Cobalt in PDB 8c31: Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition

The structure of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition, PDB code: 8c31 was solved by H.Poddar, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.18 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.114, 69.705, 204.544, 90, 90, 90
R / Rfree (%)	17 / 20.9

The structure of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Cobalt atom in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition (pdb code 8c31). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition, PDB code: 8c31:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:33.2 occ:1.00 CO A:B12302 0.0 33.2 1.0 N21 A:B12302 1.8 33.4 1.0 N23 A:B12302 1.9 31.6 1.0 N24 A:B12302 1.9 33.2 1.0 N22 A:B12302 1.9 34.5 1.0 C5' A:5AD303 2.0 31.8 1.0 NE2 A:HIS177 2.0 35.8 1.0 C19 A:B12302 2.8 33.6 1.0 C4 A:B12302 2.8 36.8 1.0 C1 A:B12302 2.9 34.8 1.0 C14 A:B12302 2.9 30.2 1.0 C11 A:B12302 2.9 33.5 1.0 C9 A:B12302 2.9 34.9 1.0 C6 A:B12302 2.9 34.6 1.0 C16 A:B12302 2.9 32.2 1.0 CD2 A:HIS177 3.0 35.6 1.0 C4' A:5AD303 3.1 33.3 1.0 CE1 A:HIS177 3.1 37.0 1.0 C5 A:B12302 3.3 35.9 1.0 C10 A:B12302 3.3 35.7 1.0 C15 A:B12302 3.3 29.6 1.0 O4' A:5AD303 3.5 32.1 1.0 C20 A:B12302 3.6 34.6 1.0 C3 A:B12302 4.1 38.8 1.0 C2 A:B12302 4.1 37.4 1.0 C18 A:B12302 4.1 31.5 1.0 C13 A:B12302 4.2 30.1 1.0 ND1 A:HIS177 4.2 39.2 1.0 C8 A:B12302 4.2 37.2 1.0 CG A:HIS177 4.2 39.2 1.0 C17 A:B12302 4.2 30.3 1.0 C7 A:B12302 4.2 36.3 1.0 C12 A:B12302 4.2 31.3 1.0 C3' A:5AD303 4.4 31.5 1.0 C26 A:B12302 4.6 33.9 1.0 C37 A:B12302 4.7 34.7 1.0 C35 A:B12302 4.8 37.6 1.0 C53 A:B12302 4.8 29.6 1.0 C1' A:5AD303 4.9 31.2 1.0 C54 A:B12302 4.9 30.8 1.0 C41 A:B12302 4.9 39.0 1.0 O3' A:5AD303 5.0 30.9 1.0

Cobalt binding site 2 out of 4 in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:46.1 occ:1.00 CO B:B12302 0.0 46.1 1.0 N21 B:B12302 1.8 48.3 1.0 N23 B:B12302 1.9 48.4 1.0 NE2 B:HIS177 2.0 40.8 1.0 N24 B:B12302 2.0 53.4 1.0 N22 B:B12302 2.0 46.9 1.0 C5' B:5AD303 2.1 48.0 1.0 C19 B:B12302 2.8 50.4 1.0 C4 B:B12302 2.8 49.9 1.0 C14 B:B12302 2.8 44.0 1.0 C1 B:B12302 2.8 48.5 1.0 C11 B:B12302 2.9 46.5 1.0 C9 B:B12302 2.9 45.4 1.0 C16 B:B12302 3.0 49.3 1.0 C6 B:B12302 3.0 48.5 1.0 CD2 B:HIS177 3.0 39.9 1.0 CE1 B:HIS177 3.0 43.5 1.0 C5 B:B12302 3.2 49.4 1.0 C4' B:5AD303 3.2 47.5 1.0 C15 B:B12302 3.3 46.7 1.0 C10 B:B12302 3.3 45.1 1.0 C20 B:B12302 3.7 45.3 1.0 O4' B:5AD303 3.7 46.8 1.0 C2 B:B12302 4.0 51.4 1.0 C3 B:B12302 4.1 53.0 1.0 C18 B:B12302 4.1 47.9 1.0 CG B:HIS177 4.1 38.5 1.0 ND1 B:HIS177 4.1 38.9 1.0 C13 B:B12302 4.1 43.7 1.0 C12 B:B12302 4.2 43.4 1.0 C17 B:B12302 4.2 50.7 1.0 C8 B:B12302 4.2 44.8 1.0 C7 B:B12302 4.2 46.3 1.0 C26 B:B12302 4.4 52.1 1.0 C3' B:5AD303 4.6 48.2 1.0 C35 B:B12302 4.7 53.4 1.0 C53 B:B12302 4.7 46.3 1.0 C37 B:B12302 4.9 49.5 1.0 C41 B:B12302 4.9 43.5 1.0 C54 B:B12302 5.0 52.3 1.0

Cobalt binding site 3 out of 4 in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ C:Co302 b:29.7 occ:1.00 CO C:B12302 0.0 29.7 1.0 N21 C:B12302 1.9 28.9 1.0 N23 C:B12302 1.9 27.9 1.0 N24 C:B12302 1.9 30.0 1.0 N22 C:B12302 1.9 29.6 1.0 C5' C:5AD303 2.0 31.1 1.0 NE2 C:HIS177 2.0 29.8 1.0 C19 C:B12302 2.8 31.3 1.0 C4 C:B12302 2.9 28.9 1.0 C9 C:B12302 2.9 28.7 1.0 C14 C:B12302 2.9 27.8 1.0 C1 C:B12302 2.9 31.3 1.0 C11 C:B12302 2.9 28.5 1.0 C16 C:B12302 3.0 28.6 1.0 C6 C:B12302 3.0 29.3 1.0 CE1 C:HIS177 3.0 30.1 1.0 CD2 C:HIS177 3.1 28.5 1.0 C4' C:5AD303 3.1 31.2 1.0 C10 C:B12302 3.3 30.2 1.0 C15 C:B12302 3.3 28.6 1.0 C5 C:B12302 3.4 29.1 1.0 C20 C:B12302 3.5 29.4 1.0 O4' C:5AD303 3.6 29.5 1.0 C18 C:B12302 4.1 30.4 1.0 C2 C:B12302 4.1 32.7 1.0 C3 C:B12302 4.1 33.2 1.0 C8 C:B12302 4.2 30.6 1.0 ND1 C:HIS177 4.2 28.9 1.0 C13 C:B12302 4.2 28.1 1.0 C17 C:B12302 4.2 30.2 1.0 CG C:HIS177 4.2 29.3 1.0 C7 C:B12302 4.2 30.6 1.0 C12 C:B12302 4.2 27.4 1.0 C3' C:5AD303 4.4 29.8 1.0 C26 C:B12302 4.6 33.8 1.0 C37 C:B12302 4.8 31.9 1.0 C41 C:B12302 4.8 28.8 1.0 C53 C:B12302 4.9 30.3 1.0 C35 C:B12302 4.9 32.9 1.0 C1' C:5AD303 4.9 30.4 1.0 C54 C:B12302 4.9 32.3 1.0 O3' C:5AD303 5.0 31.0 1.0

Cobalt binding site 4 out of 4 in the Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ D:Co702 b:32.6 occ:1.00 CO D:B12702 0.0 32.6 1.0 N21 D:B12702 1.9 36.6 1.0 N23 D:B12702 1.9 32.6 1.0 N24 D:B12702 1.9 35.2 1.0 N22 D:B12702 1.9 33.5 1.0 C5' D:5AD703 2.0 36.0 1.0 NE2 D:HIS177 2.0 30.5 1.0 C19 D:B12702 2.8 36.4 1.0 C4 D:B12702 2.8 36.1 1.0 C1 D:B12702 2.9 33.2 1.0 C14 D:B12702 2.9 32.0 1.0 C9 D:B12702 2.9 32.1 1.0 C6 D:B12702 2.9 34.7 1.0 C11 D:B12702 2.9 32.4 1.0 C16 D:B12702 3.0 32.8 1.0 CD2 D:HIS177 3.0 26.8 1.0 CE1 D:HIS177 3.1 29.3 1.0 C4' D:5AD703 3.1 35.9 1.0 C5 D:B12702 3.3 35.6 1.0 C10 D:B12702 3.4 31.3 1.0 C15 D:B12702 3.4 34.5 1.0 C20 D:B12702 3.6 31.5 1.0 O4' D:5AD703 3.6 34.1 1.0 C18 D:B12702 4.1 33.9 1.0 C2 D:B12702 4.1 37.8 1.0 C3 D:B12702 4.1 37.8 1.0 ND1 D:HIS177 4.2 29.9 1.0 CG D:HIS177 4.2 26.9 1.0 C17 D:B12702 4.2 34.3 1.0 C7 D:B12702 4.2 36.4 1.0 C8 D:B12702 4.2 33.1 1.0 C13 D:B12702 4.3 28.9 1.0 C12 D:B12702 4.3 30.8 1.0 C3' D:5AD703 4.4 36.8 1.0 C26 D:B12702 4.6 37.1 1.0 C37 D:B12702 4.8 36.4 1.0 C35 D:B12702 4.8 36.6 1.0 C53 D:B12702 4.9 32.9 1.0 C54 D:B12702 4.9 34.4 1.0 C1' D:5AD703 5.0 34.7 1.0 C41 D:B12702 5.0 33.6 1.0

H.Poddar, D.Leys. Dark State 1.8 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Aerobic Condition To Be Published.