Cobalt in PDB 6vcg: Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form, PDB code: 6vcg 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)	49.44 / 2.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	108.010, 108.010, 491.610, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 25.4

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form 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, Cobalt Form (pdb code 6vcg). 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, Cobalt Form, PDB code: 6vcg:
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, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1000 b:42.7 occ:1.00 O A:HOH1122 2.0 41.4 1.0 NE2 A:HIS467 2.1 44.6 1.0 NE2 A:HIS222 2.1 40.6 1.0 NE2 A:HIS289 2.1 41.6 1.0 NE2 A:HIS172 2.1 45.5 1.0 CD2 A:HIS222 2.9 40.5 1.0 CD2 A:HIS467 3.0 46.2 1.0 CD2 A:HIS289 3.0 41.7 1.0 CE1 A:HIS172 3.1 46.5 1.0 CE1 A:HIS467 3.1 45.4 1.0 CD2 A:HIS172 3.1 45.9 1.0 CE1 A:HIS289 3.2 40.9 1.0 CE1 A:HIS222 3.2 40.2 1.0 CG A:HIS467 4.1 47.4 1.0 ND1 A:HIS467 4.1 47.0 1.0 CG A:HIS222 4.1 40.3 1.0 ND1 A:HIS172 4.2 47.4 1.0 CG A:HIS289 4.2 41.3 1.0 CG A:HIS172 4.2 47.1 1.0 O A:HOH1209 4.2 35.8 1.0 ND1 A:HIS222 4.3 39.9 1.0 ND1 A:HIS289 4.3 40.9 1.0 CG1 A:VAL126 4.3 43.3 1.0

Cobalt binding site 2 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:38.5 occ:1.00 O B:HOH646 2.0 38.6 1.0 NE2 B:HIS222 2.1 36.2 1.0 NE2 B:HIS289 2.1 39.0 1.0 NE2 B:HIS467 2.1 41.1 1.0 NE2 B:HIS172 2.1 39.2 1.0 CD2 B:HIS222 2.9 35.8 1.0 CD2 B:HIS467 3.0 42.2 1.0 CD2 B:HIS289 3.0 38.5 1.0 CE1 B:HIS172 3.1 39.6 1.0 CE1 B:HIS467 3.1 42.1 1.0 CD2 B:HIS172 3.2 38.4 1.0 CE1 B:HIS289 3.2 38.9 1.0 CE1 B:HIS222 3.2 36.2 1.0 CG B:HIS222 4.1 35.3 1.0 CG B:HIS467 4.1 43.2 1.0 ND1 B:HIS467 4.2 42.7 1.0 CG B:HIS289 4.2 38.7 1.0 ND1 B:HIS172 4.2 39.2 1.0 CG1 B:VAL126 4.2 39.1 1.0 ND1 B:HIS289 4.2 38.8 1.0 ND1 B:HIS222 4.2 35.6 1.0 CG B:HIS172 4.3 38.7 1.0 O B:HOH732 4.4 41.6 1.0

Cobalt binding site 3 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:54.2 occ:1.00 O C:HOH619 2.0 53.4 1.0 NE2 C:HIS467 2.1 56.7 1.0 NE2 C:HIS289 2.1 54.3 1.0 NE2 C:HIS222 2.1 49.9 1.0 NE2 C:HIS172 2.1 55.0 1.0 CD2 C:HIS222 2.9 49.3 1.0 CD2 C:HIS289 3.0 54.2 1.0 CD2 C:HIS467 3.0 58.5 1.0 CE1 C:HIS467 3.1 58.0 1.0 CE1 C:HIS172 3.1 56.0 1.0 CE1 C:HIS289 3.1 53.0 1.0 CD2 C:HIS172 3.2 54.1 1.0 CE1 C:HIS222 3.3 49.4 1.0 CG C:HIS467 4.1 60.4 1.0 ND1 C:HIS467 4.1 59.3 1.0 CG C:HIS222 4.2 48.4 1.0 CG C:HIS289 4.2 53.2 1.0 ND1 C:HIS172 4.2 56.1 1.0 ND1 C:HIS289 4.2 52.9 1.0 CG C:HIS172 4.3 55.1 1.0 ND1 C:HIS222 4.3 48.6 1.0 CG1 C:VAL126 4.3 52.9 1.0

Cobalt binding site 4 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1000 b:53.8 occ:1.00 O D:HOH1125 2.0 55.0 1.0 NE2 D:HIS289 2.1 52.2 1.0 NE2 D:HIS467 2.1 55.5 1.0 NE2 D:HIS172 2.1 55.6 1.0 NE2 D:HIS222 2.1 50.0 1.0 CD2 D:HIS222 2.9 48.5 1.0 CD2 D:HIS289 3.0 51.4 1.0 CD2 D:HIS467 3.0 57.5 1.0 CE1 D:HIS172 3.1 56.3 1.0 CE1 D:HIS467 3.1 56.1 1.0 CD2 D:HIS172 3.1 55.5 1.0 CE1 D:HIS289 3.2 51.6 1.0 CE1 D:HIS222 3.3 49.9 1.0 CG D:HIS467 4.1 59.0 1.0 ND1 D:HIS467 4.1 57.3 1.0 CG D:HIS222 4.2 47.8 1.0 CG D:HIS289 4.2 50.6 1.0 ND1 D:HIS172 4.2 56.5 1.0 ND1 D:HIS289 4.2 50.7 1.0 CG D:HIS172 4.2 55.9 1.0 ND1 D:HIS222 4.3 48.6 1.0 CG1 D:VAL126 4.3 59.6 1.0 O D:HOH1183 4.4 50.7 1.0

Cobalt binding site 5 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Co501 b:61.7 occ:1.00 O E:HOH601 1.9 59.5 1.0 NE2 E:HIS467 2.1 68.3 1.0 NE2 E:HIS222 2.1 53.9 1.0 NE2 E:HIS289 2.1 66.5 1.0 NE2 E:HIS172 2.1 62.9 1.0 CD2 E:HIS222 2.9 53.3 1.0 CD2 E:HIS467 3.0 68.5 1.0 CD2 E:HIS289 3.0 67.8 1.0 CE1 E:HIS467 3.0 71.8 1.0 CE1 E:HIS172 3.1 65.2 1.0 CE1 E:HIS289 3.1 67.9 1.0 CD2 E:HIS172 3.1 61.0 1.0 CE1 E:HIS222 3.2 51.4 1.0 CG E:HIS467 4.1 71.6 1.0 ND1 E:HIS467 4.1 73.4 1.0 CG E:HIS222 4.1 51.4 1.0 CG E:HIS289 4.2 69.9 1.0 ND1 E:HIS172 4.2 64.8 1.0 ND1 E:HIS289 4.2 70.2 1.0 ND1 E:HIS222 4.2 50.2 1.0 CG E:HIS172 4.2 61.7 1.0 CG1 E:VAL126 4.3 58.5 1.0

Cobalt binding site 6 out of 6 in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Cobalt Form


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, Cobalt Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Co1000 b:71.1 occ:1.00 NE2 F:HIS222 2.1 67.7 1.0 NE2 F:HIS467 2.1 74.8 1.0 NE2 F:HIS172 2.1 71.3 1.0 NE2 F:HIS289 2.2 74.0 1.0 CD2 F:HIS222 2.9 67.3 1.0 CD2 F:HIS467 3.0 74.4 1.0 CE1 F:HIS467 3.1 76.8 1.0 CE1 F:HIS172 3.1 72.9 1.0 CD2 F:HIS289 3.1 74.0 1.0 CD2 F:HIS172 3.1 69.9 1.0 CE1 F:HIS222 3.2 66.8 1.0 CE1 F:HIS289 3.2 75.8 1.0 CG F:HIS467 4.1 76.8 1.0 CG F:HIS222 4.1 65.7 1.0 ND1 F:HIS467 4.1 77.8 1.0 ND1 F:HIS222 4.2 65.6 1.0 ND1 F:HIS172 4.2 72.2 1.0 CG1 F:VAL126 4.2 72.1 1.0 CG F:HIS172 4.3 70.2 1.0 CG F:HIS289 4.3 75.5 1.0 ND1 F:HIS289 4.3 76.8 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