Cobalt in PDB 5c8d: Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)

The structure of Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State), PDB code: 5c8d 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)	70.65 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.740, 79.720, 118.450, 90.73, 96.61, 117.29
R / Rfree (%)	18.3 / 23

The binding sites of Cobalt atom in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) (pdb code 5c8d). 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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State), PDB code: 5c8d:
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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co300 b:60.1 occ:1.00 CO A:B12300 0.0 60.1 1.0 N21 A:B12300 1.9 54.4 1.0 N24 A:B12300 1.9 66.8 1.0 N23 A:B12300 1.9 58.1 1.0 N22 A:B12300 1.9 65.5 1.0 C5' A:5AD301 2.0 71.1 1.0 NE2 A:HIS177 2.1 69.5 1.0 C19 A:B12300 2.8 71.0 1.0 C9 A:B12300 2.9 60.5 1.0 C4 A:B12300 2.9 58.0 1.0 C1 A:B12300 2.9 58.4 1.0 C11 A:B12300 2.9 58.9 1.0 C6 A:B12300 3.0 64.5 1.0 C16 A:B12300 3.0 63.4 1.0 C14 A:B12300 3.0 57.5 1.0 CE1 A:HIS177 3.1 71.9 1.0 CD2 A:HIS177 3.1 67.7 1.0 C10 A:B12300 3.2 61.9 1.0 C5 A:B12300 3.3 64.1 1.0 C4' A:5AD301 3.4 71.3 1.0 C15 A:B12300 3.4 58.3 1.0 C20 A:B12300 3.6 49.1 1.0 O4' A:5AD301 3.8 72.8 1.0 C18 A:B12300 4.1 70.2 1.0 C2 A:B12300 4.1 54.8 1.0 C3 A:B12300 4.2 55.2 1.0 C8 A:B12300 4.2 55.6 1.0 ND1 A:HIS177 4.2 70.6 1.0 C7 A:B12300 4.2 60.3 1.0 C12 A:B12300 4.2 47.7 1.0 C17 A:B12300 4.2 66.3 1.0 CG A:HIS177 4.3 69.3 1.0 C13 A:B12300 4.3 55.3 1.0 C26 A:B12300 4.5 65.9 1.0 C3' A:5AD301 4.6 69.5 1.0 C35 A:B12300 4.8 61.6 1.0 C37 A:B12300 4.8 65.3 1.0 C53 A:B12300 4.9 54.4 1.0 C41 A:B12300 4.9 57.1 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co300 b:67.3 occ:1.00 CO B:B12300 0.0 67.3 1.0 N21 B:B12300 1.9 67.4 1.0 N24 B:B12300 1.9 66.2 1.0 N23 B:B12300 1.9 56.0 1.0 N22 B:B12300 1.9 68.2 1.0 C5' B:5AD301 2.0 76.6 1.0 NE2 B:HIS177 2.2 65.3 1.0 C19 B:B12300 2.8 66.5 1.0 C9 B:B12300 2.9 63.2 1.0 C1 B:B12300 2.9 70.1 1.0 C4 B:B12300 2.9 67.7 1.0 C11 B:B12300 2.9 56.4 1.0 C16 B:B12300 3.0 64.0 1.0 C6 B:B12300 3.0 65.0 1.0 C14 B:B12300 3.0 56.6 1.0 CD2 B:HIS177 3.1 64.4 1.0 C4' B:5AD301 3.1 80.7 1.0 C10 B:B12300 3.3 57.4 1.0 CE1 B:HIS177 3.3 68.9 1.0 C5 B:B12300 3.3 66.3 1.0 C15 B:B12300 3.4 58.4 1.0 C20 B:B12300 3.5 68.0 1.0 O4' B:5AD301 3.7 84.0 1.0 C18 B:B12300 4.1 64.9 1.0 C2 B:B12300 4.1 65.1 1.0 C3 B:B12300 4.2 69.7 1.0 C8 B:B12300 4.2 61.0 1.0 C7 B:B12300 4.2 61.4 1.0 C17 B:B12300 4.2 66.0 1.0 C12 B:B12300 4.2 55.7 1.0 C13 B:B12300 4.3 54.1 1.0 CG B:HIS177 4.3 63.4 1.0 ND1 B:HIS177 4.4 67.0 1.0 C3' B:5AD301 4.5 84.2 1.0 C26 B:B12300 4.6 64.7 1.0 C37 B:B12300 4.7 63.7 1.0 C35 B:B12300 4.8 64.6 1.0 C41 B:B12300 4.8 46.8 1.0 C53 B:B12300 4.9 64.3 1.0 O3' B:5AD301 4.9 86.7 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co300 b:58.5 occ:1.00 CO C:B12300 0.0 58.5 1.0 N21 C:B12300 1.9 59.0 1.0 C5' C:5AD301 1.9 65.6 1.0 N24 C:B12300 1.9 70.8 1.0 N23 C:B12300 1.9 58.0 1.0 N22 C:B12300 1.9 62.2 1.0 NE2 C:HIS177 2.3 69.4 1.0 C9 C:B12300 2.8 63.3 1.0 C19 C:B12300 2.9 70.2 1.0 C4 C:B12300 2.9 67.7 1.0 C1 C:B12300 2.9 58.3 1.0 C11 C:B12300 2.9 59.0 1.0 C6 C:B12300 3.0 60.3 1.0 C16 C:B12300 3.0 68.1 1.0 C14 C:B12300 3.0 61.4 1.0 C4' C:5AD301 3.1 67.5 1.0 C10 C:B12300 3.3 62.3 1.0 C5 C:B12300 3.3 62.6 1.0 CE1 C:HIS177 3.3 66.8 1.0 CD2 C:HIS177 3.3 64.2 1.0 C15 C:B12300 3.4 63.3 1.0 C20 C:B12300 3.5 55.8 1.0 O4' C:5AD301 3.7 69.6 1.0 C18 C:B12300 4.1 68.7 1.0 C2 C:B12300 4.1 58.2 1.0 C3 C:B12300 4.2 70.4 1.0 C8 C:B12300 4.2 64.6 1.0 C7 C:B12300 4.2 61.7 1.0 C17 C:B12300 4.2 70.9 1.0 C12 C:B12300 4.3 57.3 1.0 C13 C:B12300 4.3 57.1 1.0 C3' C:5AD301 4.4 66.9 1.0 ND1 C:HIS177 4.4 66.0 1.0 CG C:HIS177 4.5 60.5 1.0 C26 C:B12300 4.5 58.7 1.0 C37 C:B12300 4.7 64.0 1.0 C35 C:B12300 4.7 64.2 1.0 C41 C:B12300 4.8 56.6 1.0 C53 C:B12300 4.9 60.4 1.0 O3' C:5AD301 4.9 69.5 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co300 b:71.3 occ:1.00 CO D:B12300 0.0 71.3 1.0 N21 D:B12300 1.9 64.3 1.0 N24 D:B12300 1.9 63.2 1.0 N23 D:B12300 1.9 60.0 1.0 N22 D:B12300 1.9 60.9 1.0 C5' D:5AD301 2.1 69.7 1.0 NE2 D:HIS177 2.2 71.0 1.0 C9 D:B12300 2.9 63.1 1.0 C19 D:B12300 2.9 65.0 1.0 C4 D:B12300 2.9 63.5 1.0 C1 D:B12300 2.9 61.7 1.0 C11 D:B12300 2.9 63.8 1.0 C16 D:B12300 3.0 65.1 1.0 C6 D:B12300 3.0 62.8 1.0 C14 D:B12300 3.0 59.0 1.0 CE1 D:HIS177 3.1 71.3 1.0 CD2 D:HIS177 3.2 68.6 1.0 C4' D:5AD301 3.2 72.6 1.0 C10 D:B12300 3.3 65.8 1.0 C5 D:B12300 3.3 61.0 1.0 C15 D:B12300 3.4 61.0 1.0 C20 D:B12300 3.6 57.9 1.0 O4' D:5AD301 3.7 74.9 1.0 C18 D:B12300 4.1 67.0 1.0 C2 D:B12300 4.1 64.0 1.0 C3 D:B12300 4.2 64.3 1.0 C8 D:B12300 4.2 68.0 1.0 C7 D:B12300 4.2 64.3 1.0 ND1 D:HIS177 4.2 69.1 1.0 C17 D:B12300 4.2 68.0 1.0 C12 D:B12300 4.3 54.9 1.0 C13 D:B12300 4.3 55.1 1.0 CG D:HIS177 4.3 62.0 1.0 C26 D:B12300 4.4 65.8 1.0 C3' D:5AD301 4.5 76.1 1.0 C37 D:B12300 4.7 66.0 1.0 C35 D:B12300 4.8 58.6 1.0 C41 D:B12300 4.9 68.8 1.0 C53 D:B12300 4.9 62.8 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ E:Co300 b:60.4 occ:1.00 CO E:B12300 0.0 60.4 1.0 N21 E:B12300 1.9 57.4 1.0 N24 E:B12300 1.9 66.3 1.0 N23 E:B12300 1.9 55.6 1.0 N22 E:B12300 1.9 64.1 1.0 C5' E:5AD301 1.9 68.2 1.0 NE2 E:HIS177 2.2 67.2 1.0 C19 E:B12300 2.8 66.5 1.0 C9 E:B12300 2.9 62.8 1.0 C4 E:B12300 2.9 57.1 1.0 C1 E:B12300 2.9 56.0 1.0 C11 E:B12300 2.9 57.0 1.0 C6 E:B12300 3.0 61.6 1.0 C14 E:B12300 3.0 58.1 1.0 C16 E:B12300 3.0 67.0 1.0 CE1 E:HIS177 3.1 68.7 1.0 CD2 E:HIS177 3.2 66.4 1.0 C4' E:5AD301 3.2 70.4 1.0 C10 E:B12300 3.3 60.8 1.0 C5 E:B12300 3.3 59.6 1.0 C15 E:B12300 3.4 63.0 1.0 C20 E:B12300 3.6 47.0 1.0 O4' E:5AD301 3.8 69.9 1.0 C18 E:B12300 4.1 64.3 1.0 C2 E:B12300 4.1 66.4 1.0 C3 E:B12300 4.2 54.6 1.0 C8 E:B12300 4.2 61.3 1.0 C7 E:B12300 4.2 59.0 1.0 C17 E:B12300 4.2 67.5 1.0 C12 E:B12300 4.3 48.2 1.0 ND1 E:HIS177 4.3 67.0 1.0 C13 E:B12300 4.3 54.1 1.0 CG E:HIS177 4.3 63.4 1.0 C3' E:5AD301 4.5 73.1 1.0 C26 E:B12300 4.5 74.5 1.0 C35 E:B12300 4.7 53.5 1.0 C37 E:B12300 4.8 65.4 1.0 C41 E:B12300 4.9 57.3 1.0 C53 E:B12300 4.9 63.0 1.0 O3' E:5AD301 4.9 75.1 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ F:Co300 b:66.2 occ:1.00 CO F:B12300 0.0 66.2 1.0 N21 F:B12300 1.9 69.3 1.0 N24 F:B12300 1.9 68.3 1.0 N23 F:B12300 1.9 59.8 1.0 N22 F:B12300 1.9 65.1 1.0 C5' F:5AD301 2.0 82.6 1.0 NE2 F:HIS177 2.2 66.3 1.0 C4 F:B12300 2.9 71.0 1.0 C9 F:B12300 2.9 62.8 1.0 C19 F:B12300 2.9 69.9 1.0 C1 F:B12300 2.9 67.7 1.0 C11 F:B12300 2.9 58.3 1.0 C6 F:B12300 3.0 69.3 1.0 C16 F:B12300 3.0 69.8 1.0 C14 F:B12300 3.0 58.0 1.0 CD2 F:HIS177 3.2 63.9 1.0 CE1 F:HIS177 3.2 67.6 1.0 C10 F:B12300 3.2 58.1 1.0 C5 F:B12300 3.3 69.5 1.0 C4' F:5AD301 3.4 82.4 1.0 C15 F:B12300 3.4 65.8 1.0 C20 F:B12300 3.6 65.8 1.0 O4' F:5AD301 3.9 82.2 1.0 C18 F:B12300 4.1 69.2 1.0 C2 F:B12300 4.1 65.1 1.0 C3 F:B12300 4.2 76.9 1.0 C8 F:B12300 4.2 62.9 1.0 C7 F:B12300 4.2 67.2 1.0 C17 F:B12300 4.2 70.6 1.0 C12 F:B12300 4.2 55.3 1.0 C13 F:B12300 4.3 53.7 1.0 CG F:HIS177 4.3 64.1 1.0 ND1 F:HIS177 4.3 66.0 1.0 C26 F:B12300 4.5 68.4 1.0 C3' F:5AD301 4.5 84.3 1.0 C35 F:B12300 4.7 70.4 1.0 C37 F:B12300 4.7 71.1 1.0 C53 F:B12300 4.9 65.7 1.0 C41 F:B12300 4.9 55.6 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ G:Co300 b:72.8 occ:1.00 CO G:B12300 0.0 72.8 1.0 N21 G:B12300 1.9 51.1 1.0 N24 G:B12300 1.9 58.0 1.0 N23 G:B12300 1.9 52.5 1.0 N22 G:B12300 1.9 53.7 1.0 C5' G:5AD301 2.0 69.3 1.0 NE2 G:HIS177 2.2 62.9 1.0 C9 G:B12300 2.9 55.0 1.0 C19 G:B12300 2.9 61.1 1.0 C4 G:B12300 2.9 54.0 1.0 C1 G:B12300 2.9 50.7 1.0 C11 G:B12300 2.9 50.8 1.0 C14 G:B12300 3.0 57.4 1.0 C16 G:B12300 3.0 59.9 1.0 C6 G:B12300 3.0 53.6 1.0 C4' G:5AD301 3.2 73.1 1.0 CD2 G:HIS177 3.2 63.2 1.0 CE1 G:HIS177 3.2 61.0 1.0 C10 G:B12300 3.3 53.5 1.0 C5 G:B12300 3.3 54.2 1.0 C15 G:B12300 3.4 60.6 1.0 C20 G:B12300 3.6 48.6 1.0 O4' G:5AD301 3.6 77.5 1.0 C18 G:B12300 4.1 60.2 1.0 C2 G:B12300 4.1 70.0 1.0 C3 G:B12300 4.2 54.7 1.0 C8 G:B12300 4.2 57.4 1.0 C17 G:B12300 4.2 62.9 1.0 C7 G:B12300 4.2 56.9 1.0 C12 G:B12300 4.3 47.0 1.0 C13 G:B12300 4.3 52.7 1.0 ND1 G:HIS177 4.3 63.4 1.0 CG G:HIS177 4.3 61.4 1.0 C26 G:B12300 4.5 67.0 1.0 C3' G:5AD301 4.5 75.8 1.0 C37 G:B12300 4.8 59.6 1.0 C41 G:B12300 4.8 50.0 1.0 C35 G:B12300 4.8 54.9 1.0 C53 G:B12300 4.9 64.2 1.0 C48 G:B12300 5.0 48.6 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State)


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 Full-Length Thermus Thermophilus Carh Bound to Adenosylcobalamin (Dark State) within 5.0Å range: probe atom residue distance (Å) B Occ H:Co300 b:65.0 occ:1.00 CO H:B12300 0.0 65.0 1.0 N21 H:B12300 1.9 62.5 1.0 N24 H:B12300 1.9 62.4 1.0 N22 H:B12300 1.9 59.7 1.0 N23 H:B12300 1.9 55.1 1.0 C5' H:5AD301 2.0 68.7 1.0 NE2 H:HIS177 2.3 69.1 1.0 C19 H:B12300 2.8 65.6 1.0 C4 H:B12300 2.9 59.3 1.0 C9 H:B12300 2.9 60.4 1.0 C1 H:B12300 2.9 62.2 1.0 C11 H:B12300 2.9 54.4 1.0 C6 H:B12300 3.0 58.1 1.0 C16 H:B12300 3.0 61.0 1.0 C14 H:B12300 3.0 55.5 1.0 C4' H:5AD301 3.1 67.9 1.0 CD2 H:HIS177 3.2 64.8 1.0 C10 H:B12300 3.3 53.4 1.0 CE1 H:HIS177 3.3 68.0 1.0 C5 H:B12300 3.3 55.5 1.0 C15 H:B12300 3.4 54.3 1.0 C20 H:B12300 3.6 58.9 1.0 O4' H:5AD301 3.6 67.5 1.0 C18 H:B12300 4.1 69.0 1.0 C2 H:B12300 4.1 61.9 1.0 C3 H:B12300 4.2 63.6 1.0 C8 H:B12300 4.2 66.3 1.0 C7 H:B12300 4.2 56.4 1.0 C17 H:B12300 4.2 65.9 1.0 C12 H:B12300 4.2 52.1 1.0 C13 H:B12300 4.3 57.8 1.0 CG H:HIS177 4.4 61.7 1.0 ND1 H:HIS177 4.4 66.3 1.0 C26 H:B12300 4.4 66.0 1.0 C3' H:5AD301 4.4 71.4 1.0 C35 H:B12300 4.7 55.2 1.0 C37 H:B12300 4.7 53.5 1.0 C41 H:B12300 4.9 62.6 1.0 C53 H:B12300 4.9 49.1 1.0 O3' H:5AD301 5.0 73.2 1.0 C1' H:5AD301 5.0 69.4 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