Cobalt in PDB 8c32: Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition

The structure of Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition, PDB code: 8c32 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)	57.39 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.73, 69.39, 204.14, 90, 90, 90
R / Rfree (%)	17.9 / 22.3

The structure of Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Cobalt atom in the Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition (pdb code 8c32). 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 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition, PDB code: 8c32:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic 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 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:53.0 occ:1.00 CO A:B12302 0.0 53.0 1.0 N21 A:B12302 1.9 58.1 1.0 N23 A:B12302 1.9 54.9 1.0 NE2 A:HIS177 1.9 52.7 1.0 N22 A:B12302 2.0 57.1 1.0 N24 A:B12302 2.0 52.1 1.0 C5' A:5AD303 2.0 53.4 1.0 C4 A:B12302 2.8 58.2 1.0 C19 A:B12302 2.8 50.5 1.0 C14 A:B12302 2.8 45.5 1.0 C1 A:B12302 2.9 54.1 1.0 C11 A:B12302 2.9 53.3 1.0 C9 A:B12302 3.0 54.7 1.0 CD2 A:HIS177 3.0 49.3 1.0 CE1 A:HIS177 3.0 55.5 1.0 C6 A:B12302 3.0 56.6 1.0 C16 A:B12302 3.0 50.5 1.0 C4' A:5AD303 3.1 55.0 1.0 C5 A:B12302 3.3 58.0 1.0 C15 A:B12302 3.3 47.8 1.0 C10 A:B12302 3.3 53.1 1.0 O4' A:5AD303 3.6 52.8 1.0 C20 A:B12302 3.7 49.7 1.0 C2 A:B12302 4.0 58.9 1.0 ND1 A:HIS177 4.1 55.7 1.0 C3 A:B12302 4.1 62.3 1.0 CG A:HIS177 4.1 51.9 1.0 C18 A:B12302 4.2 50.1 1.0 C13 A:B12302 4.2 48.6 1.0 C12 A:B12302 4.2 50.7 1.0 C17 A:B12302 4.2 49.2 1.0 C8 A:B12302 4.3 55.3 1.0 C7 A:B12302 4.3 57.3 1.0 C26 A:B12302 4.4 57.0 1.0 C3' A:5AD303 4.5 56.1 1.0 C35 A:B12302 4.7 57.8 1.0 C53 A:B12302 4.8 43.2 1.0 C37 A:B12302 4.8 58.0 1.0 C1' A:5AD303 4.9 51.9 1.0 C54 A:B12302 5.0 48.0 1.0

Cobalt binding site 2 out of 4 in the Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic 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 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:69.0 occ:1.00 CO B:B12301 0.0 69.0 1.0 N21 B:B12301 1.8 71.4 1.0 N23 B:B12301 1.9 68.5 1.0 NE2 B:HIS177 2.0 67.3 1.0 N24 B:B12301 2.0 72.6 1.0 N22 B:B12301 2.0 66.0 1.0 C5' B:5AD302 2.0 71.6 1.0 C19 B:B12301 2.7 71.1 1.0 C4 B:B12301 2.8 70.7 1.0 C14 B:B12301 2.8 64.0 1.0 C1 B:B12301 2.8 70.5 1.0 C11 B:B12301 2.9 68.6 1.0 C16 B:B12301 2.9 71.6 1.0 C9 B:B12301 2.9 68.1 1.0 C6 B:B12301 2.9 70.5 1.0 CE1 B:HIS177 3.0 64.3 1.0 CD2 B:HIS177 3.0 64.0 1.0 C4' B:5AD302 3.2 73.5 1.0 C5 B:B12301 3.2 72.7 1.0 C15 B:B12301 3.3 67.2 1.0 C10 B:B12301 3.3 65.4 1.0 C20 B:B12301 3.7 65.2 1.0 O4' B:5AD302 3.7 74.7 1.0 C2 B:B12301 4.0 71.6 1.0 C18 B:B12301 4.1 69.1 1.0 C3 B:B12301 4.1 76.0 1.0 ND1 B:HIS177 4.1 59.9 1.0 C17 B:B12301 4.1 71.8 1.0 CG B:HIS177 4.2 61.8 1.0 C13 B:B12301 4.2 66.0 1.0 C7 B:B12301 4.2 72.6 1.0 C8 B:B12301 4.2 73.3 1.0 C12 B:B12301 4.2 66.4 1.0 C26 B:B12301 4.4 73.2 1.0 C3' B:5AD302 4.5 76.3 1.0 C35 B:B12301 4.7 74.7 1.0 C53 B:B12301 4.7 65.5 1.0 C37 B:B12301 4.8 77.0 1.0 C41 B:B12301 4.9 72.6 1.0 C48 B:B12301 5.0 65.8 1.0

Cobalt binding site 3 out of 4 in the Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic 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 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:47.5 occ:1.00 CO C:B12301 0.0 47.5 1.0 N21 C:B12301 1.9 46.8 1.0 N23 C:B12301 1.9 49.8 1.0 NE2 C:HIS177 2.0 45.8 1.0 N22 C:B12301 2.0 46.0 1.0 N24 C:B12301 2.0 49.8 1.0 C5' C:5AD302 2.0 52.4 1.0 C4 C:B12301 2.8 47.5 1.0 C19 C:B12301 2.8 49.9 1.0 C14 C:B12301 2.8 46.3 1.0 C1 C:B12301 2.9 48.7 1.0 C11 C:B12301 2.9 47.2 1.0 CE1 C:HIS177 2.9 43.7 1.0 C9 C:B12301 2.9 47.6 1.0 C16 C:B12301 3.0 46.2 1.0 C6 C:B12301 3.0 47.2 1.0 CD2 C:HIS177 3.0 45.5 1.0 C4' C:5AD302 3.1 54.0 1.0 C5 C:B12301 3.3 48.5 1.0 C15 C:B12301 3.3 48.7 1.0 C10 C:B12301 3.3 49.4 1.0 O4' C:5AD302 3.6 59.4 1.0 C20 C:B12301 3.7 45.8 1.0 C2 C:B12301 4.0 50.4 1.0 C3 C:B12301 4.1 52.6 1.0 ND1 C:HIS177 4.1 40.7 1.0 C18 C:B12301 4.1 50.8 1.0 CG C:HIS177 4.2 44.0 1.0 C13 C:B12301 4.2 47.2 1.0 C17 C:B12301 4.2 49.3 1.0 C12 C:B12301 4.2 48.3 1.0 C8 C:B12301 4.2 48.3 1.0 C7 C:B12301 4.3 51.8 1.0 C26 C:B12301 4.5 52.6 1.0 C3' C:5AD302 4.5 51.6 1.0 C35 C:B12301 4.7 49.8 1.0 C53 C:B12301 4.8 50.2 1.0 C37 C:B12301 4.9 53.3 1.0 C54 C:B12301 4.9 44.9 1.0 C1' C:5AD302 5.0 55.2 1.0 C48 C:B12301 5.0 49.4 1.0

Cobalt binding site 4 out of 4 in the Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic 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 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:53.2 occ:1.00 CO D:B12301 0.0 53.2 1.0 N21 D:B12301 1.9 59.3 1.0 N23 D:B12301 1.9 55.9 1.0 NE2 D:HIS177 2.0 53.4 1.0 N22 D:B12301 2.0 58.9 1.0 N24 D:B12301 2.0 57.6 1.0 C5' D:5AD302 2.0 59.3 1.0 C19 D:B12301 2.8 56.4 1.0 C4 D:B12301 2.8 55.4 1.0 C14 D:B12301 2.8 54.0 1.0 C1 D:B12301 2.9 53.9 1.0 C11 D:B12301 2.9 53.6 1.0 C9 D:B12301 2.9 58.4 1.0 CE1 D:HIS177 3.0 50.3 1.0 C6 D:B12301 3.0 56.1 1.0 C16 D:B12301 3.0 52.7 1.0 CD2 D:HIS177 3.0 49.9 1.0 C4' D:5AD302 3.1 59.8 1.0 C5 D:B12301 3.3 56.1 1.0 C15 D:B12301 3.3 53.5 1.0 C10 D:B12301 3.3 52.6 1.0 O4' D:5AD302 3.6 59.6 1.0 C20 D:B12301 3.7 51.2 1.0 C2 D:B12301 4.0 58.9 1.0 C3 D:B12301 4.1 61.0 1.0 ND1 D:HIS177 4.1 48.2 1.0 C18 D:B12301 4.1 58.3 1.0 CG D:HIS177 4.1 47.0 1.0 C13 D:B12301 4.2 48.5 1.0 C7 D:B12301 4.2 61.7 1.0 C17 D:B12301 4.2 57.5 1.0 C8 D:B12301 4.2 60.1 1.0 C12 D:B12301 4.2 49.1 1.0 C26 D:B12301 4.4 62.5 1.0 C3' D:5AD302 4.5 60.0 1.0 C35 D:B12301 4.7 57.3 1.0 C53 D:B12301 4.8 51.2 1.0 C37 D:B12301 4.8 64.5 1.0 C1' D:5AD302 5.0 57.7 1.0 C41 D:B12301 5.0 57.3 1.0

H.Poddar, D.Leys. Dark State 2.2 Angstrom Crystal Structure of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh Obtained Under Anaerobic Condition To Be Published.