Cobalt in PDB 5c8e: Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment

The structure of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment, PDB code: 5c8e was solved by M.Jost, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.64 / 3.89
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.940, 141.820, 162.690, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 25.7

The binding sites of Cobalt atom in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment (pdb code 5c8e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment, PDB code: 5c8e:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ A:Co300 b:0.2 occ:1.00 CO A:B12300 0.0 0.2 1.0 N21 A:B12300 1.9 0.4 1.0 N24 A:B12300 1.9 0.4 1.0 N22 A:B12300 1.9 0.4 1.0 N23 A:B12300 1.9 0.6 1.0 C5' A:5AD301 2.0 0.1 1.0 NE2 A:HIS177 2.3 0.4 1.0 C9 A:B12300 2.9 0.8 1.0 C19 A:B12300 2.9 0.6 1.0 C1 A:B12300 2.9 1.0 1.0 C4 A:B12300 2.9 0.9 1.0 C11 A:B12300 2.9 0.8 1.0 C16 A:B12300 3.0 0.4 1.0 C14 A:B12300 3.0 0.9 1.0 C6 A:B12300 3.0 0.2 1.0 CD2 A:HIS177 3.2 0.6 1.0 CE1 A:HIS177 3.2 0.4 1.0 C10 A:B12300 3.3 0.6 1.0 C5 A:B12300 3.3 0.5 1.0 C4' A:5AD301 3.3 0.5 1.0 C15 A:B12300 3.4 0.6 1.0 C20 A:B12300 3.5 0.8 1.0 O4' A:5AD301 3.9 0.3 1.0 C18 A:B12300 4.1 0.9 1.0 C2 A:B12300 4.1 0.4 1.0 C3 A:B12300 4.2 0.7 1.0 C8 A:B12300 4.2 0.7 1.0 C7 A:B12300 4.2 0.9 1.0 C17 A:B12300 4.2 0.7 1.0 C12 A:B12300 4.2 0.4 1.0 C13 A:B12300 4.3 0.6 1.0 ND1 A:HIS177 4.4 0.3 1.0 CG A:HIS177 4.4 0.3 1.0 C3' A:5AD301 4.6 0.4 1.0 C26 A:B12300 4.7 0.3 1.0 C35 A:B12300 4.8 0.4 1.0 C37 A:B12300 4.9 0.9 1.0 C41 A:B12300 4.9 0.3 1.0 C53 A:B12300 4.9 0.9 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ B:Co300 b:0.6 occ:1.00 CO B:B12300 0.0 0.6 1.0 N21 B:B12300 1.9 0.8 1.0 N24 B:B12300 1.9 0.3 1.0 N23 B:B12300 1.9 0.6 1.0 N22 B:B12300 1.9 0.4 1.0 C5' B:5AD301 2.0 0.1 1.0 NE2 B:HIS177 2.3 0.6 1.0 C9 B:B12300 2.9 0.9 1.0 C19 B:B12300 2.9 0.7 1.0 C1 B:B12300 2.9 0.8 1.0 C4 B:B12300 2.9 0.1 1.0 C11 B:B12300 2.9 0.6 1.0 C16 B:B12300 3.0 0.0 1.0 C14 B:B12300 3.0 0.0 1.0 C6 B:B12300 3.0 0.7 1.0 CD2 B:HIS177 3.2 0.9 1.0 CE1 B:HIS177 3.2 1.0 1.0 C10 B:B12300 3.3 0.2 1.0 C5 B:B12300 3.3 0.9 1.0 C4' B:5AD301 3.3 0.7 1.0 C15 B:B12300 3.4 0.0 1.0 C20 B:B12300 3.5 0.7 1.0 O4' B:5AD301 3.9 0.6 1.0 C18 B:B12300 4.1 0.3 1.0 C2 B:B12300 4.1 0.8 1.0 C3 B:B12300 4.2 0.6 1.0 C8 B:B12300 4.2 0.9 1.0 C7 B:B12300 4.2 0.8 1.0 C17 B:B12300 4.2 0.1 1.0 C12 B:B12300 4.2 0.6 1.0 C13 B:B12300 4.3 0.1 1.0 ND1 B:HIS177 4.4 0.6 1.0 CG B:HIS177 4.4 0.9 1.0 C3' B:5AD301 4.6 0.8 1.0 C26 B:B12300 4.7 0.6 1.0 C35 B:B12300 4.8 0.3 1.0 C37 B:B12300 4.9 0.5 1.0 C41 B:B12300 4.9 0.8 1.0 C53 B:B12300 4.9 0.5 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ C:Co300 b:0.7 occ:1.00 CO C:B12300 0.0 0.7 1.0 N21 C:B12300 1.9 0.3 1.0 N24 C:B12300 1.9 0.8 1.0 N23 C:B12300 1.9 0.1 1.0 N22 C:B12300 1.9 0.1 1.0 C5' C:5AD301 2.0 1.0 1.0 NE2 C:HIS177 2.3 0.8 1.0 C19 C:B12300 2.9 0.8 1.0 C9 C:B12300 2.9 0.6 1.0 C1 C:B12300 2.9 0.0 1.0 C4 C:B12300 2.9 0.1 1.0 C11 C:B12300 2.9 0.3 1.0 C16 C:B12300 3.0 0.4 1.0 C14 C:B12300 3.0 0.7 1.0 C6 C:B12300 3.0 0.8 1.0 CD2 C:HIS177 3.2 0.9 1.0 CE1 C:HIS177 3.2 0.3 1.0 C10 C:B12300 3.3 0.8 1.0 C5 C:B12300 3.3 0.9 1.0 C4' C:5AD301 3.3 0.5 1.0 C15 C:B12300 3.4 0.5 1.0 C20 C:B12300 3.5 1.0 1.0 O4' C:5AD301 3.8 0.1 1.0 C18 C:B12300 4.1 0.9 1.0 C2 C:B12300 4.1 0.3 1.0 C3 C:B12300 4.2 0.3 1.0 C8 C:B12300 4.2 0.5 1.0 C7 C:B12300 4.2 0.6 1.0 C17 C:B12300 4.2 0.2 1.0 C12 C:B12300 4.2 0.8 1.0 C13 C:B12300 4.3 0.9 1.0 ND1 C:HIS177 4.4 0.2 1.0 CG C:HIS177 4.4 0.2 1.0 C3' C:5AD301 4.6 0.4 1.0 C26 C:B12300 4.7 0.6 1.0 C35 C:B12300 4.8 0.0 1.0 C37 C:B12300 4.9 0.9 1.0 C41 C:B12300 4.9 0.2 1.0 C53 C:B12300 4.9 0.3 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ D:Co300 b:0.2 occ:1.00 CO D:B12300 0.0 0.2 1.0 N21 D:B12300 1.9 0.6 1.0 N24 D:B12300 1.9 0.3 1.0 N22 D:B12300 1.9 0.6 1.0 N23 D:B12300 1.9 0.2 1.0 C5' D:5AD301 2.0 0.1 1.0 NE2 D:HIS177 2.3 0.9 1.0 C9 D:B12300 2.9 0.5 1.0 C19 D:B12300 2.9 0.0 1.0 C1 D:B12300 2.9 0.2 1.0 C4 D:B12300 2.9 0.1 1.0 C11 D:B12300 2.9 0.7 1.0 C16 D:B12300 3.0 0.2 1.0 C14 D:B12300 3.0 0.7 1.0 C6 D:B12300 3.0 0.3 1.0 CD2 D:HIS177 3.2 0.9 1.0 CE1 D:HIS177 3.2 0.0 1.0 C10 D:B12300 3.3 0.2 1.0 C5 D:B12300 3.3 0.0 1.0 C4' D:5AD301 3.3 0.1 1.0 C15 D:B12300 3.4 0.9 1.0 C20 D:B12300 3.5 0.7 1.0 O4' D:5AD301 3.9 0.8 1.0 C18 D:B12300 4.1 0.5 1.0 C2 D:B12300 4.1 0.7 1.0 C3 D:B12300 4.2 0.7 1.0 C8 D:B12300 4.2 0.0 1.0 C7 D:B12300 4.2 0.1 1.0 C17 D:B12300 4.2 0.8 1.0 C12 D:B12300 4.2 0.3 1.0 C13 D:B12300 4.3 0.2 1.0 ND1 D:HIS177 4.4 0.1 1.0 CG D:HIS177 4.4 0.4 1.0 C3' D:5AD301 4.6 0.5 1.0 C26 D:B12300 4.7 0.7 1.0 C35 D:B12300 4.8 0.2 1.0 C37 D:B12300 4.9 0.7 1.0 C41 D:B12300 4.9 0.6 1.0 C53 D:B12300 4.9 0.3 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ E:Co300 b:0.3 occ:1.00 CO E:B12300 0.0 0.3 1.0 N21 E:B12300 1.9 0.2 1.0 N24 E:B12300 1.9 0.7 1.0 N22 E:B12300 1.9 0.8 1.0 N23 E:B12300 1.9 0.8 1.0 C5' E:5AD301 2.0 0.6 1.0 NE2 E:HIS177 2.3 0.2 1.0 C19 E:B12300 2.9 0.2 1.0 C9 E:B12300 2.9 0.0 1.0 C1 E:B12300 2.9 0.5 1.0 C4 E:B12300 2.9 0.5 1.0 C11 E:B12300 2.9 0.3 1.0 C16 E:B12300 3.0 0.5 1.0 C14 E:B12300 3.0 0.5 1.0 C6 E:B12300 3.0 0.6 1.0 CD2 E:HIS177 3.2 0.3 1.0 CE1 E:HIS177 3.2 0.9 1.0 C10 E:B12300 3.3 0.9 1.0 C5 E:B12300 3.3 0.2 1.0 C4' E:5AD301 3.3 0.9 1.0 C15 E:B12300 3.4 0.5 1.0 C20 E:B12300 3.5 0.8 1.0 O4' E:5AD301 3.9 0.3 1.0 C18 E:B12300 4.1 0.5 1.0 C2 E:B12300 4.1 0.4 1.0 C3 E:B12300 4.2 0.1 1.0 C8 E:B12300 4.2 0.4 1.0 C7 E:B12300 4.2 0.5 1.0 C17 E:B12300 4.2 0.5 1.0 C12 E:B12300 4.2 0.4 1.0 C13 E:B12300 4.3 0.9 1.0 ND1 E:HIS177 4.3 0.9 1.0 CG E:HIS177 4.4 0.6 1.0 C3' E:5AD301 4.6 0.5 1.0 C26 E:B12300 4.7 0.8 1.0 C35 E:B12300 4.8 0.5 1.0 C37 E:B12300 4.9 0.5 1.0 C41 E:B12300 4.9 0.3 1.0 C53 E:B12300 4.9 0.3 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ F:Co300 b:0.1 occ:1.00 CO F:B12300 0.0 0.1 1.0 N21 F:B12300 1.9 0.0 1.0 N24 F:B12300 1.9 0.5 1.0 N22 F:B12300 1.9 0.3 1.0 N23 F:B12300 1.9 0.1 1.0 C5' F:5AD301 2.0 0.3 1.0 NE2 F:HIS177 2.3 0.9 1.0 C9 F:B12300 2.9 0.2 1.0 C19 F:B12300 2.9 0.1 1.0 C1 F:B12300 2.9 0.7 1.0 C4 F:B12300 2.9 0.1 1.0 C11 F:B12300 2.9 1.0 1.0 C16 F:B12300 3.0 0.6 1.0 C14 F:B12300 3.0 0.6 1.0 C6 F:B12300 3.0 0.5 1.0 CD2 F:HIS177 3.2 1.0 1.0 CE1 F:HIS177 3.3 0.3 1.0 C10 F:B12300 3.3 0.8 1.0 C5 F:B12300 3.3 0.1 1.0 C4' F:5AD301 3.3 0.8 1.0 C15 F:B12300 3.4 0.0 1.0 C20 F:B12300 3.5 0.8 1.0 O4' F:5AD301 3.9 0.6 1.0 C18 F:B12300 4.1 0.2 1.0 C2 F:B12300 4.1 0.9 1.0 C3 F:B12300 4.2 0.2 1.0 C8 F:B12300 4.2 0.9 1.0 C7 F:B12300 4.2 0.4 1.0 C17 F:B12300 4.2 0.8 1.0 C12 F:B12300 4.2 0.5 1.0 C13 F:B12300 4.3 1.0 1.0 ND1 F:HIS177 4.4 0.1 1.0 CG F:HIS177 4.4 0.7 1.0 C3' F:5AD301 4.6 0.0 1.0 C26 F:B12300 4.7 0.9 1.0 C35 F:B12300 4.8 0.6 1.0 C37 F:B12300 4.9 0.0 1.0 C41 F:B12300 4.9 0.6 1.0 C53 F:B12300 4.9 0.3 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ G:Co300 b:0.5 occ:1.00 CO G:B12300 0.0 0.5 1.0 N21 G:B12300 1.9 0.8 1.0 N24 G:B12300 1.9 0.0 1.0 N23 G:B12300 1.9 0.9 1.0 N22 G:B12300 1.9 0.0 1.0 C5' G:5AD301 2.0 0.4 1.0 NE2 G:HIS177 2.3 0.4 1.0 C19 G:B12300 2.9 0.9 1.0 C9 G:B12300 2.9 0.0 1.0 C1 G:B12300 2.9 0.2 1.0 C4 G:B12300 2.9 0.4 1.0 C11 G:B12300 2.9 0.9 1.0 C16 G:B12300 3.0 0.2 1.0 C14 G:B12300 3.0 0.6 1.0 C6 G:B12300 3.0 0.5 1.0 CD2 G:HIS177 3.2 0.7 1.0 CE1 G:HIS177 3.2 0.9 1.0 C10 G:B12300 3.3 0.4 1.0 C5 G:B12300 3.3 0.9 1.0 C4' G:5AD301 3.3 0.2 1.0 C15 G:B12300 3.4 0.3 1.0 C20 G:B12300 3.5 0.9 1.0 O4' G:5AD301 3.9 0.3 1.0 C18 G:B12300 4.1 0.2 1.0 C2 G:B12300 4.1 0.9 1.0 C3 G:B12300 4.2 0.9 1.0 C8 G:B12300 4.2 0.7 1.0 C7 G:B12300 4.2 0.8 1.0 C17 G:B12300 4.2 0.6 1.0 C12 G:B12300 4.2 0.9 1.0 C13 G:B12300 4.3 0.8 1.0 ND1 G:HIS177 4.4 0.2 1.0 CG G:HIS177 4.4 0.2 1.0 C3' G:5AD301 4.6 0.8 1.0 C26 G:B12300 4.7 0.6 1.0 C35 G:B12300 4.8 0.0 1.0 C37 G:B12300 4.9 0.2 1.0 C41 G:B12300 4.9 0.1 1.0 C53 G:B12300 4.9 0.3 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Thermus Thermophilus Carh Bound to Adenosylcobalamin and A 26-Bp Dna Segment within 5.0Å range: probe atom residue distance (Å) B Occ H:Co300 b:0.9 occ:1.00 CO H:B12300 0.0 0.9 1.0 N21 H:B12300 1.9 0.3 1.0 N24 H:B12300 1.9 0.8 1.0 N23 H:B12300 1.9 0.6 1.0 N22 H:B12300 1.9 0.7 1.0 C5' H:5AD301 2.0 0.2 1.0 NE2 H:HIS177 2.3 0.4 1.0 C9 H:B12300 2.9 0.9 1.0 C19 H:B12300 2.9 0.9 1.0 C1 H:B12300 2.9 0.2 1.0 C4 H:B12300 2.9 0.4 1.0 C11 H:B12300 2.9 0.0 1.0 C16 H:B12300 3.0 0.9 1.0 C14 H:B12300 3.0 0.9 1.0 C6 H:B12300 3.0 0.8 1.0 CD2 H:HIS177 3.2 1.0 1.0 CE1 H:HIS177 3.2 0.8 1.0 C10 H:B12300 3.3 0.8 1.0 C5 H:B12300 3.3 0.1 1.0 C4' H:5AD301 3.3 0.2 1.0 C15 H:B12300 3.4 0.4 1.0 C20 H:B12300 3.5 0.8 1.0 O4' H:5AD301 3.9 0.8 1.0 C18 H:B12300 4.1 0.9 1.0 C2 H:B12300 4.1 0.9 1.0 C3 H:B12300 4.2 0.4 1.0 C8 H:B12300 4.2 0.5 1.0 C7 H:B12300 4.2 0.8 1.0 C17 H:B12300 4.2 0.9 1.0 C12 H:B12300 4.2 0.6 1.0 C13 H:B12300 4.3 0.7 1.0 ND1 H:HIS177 4.4 0.3 1.0 CG H:HIS177 4.4 1.0 1.0 C3' H:5AD301 4.6 0.5 1.0 C26 H:B12300 4.7 0.5 1.0 C35 H:B12300 4.8 0.5 1.0 C37 H:B12300 4.9 0.1 1.0 C41 H:B12300 4.9 0.7 1.0 C53 H:B12300 4.9 0.4 1.0

M.Jost, J.Fernandez-Zapata, M.C.Polanco, J.M.Ortiz-Guerrero, P.Y.Chen, G.Kang, S.Padmanabhan, M.Elias-Arnanz, C.L.Drennan. Structural Basis For Gene Regulation By A B12-Dependent Photoreceptor. Nature V. 526 536 2015.
ISSN: ESSN 1476-4687
PubMed: 26416754
DOI: 10.1038/NATURE14950