0 34.5 1.0 C6 A:CNC701 3.0 33.5 1.0 C14 A:CNC701 3.0 34.1 1.0 N1A A:CNC701 3.0 32.4 1.0 C9B A:CNC701 3.2 34.9 1.0 C10 A:CNC701 3.3 34.3 1.0 C5 A:CNC701 3.4 32.7 1.0 C15 A:CNC701 3.4 33.9 1.0 C20 A:CNC701 3.6 32.0 1.0 C4B A:CNC701 3.8 35.0 1.0 C18 A:CNC701 4.1 32.8 1.0 C2 A:CNC701 4.2 31.9 1.0 N1B A:CNC701 4.2 35.2 1.0 C8 A:CNC701 4.2 34.3 1.0 C3 A:CNC701 4.3 32.4 1.0 C17 A:CNC701 4.3 33.2 1.0 C12 A:CNC701 4.3 34.7 1.0 C7 A:CNC701 4.3 33.7 1.0 C13 A:CNC701 4.3 35.0 1.0 C8B A:CNC701 4.4 35.1 1.0 C26 A:CNC701 4.5 31.7 1.0 C46 A:CNC701 4.8 34.4 1.0 C37 A:CNC701 4.8 33.4 1.0 C41 A:CNC701 4.9 35.7 1.0 C48 A:CNC701 4.9 36.4 1.0 C35 A:CNC701 4.9 32.5 1.0 C53 A:CNC701 5.0 33.2 1.0 C54 A:CNC701 5.0 33.0 1.0

Cobalt binding site 2 out of 5 in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Co801 b:33.9 occ:1.00 CO B:CNC801 0.0 33.9 1.0 C1A B:CNC801 1.9 33.2 1.0 N21 B:CNC801 1.9 32.6 1.0 N24 B:CNC801 1.9 32.9 1.0 N22 B:CNC801 1.9 33.0 1.0 N23 B:CNC801 2.0 33.0 1.0 N3B B:CNC801 2.1 33.4 1.0 C19 B:CNC801 2.9 33.0 1.0 C9 B:CNC801 2.9 33.1 1.0 C11 B:CNC801 2.9 33.5 1.0 C1 B:CNC801 2.9 32.8 1.0 C4 B:CNC801 2.9 32.6 1.0 C16 B:CNC801 3.0 33.0 1.0 C6 B:CNC801 3.0 32.8 1.0 C14 B:CNC801 3.0 33.5 1.0 N1A B:CNC801 3.0 32.1 1.0 C2B B:CNC801 3.1 33.8 1.0 C10 B:CNC801 3.2 33.3 1.0 C9B B:CNC801 3.3 33.8 1.0 C5 B:CNC801 3.4 32.5 1.0 C15 B:CNC801 3.4 32.9 1.0 C20 B:CNC801 3.6 33.0 1.0 C4B B:CNC801 3.9 33.7 1.0 C18 B:CNC801 4.1 33.1 1.0 C2 B:CNC801 4.2 32.9 1.0 C8 B:CNC801 4.2 33.2 1.0 C3 B:CNC801 4.2 32.8 1.0 C17 B:CNC801 4.3 33.4 1.0 C7 B:CNC801 4.3 32.9 1.0 C12 B:CNC801 4.3 33.9 1.0 N1B B:CNC801 4.3 34.4 1.0 C13 B:CNC801 4.3 34.2 1.0 C8B B:CNC801 4.4 34.1 1.0 C26 B:CNC801 4.6 33.4 1.0 C37 B:CNC801 4.7 32.5 1.0 C35 B:CNC801 4.9 32.5 1.0 C41 B:CNC801 4.9 33.7 1.0 C46 B:CNC801 4.9 34.0 1.0 C53 B:CNC801 5.0 32.7 1.0 C54 B:CNC801 5.0 33.2 1.0

Cobalt binding site 3 out of 5 in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Co901 b:44.2 occ:1.00 CO C:CNC901 0.0 44.2 1.0 C1A C:CNC901 1.9 44.1 1.0 N24 C:CNC901 1.9 43.8 1.0 N21 C:CNC901 1.9 43.8 1.0 N22 C:CNC901 1.9 44.0 1.0 N23 C:CNC901 2.0 44.4 1.0 N3B C:CNC901 2.1 44.7 1.0 C19 C:CNC901 2.9 43.6 1.0 C9 C:CNC901 2.9 44.2 1.0 C11 C:CNC901 2.9 44.4 1.0 C1 C:CNC901 2.9 43.7 1.0 C4 C:CNC901 2.9 43.6 1.0 C16 C:CNC901 3.0 43.8 1.0 C6 C:CNC901 3.0 43.7 1.0 C14 C:CNC901 3.0 44.4 1.0 C2B C:CNC901 3.0 45.1 1.0 N1A C:CNC901 3.0 43.2 1.0 C9B C:CNC901 3.3 45.3 1.0 C10 C:CNC901 3.3 44.4 1.0 C5 C:CNC901 3.4 43.6 1.0 C15 C:CNC901 3.4 44.0 1.0 C20 C:CNC901 3.6 43.8 1.0 C4B C:CNC901 3.9 45.7 1.0 C18 C:CNC901 4.1 43.7 1.0 C2 C:CNC901 4.2 43.5 1.0 C8 C:CNC901 4.2 44.3 1.0 N1B C:CNC901 4.2 45.6 1.0 C3 C:CNC901 4.2 43.8 1.0 C12 C:CNC901 4.3 44.7 1.0 C17 C:CNC901 4.3 43.9 1.0 C7 C:CNC901 4.3 43.9 1.0 C13 C:CNC901 4.3 44.9 1.0 C8B C:CNC901 4.4 45.6 1.0 C26 C:CNC901 4.6 43.2 1.0 C46 C:CNC901 4.8 44.8 1.0 C37 C:CNC901 4.8 43.7 1.0 C41 C:CNC901 4.9 45.1 1.0 C35 C:CNC901 4.9 43.5 1.0 C48 C:CNC901 4.9 45.8 1.0 C53 C:CNC901 5.0 43.9 1.0 C54 C:CNC901 5.0 43.6 1.0

Cobalt binding site 4 out of 5 in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1001 b:35.9 occ:1.00 CO D:CNC1001 0.0 35.9 1.0 C1A D:CNC1001 1.9 35.0 1.0 N24 D:CNC1001 1.9 34.8 1.0 N22 D:CNC1001 1.9 35.0 1.0 N21 D:CNC1001 1.9 34.7 1.0 N23 D:CNC1001 2.0 35.5 1.0 N3B D:CNC1001 2.1 35.3 1.0 C9 D:CNC1001 2.9 35.6 1.0 C19 D:CNC1001 2.9 34.5 1.0 C11 D:CNC1001 2.9 36.0 1.0 C4 D:CNC1001 2.9 34.1 1.0 C1 D:CNC1001 2.9 34.3 1.0 C6 D:CNC1001 3.0 35.1 1.0 C16 D:CNC1001 3.0 35.1 1.0 N1A D:CNC1001 3.0 34.5 1.0 C2B D:CNC1001 3.0 35.4 1.0 C14 D:CNC1001 3.0 36.0 1.0 C9B D:CNC1001 3.2 35.7 1.0 C10 D:CNC1001 3.3 35.5 1.0 C5 D:CNC1001 3.4 34.5 1.0 C15 D:CNC1001 3.4 35.4 1.0 C20 D:CNC1001 3.7 34.3 1.0 C4B D:CNC1001 3.9 35.7 1.0 C18 D:CNC1001 4.2 34.7 1.0 C8 D:CNC1001 4.2 35.9 1.0 N1B D:CNC1001 4.2 35.6 1.0 C2 D:CNC1001 4.2 33.9 1.0 C3 D:CNC1001 4.3 34.1 1.0 C7 D:CNC1001 4.3 35.4 1.0 C17 D:CNC1001 4.3 34.9 1.0 C12 D:CNC1001 4.3 36.5 1.0 C13 D:CNC1001 4.4 36.7 1.0 C8B D:CNC1001 4.4 35.8 1.0 C26 D:CNC1001 4.6 33.9 1.0 C37 D:CNC1001 4.8 35.5 1.0 C46 D:CNC1001 4.9 36.4 1.0 C41 D:CNC1001 4.9 36.6 1.0 C35 D:CNC1001 4.9 34.1 1.0 C53 D:CNC1001 5.0 35.7 1.0 C54 D:CNC1001 5.0 34.8 1.0

Cobalt binding site 5 out of 5 in the Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of A Vitamin B12 Binding Rna Aptamer with Ligand at 2.3 A within 5.0Å range: probe atom residue distance (Å) B Occ E:Co601 b:51.3 occ:1.00 CO E:CNC601 0.0 51.3 1.0 C1A E:CNC601 1.9 50.9 1.0 N21 E:CNC601 1.9 50.8 1.0 N24 E:CNC601 1.9 51.0 1.0 N22 E:CNC601 1.9 51.0 1.0 N23 E:CNC601 2.0 51.2 1.0 N3B E:CNC601 2.1 51.8 1.0 C9 E:CNC601 2.9 51.2 1.0 C19 E:CNC601 2.9 50.5 1.0 C11 E:CNC601 2.9 51.3 1.0 C1 E:CNC601 2.9 50.3 1.0 C4 E:CNC601 2.9 50.4 1.0 C6 E:CNC601 3.0 50.9 1.0 C2B E:CNC601 3.0 52.4 1.0 N1A E:CNC601 3.0 50.5 1.0 C16 E:CNC601 3.0 50.9 1.0 C14 E:CNC601 3.0 51.2 1.0 C9B E:CNC601 3.2 52.5 1.0 C10 E:CNC601 3.2 51.3 1.0 C5 E:CNC601 3.4 50.4 1.0 C15 E:CNC601 3.4 51.0 1.0 C20 E:CNC601 3.6 50.3 1.0 C4B E:CNC601 3.9 52.7 1.0 C18 E:CNC601 4.1 50.6 1.0 C2 E:CNC601 4.2 50.1 1.0 C8 E:CNC601 4.2 51.3 1.0 N1B E:CNC601 4.2 52.8 1.0 C3 E:CNC601 4.2 50.2 1.0 C12 E:CNC601 4.3 51.4 1.0 C17 E:CNC601 4.3 50.8 1.0 C7 E:CNC601 4.3 51.1 1.0 C13 E:CNC601 4.3 51.5 1.0 C8B E:CNC601 4.4 52.9 1.0 C26 E:CNC601 4.6 49.7 1.0 C37 E:CNC601 4.8 51.0 1.0 C46 E:CNC601 4.8 51.2 1.0 C41 E:CNC601 4.9 51.9 1.0 C35 E:CNC601 4.9 50.2 1.0 C48 E:CNC601 5.0 52.4 1.0 C54 E:CNC601 5.0 50.7 1.0 C53 E:CNC601 5.0 51.0 1.0

D.Sussman, C.Wilson. A Water Channel in the Core of the Vitamin B(12) Rna Aptamer. Structure Fold.Des. V. 8 719 2000.
ISSN: ISSN 0969-2126
PubMed: 10903943
DOI: 10.1016/S0969-2126(00)00159-3