Sodium in PDB 5wze: The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp

The structure of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp, PDB code: 5wze was solved by R.Bao, C.T.Peng, L.Liu, L.H.He, C.C.Li, T.Li, Y.L.Shen, Y.B.Zhu, Y.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.197, 123.432, 149.485, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 22.1

The structure of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp also contains other interesting chemical elements:

Manganese	(Mn)	12 atoms
Calcium	(Ca)	5 atoms

The binding sites of Sodium atom in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp (pdb code 5wze). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp, PDB code: 5wze:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:32.1 occ:1.00 ND1 A:HIS170 3.1 17.4 1.0 O C:HOH793 3.3 32.7 1.0 N A:GLY364 3.3 15.6 1.0 CB A:VAL363 3.7 12.8 1.0 CA A:VAL363 3.9 17.0 1.0 CG A:HIS170 3.9 13.9 1.0 CB A:HIS170 3.9 17.4 1.0 O A:HOH634 4.1 18.4 1.0 CE1 A:HIS170 4.1 16.8 1.0 C A:VAL363 4.1 13.4 1.0 CG1 A:VAL363 4.2 13.7 1.0 OE1 A:GLU365 4.2 46.6 1.0 CA A:GLY364 4.2 14.5 1.0 O A:GLY364 4.3 18.9 1.0 NH2 C:ARG38 4.3 28.8 1.0 C A:GLY364 4.4 15.3 1.0 NH1 C:ARG38 4.6 27.0 1.0 CZ C:ARG38 4.8 30.5 1.0 CG2 A:VAL363 4.9 13.8 1.0

Sodium binding site 2 out of 4 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:34.4 occ:1.00 N B:LYS6 3.2 25.4 1.0 O B:HOH749 3.6 26.9 1.0 CA B:PRO5 3.7 23.5 1.0 CB B:LYS6 3.8 27.2 1.0 O B:HOH673 3.9 26.3 1.0 C B:PRO5 4.0 23.6 1.0 NH2 B:ARG3 4.1 57.7 1.0 O B:HOH806 4.1 35.8 1.0 CA B:LYS6 4.1 24.1 1.0 CB B:PRO5 4.1 21.1 1.0 OE1 C:GLU80 4.2 48.1 1.0 NE B:ARG3 4.6 50.4 1.0 CZ B:ARG3 4.7 52.4 1.0 O B:ILE4 4.9 21.7 1.0 N B:PRO5 5.0 22.7 1.0

Sodium binding site 3 out of 4 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:32.1 occ:1.00 C5 B:PGE503 2.5 27.5 0.5 C6 B:PGE503 2.6 17.8 0.5 O B:HOH820 2.7 21.5 1.0 O B:HOH758 2.8 22.9 1.0 O4 B:PGE503 3.0 22.3 0.5 O3 B:PGE503 3.0 23.0 0.5 O B:MET436 3.5 20.6 1.0 CB B:MET436 3.6 18.2 1.0 CE B:MET436 3.7 13.9 1.0 C B:MET436 3.9 17.0 1.0 CD B:LYS440 4.0 39.3 1.0 CA B:GLY280 4.1 13.1 1.0 CA B:MET436 4.2 18.8 1.0 CB B:LYS440 4.2 22.0 1.0 C4 B:PGE503 4.3 25.8 0.5 O B:CYS202 4.3 21.4 1.0 N B:GLY280 4.4 17.3 1.0 CG B:MET436 4.5 13.7 1.0 O B:ASN279 4.6 19.6 1.0 C B:ASN279 4.6 18.5 1.0 C3 B:PGE503 4.6 28.5 0.5 N B:ALA437 4.6 17.6 1.0 CG B:LYS440 4.6 35.6 1.0 SD B:MET436 4.7 16.4 1.0 NZ B:LYS440 4.8 48.4 1.0 O B:HOH662 4.9 20.6 1.0 CE B:LYS440 4.9 43.5 1.0

Sodium binding site 4 out of 4 in the The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Pseudomonas Aeruginosa Aminopeptidase Pepp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:37.0 occ:1.00 O C:HOH745 3.3 30.5 1.0 O C:HOH851 3.6 54.3 1.0 NE C:ARG281 3.9 36.9 1.0 NH2 C:ARG281 4.1 36.1 1.0 CZ C:ARG281 4.5 33.0 1.0 CG C:ARG281 4.8 25.3 1.0 CD C:ARG281 5.0 31.0 1.0

C.T.Peng, L.Liu, C.C.Li, L.H.He, T.Li, Y.L.Shen, C.Gao, N.Y.Wang, Y.Xia, Y.B.Zhu, Y.J.Song, Q.Lei, L.T.Yu, R.Bao. Structure-Function Relationship of Aminopeptidase P From Pseudomonas Aeruginosa. Front Microbiol V. 8 2385 2017.
ISSN: ESSN 1664-302X
PubMed: 29259588
DOI: 10.3389/FMICB.2017.02385