Sodium in PDB 6yii: Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa

The structure of Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa, PDB code: 6yii was solved by S.Moniot, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.54 / 1.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.400, 74.680, 149.680, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 14.7

The structure of Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Manganese	(Mn)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa (pdb code 6yii). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa, PDB code: 6yii:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa


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 A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:28.1 occ:1.00 H A:THR111 2.4 27.9 1.0 HZ1 A:LYS112 2.4 44.2 1.0 H A:LYS112 2.7 32.7 1.0 O A:HOH740 2.7 53.6 1.0 HA A:PHE110 2.8 26.0 1.0 O A:HOH842 2.9 49.0 1.0 HB2 A:LYS112 3.2 35.6 1.0 N A:THR111 3.2 23.2 1.0 HG3 A:LYS112 3.2 40.0 1.0 NZ A:LYS112 3.2 36.8 1.0 HA A:ALA96 3.2 28.4 1.0 HZ2 A:LYS112 3.3 44.2 1.0 O A:ASP95 3.4 29.1 1.0 N A:LYS112 3.4 27.3 1.0 O A:HOH986 3.5 27.2 1.0 O A:HOH994 3.6 33.3 1.0 CA A:PHE110 3.7 21.7 1.0 HZ3 A:LYS112 3.8 44.2 1.0 CB A:LYS112 3.8 29.7 1.0 C A:PHE110 3.9 23.3 1.0 OG1 A:THR111 3.9 26.8 1.0 HE2 A:LYS112 3.9 43.4 1.0 CG A:LYS112 3.9 33.3 1.0 HB3 A:PHE110 4.1 28.9 1.0 CE A:LYS112 4.1 36.2 1.0 CA A:THR111 4.2 24.5 1.0 CA A:ALA96 4.2 23.7 1.0 CA A:LYS112 4.2 27.9 1.0 HD2 A:PHE110 4.2 27.5 1.0 C A:THR111 4.2 25.8 1.0 O A:LEU109 4.2 21.8 1.0 O A:LYS112 4.3 30.2 1.0 C A:ASP95 4.3 26.9 1.0 CB A:PHE110 4.4 24.1 1.0 HB2 A:ALA96 4.4 30.1 1.0 HG1 A:THR111 4.5 32.1 1.0 O A:HOH1195 4.6 49.5 1.0 N A:ALA96 4.6 23.7 1.0 CD A:LYS112 4.6 34.9 1.0 CB A:THR111 4.7 24.8 1.0 CD2 A:PHE110 4.7 22.9 1.0 HB3 A:LYS112 4.7 35.6 1.0 CB A:ALA96 4.7 25.1 1.0 HG2 A:LYS112 4.7 40.0 1.0 C A:LYS112 4.7 28.8 1.0 HE A:ARG127 4.7 43.0 1.0 N A:PHE110 4.7 21.0 1.0 HB1 A:ALA96 4.8 30.1 1.0 HD3 A:ARG127 4.8 42.6 1.0 H A:ARG97 4.8 26.4 1.0 CG A:PHE110 4.9 21.4 1.0 C A:LEU109 4.9 20.6 1.0 HE3 A:LYS112 5.0 43.4 1.0 HA A:THR111 5.0 29.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa


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 A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:55.8 occ:1.00 HZ2 A:LYS3 1.7 40.5 1.0 O A:HOH1132 2.2 27.1 1.0 NZ A:LYS3 2.5 33.8 1.0 O A:PHE329 2.5 22.8 1.0 O A:HOH718 2.6 40.9 1.0 HZ3 A:LYS3 2.6 40.5 1.0 OG A:SER345 2.8 21.3 1.0 HE2 A:LYS3 2.9 36.9 1.0 CE A:LYS3 3.1 30.8 1.0 HZ1 A:LYS3 3.2 40.5 1.0 HG A:SER345 3.2 25.5 1.0 HD3 A:LYS3 3.2 31.1 1.0 H A:CYS346 3.2 22.5 1.0 HB3 A:PHE329 3.4 24.8 1.0 HA A:SER345 3.5 20.8 1.0 C A:PHE329 3.7 21.1 1.0 CD A:LYS3 3.7 26.0 1.0 CB A:SER345 3.9 19.0 1.0 N A:CYS346 3.9 18.7 1.0 O A:CYS346 3.9 21.2 1.0 HA2 A:GLY331 4.0 23.5 1.0 N A:GLY331 4.0 20.1 1.0 HA3 A:GLY331 4.0 23.5 1.0 HE3 A:LYS3 4.0 36.9 1.0 CA A:SER345 4.1 17.4 1.0 HB2 A:SER345 4.1 22.8 1.0 HB2 A:GLU330 4.1 31.9 1.0 H A:GLY331 4.1 24.1 1.0 C A:GLU330 4.2 19.9 1.0 CA A:GLY331 4.2 19.6 1.0 O A:HOH790 4.2 20.9 1.0 CB A:PHE329 4.3 20.7 1.0 HD2 A:LYS3 4.3 31.1 1.0 HD2 A:PHE329 4.4 26.7 1.0 O A:GLU330 4.4 21.5 1.0 HB3 A:GLU361 4.4 27.3 0.3 O A:HOH1084 4.4 34.8 1.0 C A:SER345 4.5 17.4 1.0 CA A:PHE329 4.5 20.6 1.0 HG2 A:LYS3 4.5 28.6 1.0 HD22 A:LEU365 4.5 23.3 1.0 OD2 A:ASP347 4.6 24.1 1.0 HB3 A:GLU361 4.6 25.5 0.7 N A:GLU330 4.6 20.4 1.0 HA A:PHE329 4.6 24.7 1.0 HB3 A:SER345 4.7 22.8 1.0 C A:CYS346 4.7 19.0 1.0 CG A:LYS3 4.7 23.9 1.0 CA A:GLU330 4.7 22.2 1.0 HB2 A:PHE329 4.7 24.8 1.0 CB A:GLU330 4.9 26.6 1.0 CA A:CYS346 4.9 18.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa


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 A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na610 b:41.4 occ:0.58 O A:HOH1012 2.2 33.7 0.8 O A:SER2 2.3 43.0 1.0 OE2 A:GLU330 2.6 42.1 1.0 O A:ASP328 2.8 24.5 1.0 O A:SER327 2.8 23.7 0.6 O A:SER327 2.8 21.7 0.4 HA A:ASP328 3.1 26.6 1.0 C A:SER2 3.3 43.7 1.0 C A:ASP328 3.4 20.4 1.0 HA A:LYS3 3.4 30.2 1.0 O A:HOH1242 3.6 34.2 1.0 CA A:ASP328 3.7 22.2 1.0 H A:SER4 3.7 30.2 0.5 CD A:GLU330 3.7 39.2 1.0 H A:SER4 3.7 28.9 0.6 HG2 A:GLU330 3.8 37.6 1.0 HB3 A:SER2 3.8 69.6 1.0 C A:SER327 3.9 21.3 0.4 C A:SER327 3.9 21.1 0.6 OG A:SER2 4.0 59.2 1.0 HG A:SER4 4.0 37.0 0.5 N A:LYS3 4.2 32.1 1.0 CA A:LYS3 4.2 25.2 1.0 CB A:SER2 4.2 58.0 1.0 CA A:SER2 4.3 54.9 1.0 N A:ASP328 4.3 21.5 1.0 CG A:GLU330 4.3 31.4 1.0 HG A:SER2 4.3 71.0 1.0 N A:SER4 4.4 25.2 0.5 N A:SER4 4.4 24.1 0.6 N A:PHE329 4.4 20.9 1.0 H A:SER2 4.6 75.1 1.0 O A:HOH853 4.6 30.5 1.0 HA A:PHE329 4.6 24.7 1.0 N A:SER2 4.6 62.6 1.0 HG3 A:GLU330 4.6 37.6 1.0 OE1 A:GLU330 4.7 41.2 1.0 O A:SER4 4.7 25.0 0.5 O A:SER4 4.7 24.8 0.6 OG A:SER4 4.8 30.8 0.5 C A:LYS3 4.8 25.4 1.0 HG2 A:LYS3 4.8 28.6 1.0 H A:GLU330 4.9 24.4 1.0 HB3 A:SER4 4.9 28.7 0.6 CB A:ASP328 5.0 22.3 1.0 HB3 A:ASP328 5.0 26.7 1.0 H A:LYS3 5.0 38.5 1.0 H A:PHE329 5.0 25.1 1.0

J.Linder, E.Hupfeld, M.Weyand, C.Steegborn, S.Moniot. Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa. J.Struct.Biol. 07534 2020.
ISSN: ESSN 1095-8657
PubMed: 32454240
DOI: 10.1016/J.JSB.2020.107534