Cobalt in PDB 8jbs: B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State

The structure of B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State, PDB code: 8jbs was solved by S.Zhang, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.44 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.218, 125.218, 73.088, 90, 90, 120
R / Rfree (%)	18.5 / 23.6

The binding sites of Cobalt atom in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State (pdb code 8jbs). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State, PDB code: 8jbs:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:44.7 occ:1.00 CO A:B12301 0.0 44.7 1.0 N21 A:B12301 1.8 47.2 1.0 N22 A:B12301 1.9 39.8 1.0 N23 A:B12301 1.9 40.3 1.0 N24 A:B12301 1.9 43.5 1.0 C5' A:5AD302 2.2 42.6 1.0 NE2 A:HIS122 2.3 51.4 1.0 C19 A:B12301 2.7 41.6 1.0 C4 A:B12301 2.8 43.7 1.0 C1 A:B12301 2.8 47.3 1.0 C9 A:B12301 2.8 39.1 1.0 C14 A:B12301 2.9 39.2 1.0 C11 A:B12301 2.9 38.1 1.0 C6 A:B12301 2.9 44.3 1.0 C16 A:B12301 2.9 39.7 1.0 C4' A:5AD302 3.1 51.9 1.0 C10 A:B12301 3.2 38.7 1.0 CE1 A:HIS122 3.2 45.9 1.0 C5 A:B12301 3.3 42.4 1.0 C15 A:B12301 3.3 39.2 1.0 CD2 A:HIS122 3.3 55.4 1.0 O4' A:5AD302 3.6 49.9 1.0 C20 A:B12301 3.6 44.5 1.0 C2 A:B12301 4.0 51.2 1.0 C3 A:B12301 4.0 50.5 1.0 C18 A:B12301 4.1 44.0 1.0 C8 A:B12301 4.1 45.0 1.0 C17 A:B12301 4.2 42.5 1.0 C7 A:B12301 4.2 49.8 1.0 C13 A:B12301 4.2 37.4 1.0 C12 A:B12301 4.2 39.5 1.0 ND1 A:HIS122 4.4 48.8 1.0 C26 A:B12301 4.4 47.5 1.0 CG A:HIS122 4.4 47.4 1.0 C3' A:5AD302 4.5 54.5 1.0 C35 A:B12301 4.7 41.0 1.0 C37 A:B12301 4.8 43.9 1.0 C54 A:B12301 4.8 46.8 1.0 C53 A:B12301 4.8 42.2 1.0 C1' A:5AD302 4.9 50.2 1.0 O3' A:5AD302 4.9 57.5 1.0 C41 A:B12301 4.9 43.1 1.0

Cobalt binding site 2 out of 2 in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Dark State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, 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 1.8 46.8 1.0 N23 B:B12301 1.9 40.9 1.0 N24 B:B12301 1.9 39.8 1.0 N22 B:B12301 1.9 39.3 1.0 C5' B:5AD302 2.1 53.1 1.0 NE2 B:HIS122 2.3 42.4 1.0 C19 B:B12301 2.7 40.5 1.0 C4 B:B12301 2.8 47.9 1.0 C14 B:B12301 2.8 38.9 1.0 C1 B:B12301 2.8 47.7 1.0 C9 B:B12301 2.9 39.3 1.0 C16 B:B12301 2.9 41.4 1.0 C11 B:B12301 2.9 38.0 1.0 C6 B:B12301 2.9 45.0 1.0 C4' B:5AD302 3.2 47.8 1.0 CD2 B:HIS122 3.2 44.8 1.0 C15 B:B12301 3.2 38.7 1.0 CE1 B:HIS122 3.2 42.9 1.0 C10 B:B12301 3.3 37.5 1.0 C5 B:B12301 3.3 47.3 1.0 C20 B:B12301 3.6 49.0 1.0 O4' B:5AD302 3.7 42.2 1.0 C18 B:B12301 4.0 48.9 1.0 C2 B:B12301 4.0 51.0 1.0 C3 B:B12301 4.1 51.9 1.0 C17 B:B12301 4.1 45.8 1.0 C8 B:B12301 4.2 40.4 1.0 C7 B:B12301 4.2 44.2 1.0 C13 B:B12301 4.2 41.3 1.0 C12 B:B12301 4.2 37.5 1.0 ND1 B:HIS122 4.4 43.9 1.0 CG B:HIS122 4.4 46.4 1.0 C26 B:B12301 4.5 52.9 1.0 C3' B:5AD302 4.5 50.2 1.0 C37 B:B12301 4.7 44.5 1.0 C53 B:B12301 4.7 42.0 1.0 C35 B:B12301 4.7 41.9 1.0 C54 B:B12301 4.8 44.9 1.0 C41 B:B12301 4.9 42.2 1.0 O3' B:5AD302 5.0 45.5 1.0

Y.Yu, L.N.Jeffreys, H.Poddar, A.Hill, L.Johannissen, F.Dai, M.Sakuma, D.Leys, D.J.Heyes, S.Zhang, N.S.Scrutton. Signaturefinder Enables Sequence Mining to Identify Cobalamin-Dependent Photoreceptor Proteins To Be Published.