Nickel 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:

Sodium

(Na)

2 atoms

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

Nickel 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 Nickel with other atoms in the Ni 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 B:Ni401 b:36.2 occ:1.00 OE1 B:GLN337 3.2 30.9 1.0 O B:PHE215 3.3 24.6 1.0 O B:GLU213 3.5 28.5 1.0 O B:PRO216 3.7 24.6 1.0 CD B:GLN337 3.8 28.2 1.0 O B:HOH592 3.9 28.4 1.0 CA B:PRO216 4.0 20.6 1.0 NE2 B:GLN337 4.0 26.6 1.0 C B:PRO216 4.1 22.0 1.0 C B:PHE215 4.4 23.5 1.0 C B:GLU213 4.6 28.4 1.0 N B:PRO216 4.8 22.1 1.0 O B:HOH587 4.8 42.9 1.0 CG B:GLN337 4.9 26.8 1.0 CB B:GLN337 5.0 26.8 1.0

Nickel 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 Nickel with other atoms in the Ni 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 F:Ni401 b:40.2 occ:1.00 O F:PHE215 3.3 25.6 1.0 O F:GLU213 3.3 28.9 1.0 OE1 F:GLN337 3.4 31.5 1.0 NE2 F:GLN337 3.5 28.8 1.0 O F:HOH587 3.5 33.4 1.0 CD F:GLN337 3.7 27.9 1.0 O F:HOH582 3.8 31.4 1.0 O F:PRO216 4.1 30.0 1.0 C F:GLU213 4.4 29.7 1.0 C F:PHE215 4.4 23.6 1.0 CA F:PRO216 4.5 22.8 1.0 C F:PRO216 4.5 25.2 1.0 CG F:GLN337 4.8 28.6 1.0 CB F:GLN337 4.8 27.2 1.0 CA F:GLU213 5.0 32.6 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