Sodium in PDB 6vcf: Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Iron Form

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Iron Form, PDB code: 6vcf 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)	49.15 / 2.69
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	107.267, 107.267, 491.109, 90.00, 90.00, 120.00
R / Rfree (%)	25.2 / 27.1

The structure of Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Iron Form also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Nitrosotalea Devanaterra Carotenoid Cleavage Dioxygenase, Iron Form (pdb code 6vcf). 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, Iron Form, PDB code: 6vcf:
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, Iron Form


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, Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:70.5 occ:1.00 OG C:SER378 2.2 75.2 1.0 O A:ALA382 2.4 0.1 1.0 OE1 C:GLU354 2.4 75.7 1.0 O C:THR379 2.9 75.5 1.0 OE1 C:GLN388 3.0 83.1 1.0 OG A:SER383 3.1 0.7 1.0 CB C:SER378 3.5 73.9 1.0 C A:ALA382 3.5 97.5 1.0 CD C:GLU354 3.6 77.8 1.0 C C:THR379 3.7 76.4 1.0 N C:THR379 3.8 72.7 1.0 CD C:GLN388 3.9 84.1 1.0 CA A:SER383 4.0 100.0 1.0 CB A:SER383 4.0 0.4 1.0 N A:SER383 4.1 97.9 1.0 OE2 C:GLU354 4.2 81.5 1.0 O C:ALA355 4.4 66.7 1.0 N C:ALA355 4.4 67.8 1.0 CA C:THR379 4.4 73.9 1.0 NE2 C:GLN388 4.5 86.5 1.0 CA C:SER378 4.5 70.9 1.0 N C:TYR380 4.6 79.8 1.0 CA A:ALA382 4.6 94.4 1.0 C C:SER378 4.7 71.1 1.0 CB C:GLU354 4.7 73.0 1.0 CG C:GLU354 4.7 76.5 1.0 CA C:GLU354 4.8 71.8 1.0 CG C:GLN388 4.8 82.5 1.0 CA C:TYR380 4.9 83.4 1.0 CB A:ALA382 4.9 94.2 1.0 CB C:ALA355 5.0 64.9 1.0

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


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, Iron Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:80.0 occ:1.00 OG B:SER378 2.2 70.4 1.0 OE1 B:GLU354 2.4 75.3 1.0 O D:ALA382 2.5 0.4 1.0 O B:THR379 2.9 73.0 1.0 OE1 B:GLN388 2.9 77.5 1.0 OG D:SER383 3.2 0.6 1.0 CB B:SER378 3.4 69.0 1.0 C D:ALA382 3.5 0.6 1.0 CD B:GLU354 3.6 77.5 1.0 C B:THR379 3.8 73.7 1.0 N B:THR379 3.8 68.8 1.0 CD B:GLN388 3.9 78.9 1.0 CA D:SER383 4.1 0.1 1.0 OE2 B:GLU354 4.2 81.3 1.0 CB D:SER383 4.2 0.5 1.0 N D:SER383 4.2 0.8 1.0 CA B:THR379 4.5 70.7 1.0 O B:ALA355 4.5 63.2 1.0 NE2 B:GLN388 4.5 81.9 1.0 N B:ALA355 4.5 65.7 1.0 CA B:SER378 4.6 65.8 1.0 CA D:ALA382 4.6 97.8 1.0 N B:TYR380 4.6 77.4 1.0 C B:SER378 4.7 66.4 1.0 CG B:GLU354 4.7 76.0 1.0 CB B:GLU354 4.7 72.1 1.0 CG B:GLN388 4.8 76.9 1.0 CA B:GLU354 4.9 71.2 1.0 CB D:ALA382 4.9 98.2 1.0 CA B:TYR380 4.9 81.3 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