Sodium in PDB 4y0w: Yeaz From Pseudomonas Aeruginosa

The structure of Yeaz From Pseudomonas Aeruginosa, PDB code: 4y0w was solved by M.Milani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.030, 198.443, 161.350, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 25

The binding sites of Sodium atom in the Yeaz From Pseudomonas Aeruginosa (pdb code 4y0w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Yeaz From Pseudomonas Aeruginosa, PDB code: 4y0w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Yeaz 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 Yeaz From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:60.2 occ:1.00 O A:HOH424 2.1 71.4 1.0 OD1 A:ASP117 2.4 57.2 1.0 O A:ALA118 2.5 59.0 1.0 O A:GLU122 2.6 54.3 1.0 OH A:TYR169 2.8 0.3 1.0 N A:GLU122 3.4 54.1 1.0 CZ A:TYR169 3.5 91.8 1.0 CG A:ASP117 3.5 55.2 1.0 N A:ASP121 3.5 52.2 1.0 C A:ALA118 3.6 53.8 1.0 C A:GLU122 3.7 45.2 1.0 CA A:ASP121 3.7 58.0 1.0 N A:ALA118 3.7 55.2 1.0 CE1 A:TYR169 3.7 0.3 1.0 OD2 A:ASP117 3.9 73.9 1.0 C A:ASP121 3.9 54.4 1.0 O A:HOH442 4.0 66.3 1.0 CA A:GLU122 4.2 44.6 1.0 CA A:ALA118 4.3 58.5 1.0 CE2 A:TYR169 4.5 82.4 1.0 N A:MET120 4.5 78.0 1.0 C A:ARG119 4.5 77.3 1.0 C A:MET120 4.5 75.2 1.0 N A:ARG119 4.6 67.0 1.0 C A:ASP117 4.7 50.8 1.0 CB A:ASP117 4.7 50.9 1.0 CA A:ASP117 4.8 47.9 1.0 N A:VAL123 4.8 50.5 1.0 O A:ARG119 4.8 77.5 1.0 CB A:ALA118 4.9 68.2 1.0 CD1 A:TYR169 4.9 86.7 1.0 CA A:ARG119 4.9 71.5 1.0 CG1 A:VAL123 4.9 54.2 1.0

Sodium binding site 2 out of 4 in the Yeaz 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 Yeaz From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:78.7 occ:1.00 OD1 A:ASP8 2.5 65.2 1.0 O A:ALA13 2.7 69.1 1.0 O A:HOH421 2.7 57.2 1.0 OG1 A:THR11 2.8 72.8 1.0 N A:SER10 3.3 59.3 1.0 N A:THR11 3.3 58.1 1.0 OG A:SER10 3.6 77.0 1.0 CG A:ASP8 3.7 53.7 1.0 C A:ALA13 3.7 63.6 1.0 CB A:THR11 3.7 68.0 1.0 O A:ASP8 3.8 63.7 1.0 C A:THR9 3.9 45.8 1.0 C A:ASP8 3.9 52.6 1.0 CA A:THR9 3.9 51.8 1.0 N A:THR9 4.0 55.6 1.0 CA A:THR11 4.0 64.5 1.0 CG2 A:THR11 4.1 56.9 1.0 CB A:ALA13 4.1 78.4 1.0 CA A:SER10 4.1 66.0 1.0 C A:SER10 4.2 52.7 1.0 CB A:ASP8 4.2 59.5 1.0 O A:PRO186 4.2 60.5 1.0 CA A:ALA13 4.2 68.6 1.0 N A:ALA13 4.3 73.1 1.0 O A:THR11 4.3 80.7 1.0 C A:THR11 4.3 71.2 1.0 CB A:PRO186 4.4 54.5 1.0 CB A:SER10 4.5 74.4 1.0 CG A:PRO186 4.6 53.7 1.0 CD A:PRO186 4.6 52.4 1.0 CA A:ASP8 4.7 56.4 1.0 OD2 A:ASP8 4.7 58.0 1.0 N A:CYS14 4.7 61.3 1.0 O A:THR9 4.8 58.0 1.0 C A:PRO186 4.9 50.3 1.0 CA A:CYS14 5.0 51.0 1.0

Sodium binding site 3 out of 4 in the Yeaz 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 Yeaz From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:72.5 occ:1.00 OD1 B:ASP117 2.3 65.1 1.0 O B:ALA118 2.3 69.4 1.0 OH B:TYR169 2.6 0.6 1.0 O B:GLU122 2.9 50.1 1.0 CG B:ASP117 3.3 63.5 1.0 CZ B:TYR169 3.5 85.6 1.0 N B:GLU122 3.5 64.9 1.0 C B:ALA118 3.5 59.3 1.0 N B:ASP121 3.6 59.7 1.0 CA B:ASP121 3.7 71.0 1.0 OD2 B:ASP117 3.7 70.0 1.0 CE1 B:TYR169 3.8 95.8 1.0 N B:ALA118 3.9 53.9 1.0 C B:ASP121 4.0 68.3 1.0 C B:GLU122 4.0 56.0 1.0 CA B:ALA118 4.3 58.8 1.0 CA B:GLU122 4.4 56.6 1.0 C B:ARG119 4.4 89.2 1.0 N B:ARG119 4.5 74.3 1.0 O B:ARG119 4.5 73.1 1.0 CE2 B:TYR169 4.6 81.9 1.0 C B:ASP117 4.6 49.9 1.0 CA B:ARG119 4.6 84.0 1.0 CB B:ASP117 4.6 58.1 1.0 N B:MET120 4.7 79.6 1.0 C B:MET120 4.7 84.2 1.0 CA B:ASP117 4.8 51.4 1.0

Sodium binding site 4 out of 4 in the Yeaz From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Yeaz From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:76.7 occ:1.00 OD1 C:ASP117 2.1 82.1 1.0 O C:ALA118 2.4 81.9 1.0 O C:GLU122 2.4 65.0 1.0 O C:HOH418 2.4 96.2 1.0 OH C:TYR169 3.1 0.9 1.0 CG C:ASP117 3.3 78.5 1.0 N C:ALA118 3.4 58.6 1.0 C C:ALA118 3.4 67.5 1.0 CZ C:TYR169 3.5 0.9 1.0 C C:GLU122 3.5 62.8 1.0 N C:GLU122 3.5 81.2 1.0 CA C:ASP121 3.7 85.2 1.0 C C:ASP121 3.8 73.4 1.0 CA C:ALA118 4.0 53.0 1.0 N C:ASP121 4.0 80.0 1.0 CE1 C:TYR169 4.0 0.4 1.0 OD2 C:ASP117 4.0 0.7 1.0 CE2 C:TYR169 4.1 0.3 1.0 CA C:GLU122 4.2 67.5 1.0 C C:ASP117 4.3 54.4 1.0 CA C:ASP117 4.4 59.2 1.0 CG1 C:VAL123 4.4 63.8 1.0 CB C:ASP117 4.5 61.1 1.0 N C:ARG119 4.6 69.4 1.0 N C:VAL123 4.6 55.5 1.0 CB C:ALA118 4.6 59.5 1.0 O C:ASP121 4.6 96.9 1.0 OD1 C:ASP121 4.6 0.5 1.0 O C:ARG119 4.7 89.2 1.0 C C:ARG119 4.8 95.7 1.0 CA C:VAL123 4.9 56.2 1.0 CD1 C:TYR169 4.9 98.2 1.0

D.Vecchietti, S.Ferrara, R.Rusmini, R.Macchi, M.Milani, G.Bertoni. Crystal Structure of Yeaz From Pseudomonas Aeruginosa. Biochem.Biophys.Res.Commun. V. 470 460 2016.
ISSN: ESSN 1090-2104
PubMed: 26768361
DOI: 10.1016/J.BBRC.2016.01.008