Nickel in PDB 6deh: Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia)

The structure of Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia), PDB code: 6deh was solved by K.Voth, I.Y.W.Chung, K.E.Van Straaten, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.77 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.704, 84.064, 128.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.4

The binding sites of Nickel atom in the Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia) (pdb code 6deh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia), PDB code: 6deh:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:24.5 occ:1.00 NE2 A:HIS53 2.1 21.1 1.0 O A:HOH621 2.1 20.4 1.0 NE2 A:HIS52 2.1 25.5 1.0 O A:HOH619 2.2 22.8 1.0 CD2 A:HIS53 3.0 26.0 1.0 CD2 A:HIS52 3.1 26.7 1.0 CE1 A:HIS52 3.1 22.2 1.0 CE1 A:HIS53 3.1 28.5 1.0 CG A:HIS53 4.2 23.6 1.0 ND1 A:HIS53 4.2 28.6 1.0 ND1 A:HIS52 4.2 25.1 1.0 CG A:HIS52 4.2 27.8 1.0 O A:HOH516 4.4 21.9 1.0 O A:HOH641 4.5 47.7 1.0

Nickel binding site 2 out of 3 in the Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:24.6 occ:1.00 N A:HIS50 1.9 22.3 1.0 N A:HIS51 1.9 20.9 1.0 ND1 A:HIS51 1.9 26.6 1.0 N A:MET49 2.1 22.9 1.0 C A:HIS50 2.7 25.1 1.0 C A:MET49 2.8 24.7 1.0 CA A:HIS50 2.8 23.5 1.0 CA A:MET49 2.9 26.9 1.0 CE1 A:HIS51 2.9 34.1 1.0 CG A:HIS51 2.9 27.2 1.0 CA A:HIS51 3.0 25.0 1.0 CB A:HIS51 3.3 28.1 1.0 H12 A:GOL404 3.5 46.6 1.0 O A:HOH600 3.6 29.5 1.0 N A:HIS52 3.7 23.3 1.0 C A:HIS51 3.8 28.2 1.0 O A:HIS50 3.9 24.0 1.0 CG A:HIS50 3.9 23.3 1.0 CB A:HIS50 3.9 21.3 1.0 H2 A:GOL404 4.0 56.0 1.0 O A:MET49 4.0 25.2 1.0 CB A:MET49 4.0 26.9 1.0 NE2 A:HIS51 4.0 34.5 1.0 HO2 A:GOL404 4.1 48.2 1.0 O1 A:GOL404 4.1 40.4 1.0 C1 A:GOL404 4.1 38.8 1.0 CD2 A:HIS51 4.1 28.0 1.0 CD2 A:HIS50 4.2 26.0 1.0 O2 A:GOL404 4.2 40.1 1.0 ND1 A:HIS52 4.2 25.1 1.0 C2 A:GOL404 4.3 46.7 1.0 ND1 A:HIS50 4.4 24.9 1.0 O A:HOH637 4.6 37.0 1.0 CE1 A:HIS52 4.7 22.2 1.0 NE2 A:HIS50 4.8 27.2 1.0 HO1 A:GOL404 4.9 48.5 1.0 CE1 A:HIS50 4.9 29.8 1.0 CG A:HIS52 4.9 27.8 1.0 H11 A:GOL404 5.0 46.6 1.0 O A:HIS51 5.0 27.4 1.0 CG A:MET49 5.0 32.1 1.0

Nickel binding site 3 out of 3 in the Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Lpne Effector Protein From Legionella Pneumophila (Sp. Philadelphia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:21.9 occ:0.88 N B:HIS50 1.9 21.0 1.0 N B:HIS51 1.9 20.3 1.0 ND1 B:HIS51 2.0 23.8 1.0 N B:MET49 2.0 25.2 1.0 C B:MET49 2.7 27.9 1.0 C B:HIS50 2.8 24.2 1.0 CA B:MET49 2.8 26.6 1.0 CA B:HIS50 2.9 22.0 1.0 CG B:HIS51 2.9 21.8 1.0 CA B:HIS51 3.0 22.4 1.0 CE1 B:HIS51 3.0 25.8 1.0 CB B:HIS51 3.2 24.1 1.0 N B:HIS52 3.7 21.9 1.0 C B:HIS51 3.8 24.4 1.0 CB B:MET49 3.9 27.1 1.0 O B:MET49 3.9 26.1 1.0 O B:HIS50 3.9 23.1 1.0 O B:HOH628 4.0 39.5 1.0 CD2 B:HIS51 4.0 25.4 1.0 NE2 B:HIS51 4.1 25.1 1.0 CB B:HIS50 4.1 22.0 1.0 O B:HOH608 4.1 32.3 1.0 CG B:HIS50 4.2 27.2 1.0 CD2 B:HIS50 4.3 27.1 1.0 ND1 B:HIS52 4.4 20.8 1.0 CG B:MET49 4.8 29.4 1.0 O B:HIS51 4.9 22.6 1.0 CE1 B:HIS52 5.0 24.1 1.0 ND1 B:HIS50 5.0 23.4 1.0

K.A.Voth, I.Y.W.Chung, K.Van Straaten, L.Li, M.T.Boniecki, M.Cygler. The Structure of Legionella Effector Protein Lpne Provides Insights Into Its Interaction with Oculocerebrorenal Syndrome of Lowe (Ocrl) Protein. Febs J. V. 286 710 2019.
ISSN: ISSN 1742-4658
PubMed: 30479037
DOI: 10.1111/FEBS.14710