Sodium in PDB 4l3f: Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes

The structure of Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes, PDB code: 4l3f was solved by D.Neves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.100, 89.500, 186.300, 90.00, 103.50, 90.00
R / Rfree (%)	19.2 / 23.2

The structure of Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes (pdb code 4l3f). 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 Internalin K (Inlk) From Listeria Monocytogenes, PDB code: 4l3f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes


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 Internalin K (Inlk) From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ G:Na401 b:32.6 occ:1.00 O G:HOH553 2.1 33.9 1.0 O G:HOH552 2.3 23.1 1.0 O G:PRO216 4.0 30.0 1.0 OE1 G:GLN337 4.2 23.9 1.0 O G:PHE215 4.5 26.6 1.0 O G:GLU213 4.5 32.2 1.0 CD G:GLN337 4.5 25.5 1.0 C G:PRO216 4.7 24.6 1.0 NE2 G:GLN337 4.7 25.4 1.0 CB G:GLN337 4.7 24.0 1.0 CA G:PRO216 4.9 24.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Internalin K (Inlk) From Listeria Monocytogenes


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 Internalin K (Inlk) From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ H:Na401 b:29.6 occ:1.00 O H:HOH569 2.0 45.2 1.0 O H:HOH568 2.3 38.7 1.0 OE1 H:GLN337 2.9 36.1 1.0 O H:PHE215 3.3 28.0 1.0 CD H:GLN337 3.3 34.7 1.0 NE2 H:GLN337 3.6 33.0 1.0 O H:GLU213 3.6 30.3 1.0 O H:PRO216 3.6 42.8 1.0 C H:PRO216 4.2 35.4 1.0 CB H:GLN337 4.3 33.5 1.0 CA H:PRO216 4.3 32.7 1.0 CG H:GLN337 4.4 32.2 1.0 C H:PHE215 4.4 28.1 1.0 C H:GLU213 4.7 29.0 1.0 O H:HOH572 4.7 25.1 1.0 N H:PRO216 4.9 32.0 1.0

D.Neves, V.Job, L.Dortet, P.Cossart, A.Dessen. Structure of Internalin Inlk From the Human Pathogen Listeria Monocytogenes. J.Mol.Biol. V. 425 4520 2013.
ISSN: ISSN 0022-2836
PubMed: 23958637
DOI: 10.1016/J.JMB.2013.08.010