Cobalt in PDB 5d0b: Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop

All present enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop:
1.17.99.6;

The structure of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop, PDB code: 5d0b was solved by D.P.Dowling, Z.D.Miles, C.Kohrer, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.05 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.644, 110.754, 99.223, 90.00, 95.16, 90.00
R / Rfree (%)	19.2 / 22.1

The structure of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Cobalt atom in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop (pdb code 5d0b). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop, PDB code: 5d0b:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:20.1 occ:1.00 CO A:B12503 0.0 20.1 1.0 N21 A:B12503 1.9 21.1 1.0 N24 A:B12503 1.9 24.8 1.0 N23 A:B12503 1.9 21.3 1.0 N22 A:B12503 1.9 20.7 1.0 C19 A:B12503 2.8 23.0 1.0 C1 A:B12503 2.8 21.0 1.0 C9 A:B12503 2.9 20.1 1.0 C4 A:B12503 2.9 20.8 1.0 C11 A:B12503 2.9 21.3 1.0 C14 A:B12503 2.9 22.7 1.0 C6 A:B12503 3.0 18.8 1.0 C16 A:B12503 3.0 25.5 1.0 C10 A:B12503 3.3 19.8 1.0 C5 A:B12503 3.3 20.1 1.0 C20 A:B12503 3.3 20.9 1.0 C15 A:B12503 3.4 23.3 1.0 C13 F:56B34 4.0 30.4 1.0 C18 A:B12503 4.1 24.2 1.0 C2 A:B12503 4.1 21.9 1.0 C3 A:B12503 4.2 20.5 1.0 C8 A:B12503 4.2 19.1 1.0 C7 A:B12503 4.2 18.5 1.0 C12 A:B12503 4.2 23.4 1.0 C49 A:B12503 4.2 23.0 1.0 C13 A:B12503 4.2 23.0 1.0 C17 A:B12503 4.3 25.0 1.0 O12 F:56B34 4.4 30.3 1.0 C14 F:56B34 4.6 29.8 1.0 NH2 A:ARG141 4.7 21.4 1.0 C26 A:B12503 4.7 21.4 1.0 C35 A:B12503 4.7 20.9 1.0 C12 F:56B34 4.8 32.5 1.0 C37 A:B12503 4.8 18.6 1.0 C48 A:B12503 4.9 21.1 1.0 C41 A:B12503 4.9 18.3 1.0 C53 A:B12503 4.9 23.5 1.0 C46 A:B12503 4.9 23.4 1.0 C30 A:B12503 4.9 21.7 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:21.5 occ:1.00 CO B:B12503 0.0 21.5 1.0 N21 B:B12503 1.9 22.1 1.0 N24 B:B12503 1.9 22.1 1.0 N23 B:B12503 1.9 20.1 1.0 N22 B:B12503 1.9 20.9 1.0 C19 B:B12503 2.8 22.8 1.0 C1 B:B12503 2.8 22.7 1.0 C9 B:B12503 2.9 20.1 1.0 C4 B:B12503 2.9 22.3 1.0 C11 B:B12503 2.9 22.0 1.0 C14 B:B12503 2.9 21.4 1.0 C6 B:B12503 2.9 20.6 1.0 C16 B:B12503 3.0 24.0 1.0 O B:HOH625 3.2 23.5 1.0 C10 B:B12503 3.3 21.0 1.0 C5 B:B12503 3.3 22.3 1.0 C20 B:B12503 3.4 22.3 1.0 C15 B:B12503 3.4 24.5 1.0 O B:HOH627 3.9 24.6 1.0 C18 B:B12503 4.1 23.1 1.0 C2 B:B12503 4.1 22.5 1.0 C49 B:B12503 4.2 23.3 1.0 C3 B:B12503 4.2 20.6 1.0 C8 B:B12503 4.2 19.7 1.0 C7 B:B12503 4.2 20.8 1.0 C12 B:B12503 4.2 22.6 1.0 C13 B:B12503 4.2 21.2 1.0 C17 B:B12503 4.3 23.1 1.0 C26 B:B12503 4.7 24.1 1.0 C35 B:B12503 4.7 21.2 1.0 NH2 B:ARG141 4.7 21.9 1.0 C37 B:B12503 4.8 21.0 1.0 C48 B:B12503 4.8 21.6 1.0 C46 B:B12503 4.9 23.0 1.0 C53 B:B12503 4.9 26.3 1.0 C41 B:B12503 4.9 19.5 1.0 C30 B:B12503 5.0 21.8 1.0

D.P.Dowling, Z.D.Miles, C.Kohrer, S.J.Maiocco, S.J.Elliott, V.Bandarian, C.L.Drennan. Molecular Basis of Cobalamin-Dependent Rna Modification. Nucleic Acids Res. V. 44 9965 2016.
ISSN: ESSN 1362-4962
PubMed: 27638883
DOI: 10.1093/NAR/GKW806