Cobalt in PDB 6vch: Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal, PDB code: 6vch was solved by A.Daruwalla, W.Shi, P.D.Kiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.13 / 2.35
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	107.250, 107.250, 490.238, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 23.4

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal (pdb code 6vch). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal, PDB code: 6vch:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:47.2 occ:1.00 O A:HOH604 2.0 42.6 1.0 NE2 A:HIS289 2.1 43.5 1.0 NE2 A:HIS222 2.1 45.5 1.0 NE2 A:HIS467 2.1 48.2 1.0 NE2 A:HIS172 2.1 49.5 1.0 CD2 A:HIS289 2.9 43.5 1.0 CD2 A:HIS222 2.9 45.0 1.0 CD2 A:HIS467 3.0 49.8 1.0 CE1 A:HIS172 3.1 50.9 1.0 CE1 A:HIS467 3.1 48.5 1.0 CE1 A:HIS289 3.2 43.2 1.0 CD2 A:HIS172 3.2 49.2 1.0 CE1 A:HIS222 3.2 44.4 1.0 O A:QVM502 4.1 58.7 1.0 CG A:HIS289 4.1 42.3 1.0 CG A:HIS222 4.1 44.2 1.0 CG A:HIS467 4.2 51.5 1.0 ND1 A:HIS467 4.2 51.4 1.0 ND1 A:HIS172 4.2 52.1 1.0 ND1 A:HIS289 4.2 42.2 1.0 ND1 A:HIS222 4.2 44.2 1.0 CG A:HIS172 4.3 50.2 1.0 CG1 A:VAL126 4.3 47.4 1.0 C16 A:QVM502 4.6 64.7 1.0

Cobalt binding site 2 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:43.6 occ:1.00 O B:HOH601 2.0 41.8 1.0 NE2 B:HIS289 2.1 40.5 1.0 NE2 B:HIS222 2.1 40.2 1.0 NE2 B:HIS172 2.1 45.0 1.0 NE2 B:HIS467 2.1 47.4 1.0 CD2 B:HIS289 2.9 40.1 1.0 CD2 B:HIS222 3.0 38.1 1.0 CD2 B:HIS467 3.0 47.2 1.0 CE1 B:HIS172 3.0 46.4 1.0 CE1 B:HIS289 3.1 40.2 1.0 CE1 B:HIS467 3.1 48.7 1.0 CD2 B:HIS172 3.1 44.6 1.0 CE1 B:HIS222 3.2 39.5 1.0 O B:QVM503 3.9 69.3 1.0 CG B:HIS289 4.1 40.5 1.0 CG B:HIS222 4.2 37.1 1.0 ND1 B:HIS172 4.2 46.0 1.0 CG B:HIS467 4.2 48.4 1.0 ND1 B:HIS289 4.2 40.3 1.0 ND1 B:HIS467 4.2 48.8 1.0 ND1 B:HIS222 4.2 38.0 1.0 CG B:HIS172 4.2 44.9 1.0 CG1 B:VAL126 4.2 43.4 1.0 C16 B:QVM503 4.7 68.8 1.0

Cobalt binding site 3 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:52.3 occ:1.00 O C:HOH604 2.0 53.4 1.0 NE2 C:HIS172 2.1 52.1 1.0 NE2 C:HIS222 2.1 46.8 1.0 NE2 C:HIS289 2.1 51.9 1.0 NE2 C:HIS467 2.1 54.1 1.0 CD2 C:HIS222 3.0 45.8 1.0 CD2 C:HIS289 3.0 51.0 1.0 CD2 C:HIS467 3.0 55.3 1.0 CE1 C:HIS172 3.0 53.0 1.0 CD2 C:HIS172 3.1 51.9 1.0 CE1 C:HIS467 3.1 54.8 1.0 CE1 C:HIS222 3.2 46.8 1.0 CE1 C:HIS289 3.2 50.9 1.0 O C:QVM502 4.1 72.1 1.0 CG C:HIS467 4.1 57.0 1.0 ND1 C:HIS172 4.1 52.1 1.0 CG C:HIS222 4.2 45.6 1.0 ND1 C:HIS467 4.2 55.9 1.0 CG C:HIS289 4.2 50.2 1.0 CG1 C:VAL126 4.2 53.2 1.0 CG C:HIS172 4.2 52.2 1.0 ND1 C:HIS222 4.2 46.9 1.0 ND1 C:HIS289 4.2 50.1 1.0 C16 C:QVM502 4.8 74.1 1.0

Cobalt binding site 4 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ D:Co501 b:55.9 occ:1.00 O D:HOH605 2.0 57.8 1.0 NE2 D:HIS289 2.1 55.0 1.0 NE2 D:HIS172 2.1 57.7 1.0 NE2 D:HIS467 2.1 57.7 1.0 NE2 D:HIS222 2.1 51.9 1.0 CD2 D:HIS289 3.0 54.2 1.0 CD2 D:HIS222 3.0 49.7 1.0 CD2 D:HIS467 3.0 60.6 1.0 CE1 D:HIS172 3.0 58.3 1.0 CE1 D:HIS467 3.1 58.3 1.0 CD2 D:HIS172 3.1 56.9 1.0 CE1 D:HIS289 3.2 55.5 1.0 CE1 D:HIS222 3.2 52.2 1.0 CG D:HIS467 4.1 61.8 1.0 ND1 D:HIS172 4.1 58.6 1.0 O D:QVM502 4.2 76.0 1.0 ND1 D:HIS467 4.2 60.5 1.0 CG D:HIS289 4.2 54.2 1.0 CG D:HIS222 4.2 49.2 1.0 CG D:HIS172 4.2 57.1 1.0 CG1 D:VAL126 4.2 64.5 1.0 ND1 D:HIS289 4.3 55.4 1.0 ND1 D:HIS222 4.3 49.6 1.0 C16 D:QVM502 4.9 79.3 1.0

Cobalt binding site 5 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ E:Co501 b:72.8 occ:1.00 O E:HOH605 2.0 67.7 1.0 NE2 E:HIS467 2.1 80.0 1.0 NE2 E:HIS222 2.1 61.5 1.0 NE2 E:HIS172 2.1 74.2 1.0 NE2 E:HIS289 2.2 79.1 1.0 CD2 E:HIS467 3.0 80.2 1.0 CD2 E:HIS222 3.0 60.4 1.0 CD2 E:HIS289 3.1 78.6 1.0 CE1 E:HIS172 3.1 75.9 1.0 CE1 E:HIS467 3.1 82.3 1.0 CE1 E:HIS222 3.1 58.6 1.0 CD2 E:HIS172 3.2 71.1 1.0 CE1 E:HIS289 3.2 80.2 1.0 CG E:HIS467 4.1 82.1 1.0 ND1 E:HIS467 4.1 84.0 1.0 CG E:HIS222 4.2 57.8 1.0 ND1 E:HIS172 4.2 74.4 1.0 ND1 E:HIS222 4.2 57.1 1.0 CG1 E:VAL126 4.2 62.2 1.0 CG E:HIS289 4.2 79.7 1.0 CG E:HIS172 4.3 70.2 1.0 ND1 E:HIS289 4.3 81.4 1.0

Cobalt binding site 6 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal


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 Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase in Complex with 3-Hydroxy-Beta-Apo-14'-Carotenal within 5.0Å range: probe atom residue distance (Å) B Occ F:Co1000 b:89.3 occ:1.00 NE2 F:HIS222 2.1 81.0 1.0 NE2 F:HIS467 2.1 94.9 1.0 NE2 F:HIS172 2.1 87.7 1.0 NE2 F:HIS289 2.2 96.0 1.0 CD2 F:HIS467 3.0 94.0 1.0 CD2 F:HIS222 3.0 81.1 1.0 CD2 F:HIS289 3.1 96.2 1.0 CE1 F:HIS172 3.1 90.1 1.0 CE1 F:HIS467 3.1 98.8 1.0 CE1 F:HIS222 3.1 78.3 1.0 CD2 F:HIS172 3.2 84.4 1.0 CE1 F:HIS289 3.2 99.4 1.0 CG F:HIS467 4.1 96.7 1.0 ND1 F:HIS467 4.2 0.0 1.0 CG F:HIS222 4.2 78.3 1.0 CG1 F:VAL126 4.2 83.3 1.0 ND1 F:HIS222 4.2 77.1 1.0 ND1 F:HIS172 4.2 88.3 1.0 CG F:HIS289 4.3 98.7 1.0 CG F:HIS172 4.3 85.1 1.0 ND1 F:HIS289 4.3 0.4 1.0

A.Daruwalla, J.Zhang, H.J.Lee, N.Khadka, E.R.Farquhar, W.Shi, J.Von Lintig, P.D.Kiser. Structural Basis For Carotenoid Cleavage By An Archaeal Carotenoid Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 117 19914 2020.
ISSN: ESSN 1091-6490
PubMed: 32747548
DOI: 10.1073/PNAS.2004116117