Sodium 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:

Cobalt	(Co)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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 B:Na502 b:73.5 occ:1.00 OE1 B:GLU354 2.3 73.2 1.0 O B:THR379 2.3 65.9 1.0 OG B:SER378 2.4 65.1 1.0 O D:ALA382 2.6 66.6 1.0 OE1 B:GLN388 2.7 68.4 1.0 OG D:SER383 2.7 73.6 1.0 C B:THR379 3.3 66.3 1.0 CD B:GLU354 3.4 74.7 1.0 C D:ALA382 3.4 66.0 1.0 CB B:SER378 3.4 62.7 1.0 N B:THR379 3.5 61.7 1.0 CD B:GLN388 3.7 69.1 1.0 OE2 B:GLU354 3.8 79.0 1.0 CB D:SER383 3.9 72.5 1.0 CA D:SER383 3.9 69.7 1.0 N D:SER383 4.0 66.2 1.0 CA B:THR379 4.1 63.5 1.0 NE2 B:GLN388 4.1 70.8 1.0 N B:TYR380 4.1 68.6 1.0 C B:SER378 4.3 60.2 1.0 CA B:SER378 4.4 61.0 1.0 CA D:ALA382 4.4 63.9 1.0 CA B:TYR380 4.4 72.0 1.0 O B:HOH608 4.5 80.0 1.0 CB D:ALA382 4.5 64.6 1.0 O B:ALA355 4.6 62.0 1.0 N B:ALA355 4.7 61.5 1.0 CG B:GLU354 4.7 72.8 1.0 CG B:GLN388 4.9 69.2 1.0 CB B:GLU354 4.9 68.9 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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 C:Na503 b:62.5 occ:1.00 OE1 C:GLU354 2.2 63.4 1.0 O C:THR379 2.4 64.3 1.0 OG C:SER378 2.4 64.3 1.0 OG A:SER383 2.6 68.2 1.0 OE1 C:GLN388 2.6 68.8 1.0 O A:ALA382 2.7 62.5 1.0 C C:THR379 3.3 64.8 1.0 CD C:GLU354 3.3 64.7 1.0 CB C:SER378 3.4 64.0 1.0 C A:ALA382 3.5 61.4 1.0 N C:THR379 3.6 62.2 1.0 CD C:GLN388 3.6 71.1 1.0 CB A:SER383 3.7 66.3 1.0 OE2 C:GLU354 3.8 69.1 1.0 CA A:SER383 3.9 64.2 1.0 N A:SER383 4.0 61.8 1.0 NE2 C:GLN388 4.1 72.3 1.0 CA C:THR379 4.1 63.6 1.0 N C:TYR380 4.1 66.2 1.0 C C:SER378 4.3 62.1 1.0 CA C:TYR380 4.4 68.2 1.0 CA C:SER378 4.4 62.4 1.0 CA A:ALA382 4.5 59.8 1.0 CB A:ALA382 4.6 60.0 1.0 CG C:GLU354 4.6 64.3 1.0 N C:ALA355 4.7 57.5 1.0 O C:ALA355 4.7 59.4 1.0 O C:HOH607 4.8 80.0 1.0 CB C:GLU354 4.9 61.2 1.0 CG C:GLN388 4.9 72.1 1.0 CA C:GLU354 5.0 59.6 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