Sodium in PDB 6rp4: Cdt of Sidd, Deampylase From Legionella Pneumophila

The structure of Cdt of Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rp4 was solved by I.Tascon, M.Lucas, A.L.Rojas, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 2.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	165.579, 165.579, 68.712, 90.00, 90.00, 120.00
R / Rfree (%)	26.3 / 29.6

The structure of Cdt of Sidd, Deampylase From Legionella Pneumophila also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Cdt of Sidd, Deampylase From Legionella Pneumophila (pdb code 6rp4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cdt of Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rp4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:41.9 occ:1.00 O A:ASN392 3.3 56.2 1.0 C A:ASN392 3.4 47.5 1.0 O A:HOH701 3.4 38.3 1.0 N A:LEU393 3.6 46.3 1.0 CB A:ASN392 3.6 47.2 1.0 NE2 A:HIS486 3.6 61.7 1.0 CA A:LEU393 3.8 43.2 1.0 CA A:ASN392 4.1 42.0 1.0 CD2 A:LEU393 4.1 44.3 1.0 CE1 A:HIS486 4.2 64.6 1.0 CG A:LEU393 4.3 44.9 1.0 NA A:NA605 4.4 47.0 1.0 CB A:LEU393 4.6 44.4 1.0 CD2 A:HIS486 4.8 64.1 1.0 CB A:LYS396 4.9 52.1 1.0 CG A:ASN392 4.9 43.6 1.0 OH A:TYR476 4.9 42.4 1.0

Sodium binding site 2 out of 3 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:47.0 occ:1.00 ND2 A:ASN392 2.5 41.2 1.0 O A:HOH701 3.2 38.3 1.0 CB A:ASN392 3.3 47.2 1.0 CG A:ASN392 3.3 43.6 1.0 CD2 A:LEU389 3.7 49.7 1.0 CA A:LEU389 4.1 40.8 1.0 OH A:TYR476 4.3 42.4 1.0 O A:THR388 4.4 40.8 1.0 NA A:NA604 4.4 41.9 1.0 OD1 A:ASN392 4.5 42.1 1.0 O A:LEU389 4.6 41.3 1.0 N A:LEU389 4.7 40.4 1.0 CA A:ASN392 4.7 42.0 1.0 CB A:LEU389 4.8 41.6 1.0 C A:THR388 4.8 42.5 1.0 CG A:LEU389 4.8 43.1 1.0 C A:LEU389 4.9 40.8 1.0 CG2 A:THR388 4.9 48.6 1.0

Sodium binding site 3 out of 3 in the Cdt of Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cdt of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:52.4 occ:1.00 O A:HOH716 2.7 48.4 1.0 CB A:ALA481 3.5 47.8 1.0 OD1 A:ASN479 4.7 57.1 1.0 CA A:ALA481 4.9 44.7 1.0

I.Tascon, X.Li, M.Lucas, D.Nelson, A.Vidaurrazaga, Y.H.Lin, A.L.Rojas, A.Hierro, M.P.Machner. Structural Insight Into the Membrane Targeting Domain of the Legionella Deampylase Sidd. Plos Pathog. V. 16 08734 2020.
ISSN: ESSN 1553-7374
PubMed: 32853279
DOI: 10.1371/JOURNAL.PPAT.1008734