Cobalt in PDB 8jbt: B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Anaerobic Light State

The structure of B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Anaerobic Light State, PDB code: 8jbt 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)	106.94 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.485, 123.485, 73.105, 90, 90, 120
R / Rfree (%)	20.6 / 22.5

The binding sites of Cobalt atom in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Anaerobic Light State (pdb code 8jbt). 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, Anaerobic Light State, PDB code: 8jbt:
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, Anaerobic Light 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, Anaerobic Light State within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:33.6 occ:1.00 CO A:B12301 0.0 33.6 1.0 N24 A:B12301 1.8 31.1 1.0 N21 A:B12301 1.8 32.6 1.0 N23 A:B12301 1.9 33.8 1.0 N22 A:B12301 1.9 34.3 1.0 O A:HOH401 2.2 35.8 1.0 NE2 A:HIS122 2.2 29.2 1.0 C19 A:B12301 2.8 31.9 1.0 C1 A:B12301 2.8 32.3 1.0 C16 A:B12301 2.9 33.6 1.0 C4 A:B12301 2.9 32.1 1.0 C9 A:B12301 2.9 34.8 1.0 C11 A:B12301 2.9 32.4 1.0 C6 A:B12301 2.9 36.9 1.0 C14 A:B12301 3.0 30.2 1.0 CD2 A:HIS122 3.2 32.7 1.0 CE1 A:HIS122 3.2 30.4 1.0 C10 A:B12301 3.3 31.6 1.0 C5 A:B12301 3.3 35.7 1.0 C15 A:B12301 3.3 33.6 1.0 C20 A:B12301 3.5 33.7 1.0 OE1 A:GLU84 3.9 47.2 1.0 C18 A:B12301 4.0 34.3 1.0 C2 A:B12301 4.1 34.9 1.0 C17 A:B12301 4.1 36.4 1.0 C3 A:B12301 4.1 34.5 1.0 C7 A:B12301 4.2 37.7 1.0 C8 A:B12301 4.2 37.7 1.0 C12 A:B12301 4.2 32.4 1.0 C13 A:B12301 4.3 33.1 1.0 CG A:HIS122 4.4 33.6 1.0 ND1 A:HIS122 4.4 32.7 1.0 C26 A:B12301 4.6 34.8 1.0 C37 A:B12301 4.7 37.5 1.0 C35 A:B12301 4.8 32.1 1.0 CD A:GLU84 4.8 46.0 1.0 C53 A:B12301 4.8 31.8 1.0 OE2 A:GLU84 5.0 44.5 1.0 C41 A:B12301 5.0 37.8 1.0 C46 A:B12301 5.0 32.3 1.0 C55 A:B12301 5.0 42.6 1.0

Cobalt binding site 2 out of 2 in the B12-Binding Domain From Chloracidobacterium Thermophilum Merr Family Protein, Anaerobic Light 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, Anaerobic Light State within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:34.9 occ:1.00 CO B:B12302 0.0 34.9 1.0 N21 B:B12302 1.9 33.8 1.0 N24 B:B12302 1.9 34.4 1.0 N23 B:B12302 1.9 35.0 1.0 N22 B:B12302 1.9 35.8 1.0 NE2 B:HIS122 2.2 35.6 1.0 O B:HOH404 2.3 39.0 1.0 C19 B:B12302 2.8 37.8 1.0 C1 B:B12302 2.8 34.5 1.0 C9 B:B12302 2.9 38.0 1.0 C11 B:B12302 2.9 33.9 1.0 C4 B:B12302 2.9 35.7 1.0 C14 B:B12302 2.9 34.0 1.0 C6 B:B12302 3.0 35.0 1.0 C16 B:B12302 3.0 35.0 1.0 CD2 B:HIS122 3.2 39.7 1.0 C10 B:B12302 3.2 32.0 1.0 CE1 B:HIS122 3.3 40.6 1.0 C5 B:B12302 3.3 38.3 1.0 C15 B:B12302 3.4 34.7 1.0 C20 B:B12302 3.5 33.7 1.0 OE1 B:GLU84 3.8 53.7 1.0 C18 B:B12302 4.1 35.4 1.0 C2 B:B12302 4.1 37.3 1.0 C3 B:B12302 4.2 37.6 1.0 C12 B:B12302 4.2 37.2 1.0 C17 B:B12302 4.2 35.5 1.0 C13 B:B12302 4.2 37.3 1.0 C8 B:B12302 4.2 36.3 1.0 C7 B:B12302 4.2 36.3 1.0 CG B:HIS122 4.4 34.1 1.0 ND1 B:HIS122 4.4 35.2 1.0 C26 B:B12302 4.6 37.1 1.0 C37 B:B12302 4.7 37.8 1.0 CD B:GLU84 4.8 50.5 1.0 C35 B:B12302 4.8 28.5 1.0 C53 B:B12302 4.9 29.0 1.0 C54 B:B12302 4.9 34.2 1.0 C41 B:B12302 4.9 35.9 1.0 C46 B:B12302 4.9 40.5 1.0 OE2 B:GLU84 4.9 43.7 1.0 C48 B:B12302 5.0 37.0 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.