Cobalt in PDB 5c8a: Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)

The structure of Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State), PDB code: 5c8a was solved by M.Jost, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.96 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.430, 99.680, 143.990, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.7

The binding sites of Cobalt atom in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) (pdb code 5c8a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State), PDB code: 5c8a:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co300 b:37.9 occ:1.00 CO A:B12300 0.0 37.9 1.0 N21 A:B12300 1.9 41.6 1.0 N24 A:B12300 1.9 37.2 1.0 N22 A:B12300 1.9 38.8 1.0 N23 A:B12300 1.9 39.9 1.0 C5' A:5AD301 2.0 42.4 1.0 NE2 A:HIS177 2.2 36.7 1.0 C19 A:B12300 2.9 39.0 1.0 C9 A:B12300 2.9 38.8 1.0 C1 A:B12300 2.9 39.1 1.0 C4 A:B12300 2.9 41.3 1.0 C11 A:B12300 2.9 39.4 1.0 C6 A:B12300 3.0 40.2 1.0 C16 A:B12300 3.0 35.7 1.0 C14 A:B12300 3.0 38.1 1.0 C4' A:5AD301 3.1 44.0 1.0 CD2 A:HIS177 3.2 38.5 1.0 CE1 A:HIS177 3.2 37.3 1.0 C10 A:B12300 3.3 39.9 1.0 C5 A:B12300 3.3 40.8 1.0 C15 A:B12300 3.4 35.1 1.0 C20 A:B12300 3.5 37.8 1.0 O4' A:5AD301 3.6 43.9 1.0 C18 A:B12300 4.1 37.8 1.0 C2 A:B12300 4.1 39.9 1.0 C3 A:B12300 4.2 43.4 1.0 C8 A:B12300 4.2 40.2 1.0 C7 A:B12300 4.2 41.3 1.0 C17 A:B12300 4.2 39.2 1.0 C12 A:B12300 4.2 39.1 1.0 C13 A:B12300 4.3 37.3 1.0 CG A:HIS177 4.3 37.5 1.0 ND1 A:HIS177 4.3 36.7 1.0 C3' A:5AD301 4.5 46.2 1.0 C26 A:B12300 4.6 43.9 1.0 C37 A:B12300 4.7 41.8 1.0 C35 A:B12300 4.8 42.5 1.0 C41 A:B12300 4.9 40.2 1.0 C53 A:B12300 4.9 36.1 1.0 O3' A:5AD301 5.0 47.8 1.0 C1' A:5AD301 5.0 43.1 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:43.1 occ:1.00 CO B:B12301 0.0 43.1 1.0 N21 B:B12301 1.9 48.8 1.0 N24 B:B12301 1.9 45.4 1.0 N22 B:B12301 1.9 43.0 1.0 N23 B:B12301 1.9 41.3 1.0 C5' B:5AD302 2.0 53.1 1.0 NE2 B:HIS177 2.2 46.1 1.0 C19 B:B12301 2.8 46.1 1.0 C9 B:B12301 2.8 43.8 1.0 C4 B:B12301 2.9 49.6 1.0 C1 B:B12301 2.9 49.0 1.0 C11 B:B12301 2.9 41.0 1.0 C6 B:B12301 3.0 46.4 1.0 C16 B:B12301 3.0 41.6 1.0 C14 B:B12301 3.0 40.4 1.0 CD2 B:HIS177 3.1 45.1 1.0 C4' B:5AD302 3.1 52.8 1.0 C10 B:B12301 3.2 41.7 1.0 C5 B:B12301 3.3 47.8 1.0 CE1 B:HIS177 3.3 44.5 1.0 C15 B:B12301 3.4 40.6 1.0 C20 B:B12301 3.5 47.8 1.0 O4' B:5AD302 3.6 54.0 1.0 C18 B:B12301 4.1 44.9 1.0 C2 B:B12301 4.1 46.0 1.0 C3 B:B12301 4.2 53.4 1.0 C8 B:B12301 4.2 44.3 1.0 C7 B:B12301 4.2 48.0 1.0 C17 B:B12301 4.2 44.7 1.0 C12 B:B12301 4.2 48.3 1.0 CG B:HIS177 4.3 43.9 1.0 C13 B:B12301 4.3 39.7 1.0 ND1 B:HIS177 4.4 44.1 1.0 C3' B:5AD302 4.5 55.4 1.0 C26 B:B12301 4.6 47.5 1.0 C35 B:B12301 4.7 48.2 1.0 C37 B:B12301 4.8 50.3 1.0 C41 B:B12301 4.9 45.3 1.0 C53 B:B12301 4.9 44.9 1.0 C1' B:5AD302 5.0 52.9 1.0 O3' B:5AD302 5.0 57.0 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co300 b:40.5 occ:1.00 CO C:B12300 0.0 40.5 1.0 N21 C:B12300 1.9 38.3 1.0 N24 C:B12300 1.9 41.1 1.0 N23 C:B12300 1.9 35.7 1.0 N22 C:B12300 1.9 44.2 1.0 C5' C:5AD301 2.0 45.4 1.0 NE2 C:HIS177 2.3 38.6 1.0 C19 C:B12300 2.8 41.5 1.0 C4 C:B12300 2.9 39.5 1.0 C9 C:B12300 2.9 37.2 1.0 C1 C:B12300 2.9 38.5 1.0 C11 C:B12300 2.9 38.8 1.0 C6 C:B12300 2.9 43.5 1.0 C14 C:B12300 3.0 35.0 1.0 C16 C:B12300 3.0 36.0 1.0 C4' C:5AD301 3.2 44.1 1.0 CD2 C:HIS177 3.2 39.3 1.0 C10 C:B12300 3.3 36.4 1.0 C5 C:B12300 3.3 39.9 1.0 CE1 C:HIS177 3.3 38.7 1.0 C15 C:B12300 3.4 35.1 1.0 C20 C:B12300 3.6 37.8 1.0 O4' C:5AD301 3.6 44.1 1.0 C18 C:B12300 4.1 41.1 1.0 C2 C:B12300 4.1 40.3 1.0 C3 C:B12300 4.2 44.9 1.0 C7 C:B12300 4.2 42.8 1.0 C8 C:B12300 4.2 38.1 1.0 C12 C:B12300 4.2 38.2 1.0 C17 C:B12300 4.2 42.5 1.0 C13 C:B12300 4.3 34.4 1.0 CG C:HIS177 4.4 39.1 1.0 ND1 C:HIS177 4.4 35.2 1.0 C3' C:5AD301 4.5 46.9 1.0 C26 C:B12300 4.6 41.1 1.0 C37 C:B12300 4.7 40.2 1.0 C35 C:B12300 4.7 41.6 1.0 C53 C:B12300 4.9 34.4 1.0 C41 C:B12300 4.9 37.7 1.0 C46 C:B12300 5.0 39.9 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of A Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Truncated Form of Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co300 b:39.0 occ:1.00 CO D:B12300 0.0 39.0 1.0 N21 D:B12300 1.9 37.4 1.0 N24 D:B12300 1.9 37.3 1.0 N22 D:B12300 1.9 37.3 1.0 N23 D:B12300 1.9 35.4 1.0 C5' D:5AD301 2.0 38.3 1.0 NE2 D:HIS177 2.3 41.7 1.0 C9 D:B12300 2.8 37.1 1.0 C19 D:B12300 2.8 38.8 1.0 C4 D:B12300 2.9 41.7 1.0 C1 D:B12300 2.9 37.4 1.0 C11 D:B12300 2.9 36.2 1.0 C6 D:B12300 3.0 38.5 1.0 C16 D:B12300 3.0 35.1 1.0 C14 D:B12300 3.0 34.6 1.0 C4' D:5AD301 3.1 38.3 1.0 CD2 D:HIS177 3.2 38.9 1.0 C10 D:B12300 3.2 36.4 1.0 C5 D:B12300 3.3 43.2 1.0 CE1 D:HIS177 3.4 41.3 1.0 C15 D:B12300 3.4 34.5 1.0 C20 D:B12300 3.5 41.1 1.0 O4' D:5AD301 3.6 39.6 1.0 C18 D:B12300 4.1 38.6 1.0 C2 D:B12300 4.1 46.6 1.0 C3 D:B12300 4.2 43.0 1.0 C8 D:B12300 4.2 38.1 1.0 C7 D:B12300 4.2 39.3 1.0 C17 D:B12300 4.2 38.8 1.0 C12 D:B12300 4.2 35.7 1.0 C13 D:B12300 4.3 34.3 1.0 CG D:HIS177 4.4 37.6 1.0 ND1 D:HIS177 4.4 38.4 1.0 C3' D:5AD301 4.5 41.0 1.0 C26 D:B12300 4.6 43.3 1.0 C35 D:B12300 4.8 47.3 1.0 C37 D:B12300 4.8 40.2 1.0 C41 D:B12300 4.8 37.7 1.0 C53 D:B12300 4.9 34.3 1.0 C1' D:5AD301 5.0 41.2 1.0

M.Jost, J.Fernandez-Zapata, M.C.Polanco, J.M.Ortiz-Guerrero, P.Y.Chen, G.Kang, S.Padmanabhan, M.Elias-Arnanz, C.L.Drennan. Structural Basis For Gene Regulation By A B12-Dependent Photoreceptor. Nature V. 526 536 2015.
ISSN: ESSN 1476-4687
PubMed: 26416754
DOI: 10.1038/NATURE14950