Cobalt in PDB 5d08: Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase

All present enzymatic activity of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase:
1.17.99.6;

The structure of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase, PDB code: 5d08 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)	46.41 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.301, 95.780, 111.175, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.6

The structure of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase (pdb code 5d08). 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 Selenomethionine-Labeled Epoxyqueuosine Reductase, PDB code: 5d08:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:15.2 occ:1.00 CO A:B12503 0.0 15.2 1.0 N21 A:B12503 1.9 11.5 1.0 N24 A:B12503 1.9 15.2 1.0 N23 A:B12503 1.9 14.4 1.0 N22 A:B12503 1.9 14.7 1.0 O A:HOH770 2.6 22.9 1.0 C1 A:B12503 2.8 13.0 1.0 C19 A:B12503 2.9 12.3 1.0 C9 A:B12503 2.9 13.8 1.0 C4 A:B12503 2.9 12.2 1.0 C11 A:B12503 2.9 13.3 1.0 C14 A:B12503 2.9 15.7 1.0 C16 A:B12503 3.0 13.1 1.0 C6 A:B12503 3.0 15.4 1.0 C10 A:B12503 3.3 13.7 1.0 C20 A:B12503 3.3 13.4 1.0 C5 A:B12503 3.3 13.9 1.0 C15 A:B12503 3.4 14.1 1.0 C18 A:B12503 4.1 11.7 1.0 C2 A:B12503 4.1 15.0 1.0 O A:HOH800 4.2 18.6 1.0 C3 A:B12503 4.2 9.6 1.0 C8 A:B12503 4.2 12.7 1.0 C13 A:B12503 4.2 14.2 1.0 C12 A:B12503 4.2 14.4 1.0 C7 A:B12503 4.2 12.2 1.0 C17 A:B12503 4.3 13.0 1.0 C49 A:B12503 4.3 16.7 1.0 O2 A:GOL504 4.3 18.7 1.0 O A:HOH889 4.6 28.6 1.0 C26 A:B12503 4.7 18.2 1.0 C35 A:B12503 4.8 15.9 1.0 C41 A:B12503 4.8 14.2 1.0 C37 A:B12503 4.8 13.5 1.0 C48 A:B12503 4.8 14.2 1.0 C46 A:B12503 4.9 17.5 1.0 C53 A:B12503 4.9 12.8 1.0 C30 A:B12503 4.9 11.6 1.0 C2 A:GOL504 5.0 16.9 1.0 NH2 A:ARG141 5.0 15.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:15.9 occ:1.00 CO B:B12503 0.0 15.9 1.0 N21 B:B12503 1.9 13.5 1.0 N24 B:B12503 1.9 12.9 1.0 N23 B:B12503 1.9 13.6 1.0 N22 B:B12503 1.9 15.7 1.0 O B:HOH659 2.7 23.2 1.0 C1 B:B12503 2.8 11.5 1.0 C19 B:B12503 2.8 11.5 1.0 C9 B:B12503 2.9 15.2 1.0 C4 B:B12503 2.9 15.1 1.0 C11 B:B12503 2.9 13.5 1.0 C14 B:B12503 2.9 14.7 1.0 C6 B:B12503 3.0 13.5 1.0 C16 B:B12503 3.0 15.2 1.0 C10 B:B12503 3.3 15.3 1.0 C20 B:B12503 3.3 15.8 1.0 C5 B:B12503 3.3 14.2 1.0 C15 B:B12503 3.4 14.7 1.0 C18 B:B12503 4.1 13.7 1.0 O B:HOH806 4.1 20.3 1.0 C2 B:B12503 4.1 12.0 1.0 C3 B:B12503 4.2 11.8 1.0 C8 B:B12503 4.2 16.8 1.0 C13 B:B12503 4.2 14.1 1.0 C12 B:B12503 4.2 13.2 1.0 C7 B:B12503 4.2 13.9 1.0 C17 B:B12503 4.3 13.1 1.0 O2 B:GOL504 4.3 19.4 1.0 C49 B:B12503 4.3 17.3 1.0 O B:HOH869 4.5 24.5 1.0 C26 B:B12503 4.7 14.7 1.0 C35 B:B12503 4.8 15.4 1.0 C41 B:B12503 4.8 16.5 1.0 C37 B:B12503 4.8 15.1 1.0 C48 B:B12503 4.9 14.7 1.0 C46 B:B12503 4.9 15.5 1.0 NH2 B:ARG141 4.9 15.6 1.0 C53 B:B12503 4.9 13.8 1.0 C2 B:GOL504 4.9 21.6 1.0 C30 B:B12503 5.0 14.8 1.0 C3 B:GOL504 5.0 22.3 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