Sodium in PDB 6oqq: Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq was solved by D.R.Tomchick, V.S.Tagliabracci, M.Black, A.Osinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.490, 104.749, 107.770, 90.00, 103.97, 90.00
R / Rfree (%)	20.2 / 23.4

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex (pdb code 6oqq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:40.0 occ:1.00 H A:ASN733 2.1 43.5 1.0 HE A:ARG522 2.4 57.5 1.0 O A:HOH1043 2.7 26.6 1.0 N A:ASN733 3.0 36.2 1.0 HA A:ASN733 3.1 24.1 1.0 HH21 A:ARG522 3.1 54.0 1.0 NE A:ARG522 3.2 47.9 1.0 HD1 A:TYR732 3.3 48.1 1.0 HB3 A:ARG522 3.4 15.7 1.0 HA A:TYR732 3.4 22.9 1.0 HE2 A:HIS492 3.4 21.7 1.0 CA A:ASN733 3.6 20.1 1.0 NE2 A:HIS492 3.8 18.1 1.0 NH2 A:ARG522 3.8 45.0 1.0 HD3 A:ARG522 3.9 17.6 1.0 CD1 A:TYR732 3.9 40.1 1.0 HB A:THR493 3.9 27.9 1.0 HG1 A:THR493 3.9 65.5 1.0 CZ A:ARG522 3.9 18.7 1.0 H A:ARG734 4.0 22.5 1.0 HE1 A:TYR732 4.0 38.7 1.0 C A:TYR732 4.0 41.7 1.0 HB2 A:ARG522 4.1 15.7 1.0 CD A:ARG522 4.1 14.8 1.0 CB A:ARG522 4.1 13.2 1.0 CA A:TYR732 4.2 19.2 1.0 CE1 A:TYR732 4.2 32.2 1.0 MG A:MG906 4.2 76.9 1.0 CE1 A:HIS492 4.2 17.4 1.0 O A:HIS492 4.3 33.0 1.0 HE1 A:HIS492 4.3 20.9 1.0 OG1 A:THR493 4.3 54.5 1.0 O A:GLY731 4.4 17.0 1.0 OD1 A:ASN733 4.5 0.4 1.0 CD2 A:HIS492 4.5 16.3 1.0 HE2 A:PHE495 4.5 91.2 1.0 O2P A:AMP901 4.5 75.3 1.0 N A:ARG734 4.5 18.7 1.0 C A:ASN733 4.5 26.7 1.0 HH22 A:ARG522 4.6 54.0 1.0 CB A:THR493 4.6 23.2 1.0 CB A:ASN733 4.7 26.6 1.0 HD2 A:HIS492 4.7 19.6 1.0 CG A:ASN733 4.7 33.0 1.0 H A:ARG522 4.7 14.2 1.0 CG A:ARG522 4.7 13.7 1.0 HD2 A:PHE495 4.7 0.7 1.0 CG A:TYR732 4.8 55.2 1.0 HD2 A:ARG522 4.9 17.6 1.0 HB2 A:ASN733 5.0 32.0 1.0

Sodium binding site 2 out of 2 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:49.3 occ:1.00 HD21 B:ASN24 2.2 71.2 1.0 O B:HOH330 2.4 34.4 1.0 OD1 B:ASN24 2.5 29.5 1.0 ND2 B:ASN24 2.5 59.3 1.0 O B:ASP21 2.5 28.3 1.0 O B:ALA18 2.6 19.0 1.0 CG B:ASN24 2.7 76.2 1.0 O B:HOH313 3.1 37.1 1.0 HB3 B:ASP21 3.1 31.9 1.0 O B:HOH323 3.2 44.9 1.0 HD22 B:ASN24 3.2 71.2 1.0 HA B:ASN24 3.5 32.9 1.0 C B:ASP21 3.6 28.1 1.0 C B:ALA18 3.7 18.8 1.0 O B:HOH306 3.8 29.4 1.0 CB B:ASP21 3.9 26.7 1.0 CB B:ASN24 3.9 46.2 1.0 HA B:ALA18 4.0 27.3 1.0 H B:ASP21 4.1 33.6 1.0 CA B:ASN24 4.1 27.4 1.0 H B:ASN24 4.1 42.1 1.0 HB1 B:ALA18 4.2 23.3 1.0 CA B:ASP21 4.2 27.4 1.0 CG B:ASP21 4.2 26.2 1.0 OD2 B:ASP21 4.3 25.9 1.0 CA B:ALA18 4.4 22.7 1.0 HA B:LEU19 4.4 22.8 1.0 N B:ASN24 4.4 35.0 1.0 O B:LYS22 4.4 48.4 1.0 HB3 B:ASN24 4.5 55.5 1.0 N B:ASP21 4.5 28.2 1.0 HB2 B:ASN24 4.5 55.5 1.0 HA B:LYS22 4.7 42.4 1.0 N B:LEU19 4.7 18.5 1.0 HH22 A:ARG479 4.7 42.6 1.0 HB2 B:ASP21 4.7 31.9 1.0 O B:LEU19 4.7 18.9 1.0 N B:LYS22 4.7 66.0 1.0 CB B:ALA18 4.8 19.5 1.0 C B:LYS22 4.8 39.6 1.0 CA B:LEU19 4.8 18.9 1.0 C B:LEU19 4.9 28.5 1.0 OD1 B:ASP21 4.9 26.5 1.0 CA B:LYS22 5.0 35.3 1.0

M.H.Black, A.Osinski, M.Gradowski, K.A.Servage, K.Pawlowski, D.R.Tomchick, V.S.Tagliabracci. Bacterial Pseudokinase Catalyzes Protein Polyglutamylation to Inhibit the Side-Family Ubiquitin Ligases. Science V. 364 787 2019.
ISSN: ESSN 1095-9203
PubMed: 31123136
DOI: 10.1126/SCIENCE.AAW7446