Cobalt in PDB 5d6s: Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.

The structure of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus., PDB code: 5d6s was solved by K.A.P.Payne, K.Fisher, M.S.Dunstan, H.Sjuts, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.58 / 2.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.120, 106.120, 332.280, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.3

The structure of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. also contains other interesting chemical elements:

Iron

(Fe)

40 atoms

The binding sites of Cobalt atom in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. (pdb code 5d6s). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus., PDB code: 5d6s:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:51.0 occ:1.00 CO A:B12403 0.0 51.0 1.0 N21 A:B12403 1.9 52.9 1.0 N24 A:B12403 1.9 44.0 1.0 N22 A:B12403 1.9 48.4 1.0 N23 A:B12403 1.9 50.2 1.0 O A:HOH518 2.6 61.3 1.0 C9 A:B12403 2.8 48.8 1.0 C19 A:B12403 2.8 49.0 1.0 C4 A:B12403 2.8 58.0 1.0 C11 A:B12403 2.9 47.2 1.0 C1 A:B12403 2.9 49.5 1.0 C14 A:B12403 2.9 51.7 1.0 C6 A:B12403 2.9 47.4 1.0 C16 A:B12403 3.0 51.2 1.0 C10 A:B12403 3.2 45.6 1.0 C5 A:B12403 3.3 52.1 1.0 C15 A:B12403 3.4 52.0 1.0 C20 A:B12403 3.5 49.1 1.0 C18 A:B12403 4.1 48.2 1.0 C3 A:B12403 4.1 59.4 1.0 C2 A:B12403 4.2 54.0 1.0 C8 A:B12403 4.2 48.1 1.0 C12 A:B12403 4.2 53.3 1.0 C7 A:B12403 4.2 47.0 1.0 C13 A:B12403 4.2 56.4 1.0 C17 A:B12403 4.2 48.6 1.0 C49 A:B12403 4.4 66.4 1.0 C26 A:B12403 4.7 55.2 1.0 C35 A:B12403 4.7 49.8 1.0 C37 A:B12403 4.8 47.5 1.0 C46 A:B12403 4.9 58.5 1.0 C53 A:B12403 4.9 49.8 1.0 C48 A:B12403 4.9 58.2 1.0 C30 A:B12403 4.9 61.2 1.0 C41 A:B12403 5.0 49.0 1.0

Cobalt binding site 2 out of 5 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co403 b:47.4 occ:1.00 CO B:B12403 0.0 47.4 1.0 N21 B:B12403 1.9 42.7 1.0 N24 B:B12403 1.9 39.4 1.0 N22 B:B12403 1.9 40.2 1.0 N23 B:B12403 1.9 38.9 1.0 C9 B:B12403 2.8 40.9 1.0 C19 B:B12403 2.8 43.6 1.0 C1 B:B12403 2.8 46.8 1.0 C11 B:B12403 2.9 39.4 1.0 C4 B:B12403 2.9 43.9 1.0 C14 B:B12403 2.9 41.4 1.0 C6 B:B12403 2.9 39.8 1.0 C16 B:B12403 3.0 39.0 1.0 C10 B:B12403 3.2 37.8 1.0 C5 B:B12403 3.3 39.5 1.0 C15 B:B12403 3.3 41.0 1.0 C20 B:B12403 3.3 43.0 1.0 C18 B:B12403 4.1 44.8 1.0 C2 B:B12403 4.1 47.9 1.0 C8 B:B12403 4.1 43.9 1.0 C7 B:B12403 4.1 44.5 1.0 C3 B:B12403 4.2 47.8 1.0 C12 B:B12403 4.2 43.6 1.0 C13 B:B12403 4.2 45.5 1.0 C17 B:B12403 4.2 42.5 1.0 C49 B:B12403 4.5 60.0 1.0 C26 B:B12403 4.6 51.0 1.0 C37 B:B12403 4.7 40.2 1.0 C35 B:B12403 4.8 45.0 1.0 C53 B:B12403 4.8 41.4 1.0 C41 B:B12403 4.9 44.3 1.0 C46 B:B12403 4.9 43.9 1.0 C48 B:B12403 4.9 52.1 1.0 C30 B:B12403 5.0 52.8 1.0

Cobalt binding site 3 out of 5 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co403 b:65.4 occ:1.00 CO C:B12403 0.0 65.4 1.0 N21 C:B12403 1.9 65.7 1.0 N24 C:B12403 1.9 64.8 1.0 N23 C:B12403 1.9 53.5 1.0 N22 C:B12403 1.9 67.4 1.0 C1 C:B12403 2.8 64.2 1.0 C11 C:B12403 2.8 57.9 1.0 C9 C:B12403 2.8 64.4 1.0 C19 C:B12403 2.8 66.8 1.0 C4 C:B12403 2.9 71.5 1.0 C14 C:B12403 2.9 55.2 1.0 C6 C:B12403 2.9 69.7 1.0 C16 C:B12403 2.9 67.2 1.0 C10 C:B12403 3.2 62.8 1.0 C20 C:B12403 3.2 58.4 1.0 C5 C:B12403 3.3 65.0 1.0 C15 C:B12403 3.4 57.0 1.0 C18 C:B12403 4.1 67.7 1.0 C12 C:B12403 4.1 54.4 1.0 C2 C:B12403 4.1 66.5 1.0 C8 C:B12403 4.2 70.6 1.0 C3 C:B12403 4.2 71.7 1.0 C7 C:B12403 4.2 75.2 1.0 C13 C:B12403 4.2 55.4 1.0 C17 C:B12403 4.2 63.0 1.0 C49 C:B12403 4.7 71.3 1.0 C46 C:B12403 4.7 56.6 1.0 C26 C:B12403 4.7 64.8 1.0 C37 C:B12403 4.8 73.8 1.0 C41 C:B12403 4.8 66.0 1.0 C35 C:B12403 4.8 60.4 1.0 C53 C:B12403 4.8 54.6 1.0

Cobalt binding site 4 out of 5 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ D:Co403 b:55.9 occ:1.00 CO D:B12403 0.0 55.9 1.0 N21 D:B12403 1.9 57.5 1.0 N24 D:B12403 1.9 48.5 1.0 N23 D:B12403 1.9 51.5 1.0 N22 D:B12403 1.9 55.5 1.0 C9 D:B12403 2.8 59.6 1.0 C19 D:B12403 2.8 54.1 1.0 C4 D:B12403 2.9 59.9 1.0 C1 D:B12403 2.9 54.9 1.0 C11 D:B12403 2.9 50.8 1.0 C14 D:B12403 2.9 50.9 1.0 C6 D:B12403 2.9 57.2 1.0 C16 D:B12403 2.9 55.6 1.0 C10 D:B12403 3.2 57.0 1.0 C5 D:B12403 3.3 58.8 1.0 C15 D:B12403 3.3 53.0 1.0 C20 D:B12403 3.5 53.2 1.0 C2 D:B12403 4.1 57.4 1.0 C18 D:B12403 4.1 54.0 1.0 C3 D:B12403 4.2 61.9 1.0 C8 D:B12403 4.2 56.5 1.0 C12 D:B12403 4.2 53.7 1.0 C7 D:B12403 4.2 57.3 1.0 C13 D:B12403 4.2 49.6 1.0 C17 D:B12403 4.2 54.2 1.0 O D:HOH514 4.5 55.5 1.0 C26 D:B12403 4.5 51.6 1.0 C49 D:B12403 4.6 59.1 1.0 C35 D:B12403 4.7 58.0 1.0 C37 D:B12403 4.8 61.5 1.0 C53 D:B12403 4.8 52.1 1.0 C46 D:B12403 4.9 59.9 1.0 C41 D:B12403 4.9 61.5 1.0 C48 D:B12403 5.0 53.6 1.0

Cobalt binding site 5 out of 5 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ E:Co403 b:72.7 occ:1.00 CO E:B12403 0.0 72.7 1.0 O E:HOH507 1.8 54.5 1.0 N21 E:B12403 1.9 82.6 1.0 N24 E:B12403 1.9 71.3 1.0 N23 E:B12403 1.9 69.8 1.0 N22 E:B12403 1.9 73.8 1.0 C9 E:B12403 2.8 78.3 1.0 C11 E:B12403 2.8 68.8 1.0 C1 E:B12403 2.9 75.6 1.0 C19 E:B12403 2.9 74.6 1.0 C4 E:B12403 2.9 80.2 1.0 C6 E:B12403 2.9 76.4 1.0 C14 E:B12403 2.9 63.3 1.0 C16 E:B12403 3.0 68.6 1.0 C10 E:B12403 3.2 75.1 1.0 C5 E:B12403 3.3 79.5 1.0 C20 E:B12403 3.3 71.5 1.0 C15 E:B12403 3.4 64.9 1.0 C12 E:B12403 4.1 61.8 1.0 C18 E:B12403 4.1 68.5 1.0 C8 E:B12403 4.1 72.5 1.0 C2 E:B12403 4.2 77.7 1.0 C3 E:B12403 4.2 81.8 1.0 C7 E:B12403 4.2 71.1 1.0 C13 E:B12403 4.2 60.4 1.0 C17 E:B12403 4.3 65.2 1.0 C49 E:B12403 4.5 66.6 1.0 C46 E:B12403 4.7 62.8 1.0 C26 E:B12403 4.7 73.9 1.0 C35 E:B12403 4.7 81.2 1.0 C37 E:B12403 4.8 73.7 1.0 C41 E:B12403 4.8 68.0 1.0 C53 E:B12403 4.9 63.5 1.0 C48 E:B12403 4.9 59.5 1.0

K.A.Payne, K.Fisher, H.Sjuts, M.S.Dunstan, B.Bellina, L.Johannissen, P.Barran, S.Hay, S.E.Rigby, D.Leys. Epoxyqueuosine Reductase Structure Suggests A Mechanism For Cobalamin-Dependent Trna Modification. J.Biol.Chem. V. 290 27572 2015.
ISSN: ESSN 1083-351X
PubMed: 26378237
DOI: 10.1074/JBC.M115.685693