Cobalt in PDB 8c35: Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh

The structure of Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh, PDB code: 8c35 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)	51.19 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.924, 69.97, 204.555, 90, 90, 90
R / Rfree (%)	18.6 / 22.3

The binding sites of Cobalt atom in the Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh (pdb code 8c35). 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 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh, PDB code: 8c35:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:35.5 occ:1.00 CO A:B12301 0.0 35.5 1.0 N21 A:B12301 1.8 36.3 1.0 N23 A:B12301 1.9 35.8 1.0 N24 A:B12301 1.9 35.7 1.0 N22 A:B12301 1.9 36.6 1.0 NE2 A:HIS177 2.0 35.6 1.0 C5' A:5AD302 2.0 36.1 1.0 C19 A:B12301 2.8 35.1 1.0 C14 A:B12301 2.8 34.4 1.0 C4 A:B12301 2.8 37.7 1.0 C1 A:B12301 2.8 36.6 1.0 C11 A:B12301 2.9 36.5 1.0 C9 A:B12301 2.9 36.3 1.0 C16 A:B12301 3.0 34.5 1.0 CE1 A:HIS177 3.0 36.3 1.0 C6 A:B12301 3.0 36.4 1.0 CD2 A:HIS177 3.0 35.1 1.0 C4' A:5AD302 3.1 35.2 1.0 C10 A:B12301 3.2 38.4 1.0 C15 A:B12301 3.3 32.8 1.0 C5 A:B12301 3.4 38.1 1.0 C20 A:B12301 3.6 36.1 1.0 O4' A:5AD302 3.7 36.8 1.0 C2 A:B12301 4.1 37.0 1.0 ND1 A:HIS177 4.1 35.4 1.0 C3 A:B12301 4.1 38.5 1.0 C13 A:B12301 4.1 32.0 1.0 C18 A:B12301 4.1 34.8 1.0 CG A:HIS177 4.2 34.7 1.0 C12 A:B12301 4.2 33.2 1.0 C8 A:B12301 4.2 39.1 1.0 C7 A:B12301 4.2 38.5 1.0 C17 A:B12301 4.2 36.2 1.0 C3' A:5AD302 4.4 35.5 1.0 C26 A:B12301 4.5 35.8 1.0 C37 A:B12301 4.7 38.2 1.0 C53 A:B12301 4.8 30.8 1.0 C35 A:B12301 4.9 38.1 1.0 C41 A:B12301 4.9 38.4 1.0 C48 A:B12301 5.0 32.6 1.0 O3' A:5AD302 5.0 34.2 1.0 C1' A:5AD302 5.0 35.0 1.0

Cobalt binding site 2 out of 4 in the Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:40.7 occ:1.00 CO B:B12301 0.0 40.7 1.0 N21 B:B12301 1.9 42.6 1.0 N23 B:B12301 1.9 39.9 1.0 N24 B:B12301 1.9 44.4 1.0 N22 B:B12301 1.9 40.6 1.0 NE2 B:HIS177 2.0 47.1 1.0 C5' B:5AD302 2.0 42.7 1.0 C19 B:B12301 2.8 44.5 1.0 C4 B:B12301 2.8 43.9 1.0 C1 B:B12301 2.9 41.6 1.0 C14 B:B12301 2.9 38.8 1.0 C11 B:B12301 2.9 39.4 1.0 C9 B:B12301 2.9 39.5 1.0 C16 B:B12301 2.9 44.1 1.0 CD2 B:HIS177 3.0 43.5 1.0 C6 B:B12301 3.0 41.7 1.0 CE1 B:HIS177 3.0 45.3 1.0 C4' B:5AD302 3.1 43.7 1.0 C10 B:B12301 3.3 40.2 1.0 C15 B:B12301 3.3 40.4 1.0 C5 B:B12301 3.3 43.2 1.0 C20 B:B12301 3.6 39.0 1.0 O4' B:5AD302 3.7 44.0 1.0 C18 B:B12301 4.1 45.8 1.0 ND1 B:HIS177 4.1 40.7 1.0 C2 B:B12301 4.1 41.5 1.0 C3 B:B12301 4.1 44.9 1.0 CG B:HIS177 4.1 39.4 1.0 C17 B:B12301 4.2 45.5 1.0 C13 B:B12301 4.2 38.5 1.0 C8 B:B12301 4.2 39.5 1.0 C7 B:B12301 4.2 42.9 1.0 C12 B:B12301 4.2 39.4 1.0 C3' B:5AD302 4.5 48.1 1.0 C26 B:B12301 4.7 40.4 1.0 C37 B:B12301 4.7 47.6 1.0 C53 B:B12301 4.8 39.0 1.0 C35 B:B12301 4.8 42.2 1.0 C54 B:B12301 4.9 46.1 1.0 C41 B:B12301 5.0 37.7 1.0 C46 B:B12301 5.0 41.5 1.0

Cobalt binding site 3 out of 4 in the Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:34.2 occ:1.00 CO C:B12301 0.0 34.2 1.0 N21 C:B12301 1.8 36.1 1.0 N23 C:B12301 1.9 36.2 1.0 N24 C:B12301 1.9 36.0 1.0 N22 C:B12301 1.9 37.3 1.0 C5' C:5AD302 2.0 35.9 1.0 NE2 C:HIS177 2.0 34.0 1.0 C19 C:B12301 2.8 35.9 1.0 C4 C:B12301 2.8 36.3 1.0 C1 C:B12301 2.8 36.0 1.0 C14 C:B12301 2.9 33.8 1.0 C9 C:B12301 2.9 35.6 1.0 C11 C:B12301 2.9 35.5 1.0 C16 C:B12301 2.9 35.2 1.0 C6 C:B12301 3.0 36.1 1.0 CE1 C:HIS177 3.0 34.1 1.0 C4' C:5AD302 3.0 35.4 1.0 CD2 C:HIS177 3.1 33.0 1.0 C10 C:B12301 3.3 36.9 1.0 C15 C:B12301 3.3 34.4 1.0 C5 C:B12301 3.3 36.3 1.0 C20 C:B12301 3.5 34.7 1.0 O4' C:5AD302 3.5 35.4 1.0 C2 C:B12301 4.1 37.3 1.0 C3 C:B12301 4.1 37.3 1.0 C18 C:B12301 4.1 36.3 1.0 ND1 C:HIS177 4.2 31.1 1.0 C17 C:B12301 4.2 37.6 1.0 C13 C:B12301 4.2 34.2 1.0 C8 C:B12301 4.2 37.1 1.0 CG C:HIS177 4.2 31.1 1.0 C7 C:B12301 4.2 37.2 1.0 C12 C:B12301 4.3 35.0 1.0 C3' C:5AD302 4.4 33.5 1.0 C26 C:B12301 4.5 38.3 1.0 C35 C:B12301 4.8 38.0 1.0 C37 C:B12301 4.8 39.6 1.0 C53 C:B12301 4.8 32.4 1.0 C1' C:5AD302 4.8 34.1 1.0 C54 C:B12301 4.9 36.7 1.0 C41 C:B12301 4.9 37.1 1.0 O3' C:5AD302 4.9 31.7 1.0

Cobalt binding site 4 out of 4 in the Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:37.3 occ:1.00 CO D:B12301 0.0 37.3 1.0 N21 D:B12301 1.9 38.9 1.0 N23 D:B12301 1.9 38.6 1.0 N24 D:B12301 1.9 39.2 1.0 N22 D:B12301 1.9 38.4 1.0 NE2 D:HIS177 2.0 36.7 1.0 C5' D:5AD302 2.0 40.5 1.0 C19 D:B12301 2.8 41.2 1.0 C14 D:B12301 2.8 37.2 1.0 C4 D:B12301 2.9 40.1 1.0 C1 D:B12301 2.9 39.3 1.0 C11 D:B12301 2.9 36.3 1.0 C9 D:B12301 2.9 37.7 1.0 C16 D:B12301 2.9 37.2 1.0 C6 D:B12301 3.0 40.2 1.0 CE1 D:HIS177 3.0 36.0 1.0 CD2 D:HIS177 3.1 35.0 1.0 C4' D:5AD302 3.1 41.8 1.0 C10 D:B12301 3.2 37.9 1.0 C15 D:B12301 3.3 37.8 1.0 C5 D:B12301 3.4 40.5 1.0 C20 D:B12301 3.5 38.5 1.0 O4' D:5AD302 3.6 42.3 1.0 C2 D:B12301 4.1 42.2 1.0 C18 D:B12301 4.1 42.2 1.0 C3 D:B12301 4.1 43.0 1.0 ND1 D:HIS177 4.1 34.0 1.0 C17 D:B12301 4.2 41.4 1.0 C13 D:B12301 4.2 35.4 1.0 CG D:HIS177 4.2 33.8 1.0 C12 D:B12301 4.2 34.4 1.0 C8 D:B12301 4.2 40.1 1.0 C7 D:B12301 4.3 42.6 1.0 C3' D:5AD302 4.5 40.8 1.0 C26 D:B12301 4.5 42.2 1.0 C37 D:B12301 4.8 42.8 1.0 C53 D:B12301 4.8 34.7 1.0 C35 D:B12301 4.8 40.4 1.0 C54 D:B12301 4.9 41.4 1.0 C1' D:5AD302 4.9 43.4 1.0 C41 D:B12301 5.0 39.3 1.0

H.Poddar, D.Leys. Dark State 2.1 Angstrom Crystal Structure of H132A Variant of Cobalamin Binding Domain Belonging to A Light-Dependent Transcription Regulator Ttcarh To Be Published.