Sodium in PDB 5miy: Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila

All present enzymatic activity of Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila:
6.3.2.19;

The structure of Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila, PDB code: 5miy was solved by M.Lucas, G.Abascal-Palacios, A.L.Rojas, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 1.72
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.160, 177.010, 79.450, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

The binding sites of Sodium atom in the Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila (pdb code 5miy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila, PDB code: 5miy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the E3 Ubiquitin Ligase Ravn 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 Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:66.7 occ:1.00 O C:HOH365 2.6 65.0 1.0 O A:SER45 3.1 40.9 1.0 O A:HOH355 3.2 64.4 1.0 OG A:SER45 3.3 45.4 1.0 CD A:PRO44 3.9 33.9 1.0 C A:SER45 3.9 39.4 1.0 N A:SER45 4.1 35.8 1.0 CG A:PRO44 4.1 33.0 1.0 CD2 A:LEU43 4.2 36.9 1.0 CA A:PRO47 4.2 44.1 1.0 CA A:SER45 4.4 37.5 1.0 O A:ASP46 4.4 43.4 1.0 N A:PRO47 4.4 41.8 1.0 C A:ASP46 4.4 42.5 1.0 CB A:SER45 4.4 42.6 1.0 CD2 A:HIS50 4.5 65.8 1.0 CB A:LEU43 4.6 32.3 1.0 O A:HOH327 4.6 62.3 1.0 N A:PRO44 4.6 32.8 1.0 CG2 C:ILE88 4.7 29.9 1.0 NE2 A:HIS50 4.8 70.7 1.0 CG A:LEU43 4.8 33.6 1.0 CG A:PRO47 4.8 39.5 1.0 N A:ASP46 4.8 42.2 1.0 CD A:PRO47 4.9 38.4 1.0 CD1 C:ILE88 4.9 33.1 1.0 CD1 A:LEU43 5.0 37.5 1.0 CB A:PRO47 5.0 42.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the E3 Ubiquitin Ligase Ravn 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 Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:45.4 occ:1.00 O C:ILE88 2.6 30.9 1.0 O C:HOH380 2.7 40.9 1.0 O A:HIS42 2.7 38.5 1.0 C C:ILE88 3.5 30.8 1.0 CD A:PRO44 3.6 33.9 1.0 CB A:VAL107 3.6 29.9 1.0 CG2 C:ILE88 3.7 29.9 1.0 C A:HIS42 3.8 36.9 1.0 CA C:ALA92 3.9 32.3 0.6 CG1 A:VAL107 3.9 29.1 1.0 CA C:ALA92 3.9 32.2 0.4 CB C:ALA92 4.0 30.4 0.4 CG2 A:VAL107 4.0 33.5 1.0 O A:HOH335 4.0 34.5 1.0 CA A:LEU43 4.0 34.6 1.0 CA C:GLU89 4.0 28.2 1.0 O A:HOH319 4.0 37.3 1.0 N C:GLU89 4.1 30.2 1.0 N A:PRO44 4.1 32.8 1.0 O C:GLU89 4.2 33.6 1.0 N C:ALA92 4.3 31.1 0.6 N C:ALA92 4.3 32.0 0.4 C A:LEU43 4.3 32.5 1.0 C C:GLU89 4.3 32.1 1.0 N A:LEU43 4.4 35.2 1.0 CG A:PRO44 4.4 33.0 1.0 CB C:ALA92 4.5 30.0 0.6 CA C:ILE88 4.5 29.4 1.0 CB C:ILE88 4.7 29.8 1.0 CB A:PRO44 4.8 33.0 1.0 CA A:HIS42 4.9 38.5 1.0 C C:ALA92 4.9 35.9 0.6 O C:ALA92 4.9 38.4 0.6 O C:HOH375 5.0 63.2 1.0 CA A:VAL107 5.0 32.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the E3 Ubiquitin Ligase Ravn 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 Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ C:Na206 b:37.9 occ:1.00 O A:HOH301 2.7 31.7 1.0 O C:HOH318 2.7 55.7 1.0 O C:ILE57 2.8 29.4 1.0 N C:VAL21 3.1 33.6 1.0 O C:VAL21 3.3 28.2 1.0 CA C:ILE20 3.8 31.6 1.0 O C:HOH356 3.8 48.0 1.0 C C:ILE57 3.9 27.0 1.0 O C:THR19 3.9 35.3 1.0 C C:ILE20 3.9 35.6 1.0 CA C:VAL21 3.9 27.8 1.0 N C:ALA59 4.1 29.1 1.0 C C:VAL21 4.1 28.0 1.0 CB C:VAL21 4.2 27.6 1.0 CA C:PRO58 4.2 26.0 1.0 O C:HOH322 4.4 44.0 1.0 C C:PRO58 4.5 28.3 1.0 CG2 C:ILE20 4.5 31.4 1.0 N C:PRO58 4.5 26.2 1.0 OE1 A:GLU118 4.5 48.8 1.0 CH2 A:TRP115 4.6 27.9 1.0 CG2 C:VAL21 4.6 29.3 1.0 N C:ILE57 4.6 25.9 1.0 CD1 C:ILE20 4.7 33.5 1.0 CB C:ILE20 4.7 30.8 1.0 C C:THR19 4.8 34.4 1.0 N C:ILE20 4.8 33.8 1.0 CA C:ALA59 4.9 29.5 1.0 CA C:ILE57 4.9 26.1 0.4 CA C:ILE57 4.9 26.0 0.6 OG1 C:THR112 5.0 26.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the E3 Ubiquitin Ligase Ravn From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ C:Na207 b:69.0 occ:1.00 N C:ARG109 2.9 31.9 1.0 O C:HOH348 3.2 44.8 1.0 CA C:GLY39 3.4 35.7 1.0 CA C:LYS108 3.6 32.6 1.0 C C:LYS108 3.7 30.8 1.0 CB C:ARG109 3.8 36.1 1.0 N C:GLY39 3.8 38.5 1.0 CA C:ARG109 3.9 33.7 1.0 CB C:LYS108 4.2 37.4 1.0 O C:VAL107 4.2 42.9 1.0 OE1 C:GLU110 4.3 67.9 1.0 CD C:LYS108 4.4 62.1 1.0 C C:GLY39 4.4 37.4 1.0 N C:LYS108 4.7 34.6 1.0 CD1 C:ILE20 4.7 33.5 1.0 NH2 C:ARG109 4.7 38.4 1.0 CG C:LYS108 4.9 52.4 1.0 C C:VAL107 4.9 34.8 1.0 O C:LYS108 4.9 27.9 1.0 O C:GLY39 5.0 36.5 1.0

Y.H.Lin, M.Lucas, T.R.Evans, G.Abascal-Palacios, A.G.Doms, N.A.Beauchene, A.L.Rojas, A.Hierro, M.P.Machner. Ravn Is A Member of A Previously Unrecognized Group of Legionella Pneumophila E3 Ubiquitin Ligases. Plos Pathog. V. 14 06897 2018.
ISSN: ESSN 1553-7374
PubMed: 29415051
DOI: 10.1371/JOURNAL.PPAT.1006897