Potassium in PDB 8evx: Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine

All present enzymatic activity of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine:
6.3.2.4;

The structure of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine, PDB code: 8evx was solved by J.L.Pederick, J.C.Woolman, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.18 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.467, 133.053, 53.852, 90, 109.17, 90
R / Rfree (%)	19.8 / 21.8

The structure of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Potassium atom in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine (pdb code 8evx). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine, PDB code: 8evx:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range: probe atom residue distance (Å) B Occ A:K405 b:12.4 occ:0.85 O A:VAL300 2.8 14.1 1.0 OE1 A:GLU299 2.8 12.1 1.0 O A:ALA131 2.9 12.6 1.0 O A:HOH626 2.9 15.5 1.0 O A:HOH589 2.9 16.4 1.0 O A:HOH606 3.1 12.8 1.0 OD1 A:ASN301 3.4 15.6 1.0 O A:HOH580 3.8 14.5 1.0 MG A:MG403 3.8 11.8 0.9 C A:ALA131 3.8 11.5 1.0 C A:VAL300 3.8 16.2 1.0 CD A:GLU299 4.0 11.3 1.0 CA A:MET132 4.1 15.1 1.0 SD A:MET132 4.1 20.6 1.0 CA A:ASN301 4.1 10.2 1.0 CG A:ASN301 4.2 16.2 1.0 N A:MET132 4.3 10.5 1.0 N A:ASN301 4.4 11.4 1.0 CB A:GLU299 4.4 13.4 1.0 NZ A:LYS134 4.4 11.8 1.0 N A:VAL300 4.7 8.8 1.0 CB A:ASN301 4.7 11.2 1.0 CG A:GLU299 4.8 11.5 1.0 C A:MET132 4.8 16.0 1.0 CB A:ALA131 4.8 11.1 1.0 O A:MET132 4.8 14.5 1.0 OE2 A:GLU299 4.8 11.4 1.0 CA A:ALA131 4.8 11.2 1.0 CG A:MET132 4.9 14.3 1.0 O A:GLN176 4.9 14.3 1.0 O3B A:ADP401 4.9 12.0 1.0 CA A:VAL300 4.9 12.1 1.0 CE A:MET132 5.0 11.7 1.0 CE A:LYS134 5.0 11.2 1.0

Potassium binding site 2 out of 2 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range: probe atom residue distance (Å) B Occ B:K405 b:12.5 occ:0.90 O B:VAL300 2.7 10.9 1.0 OE1 B:GLU299 2.8 11.4 1.0 O B:ALA131 2.8 13.0 1.0 O B:HOH555 2.9 14.5 1.0 O B:HOH593 2.9 13.8 1.0 O B:HOH618 3.1 13.2 1.0 OD1 B:ASN301 3.5 11.4 1.0 O B:HOH599 3.7 13.7 1.0 C B:ALA131 3.8 13.1 1.0 MG B:MG403 3.8 12.0 1.0 C B:VAL300 3.8 10.3 1.0 SD B:MET132 4.0 23.8 1.0 CD B:GLU299 4.0 11.1 1.0 CA B:MET132 4.1 10.4 1.0 CA B:ASN301 4.2 9.8 1.0 CG B:ASN301 4.2 10.5 1.0 N B:MET132 4.3 12.9 1.0 N B:ASN301 4.4 9.9 1.0 NZ B:LYS134 4.5 13.2 1.0 CB B:GLU299 4.5 9.5 1.0 N B:VAL300 4.6 8.6 1.0 O B:MET132 4.7 13.5 1.0 C B:MET132 4.8 10.2 1.0 CB B:ASN301 4.8 9.3 1.0 CB B:ALA131 4.8 11.9 1.0 OE2 B:GLU299 4.8 10.2 1.0 CA B:ALA131 4.8 12.2 1.0 CG B:GLU299 4.8 9.8 1.0 O B:GLN176 4.9 14.1 1.0 O2B B:ADP401 4.9 11.9 1.0 CA B:VAL300 4.9 9.7 1.0 CG B:MET132 4.9 17.2 1.0 O B:HOH586 5.0 14.6 1.0 CE B:LYS134 5.0 13.4 1.0

J.L.Pederick, J.C.Woolman, J.B.Bruning. Comparative Functional and Structural Analysis of Pseudomonas Aeruginosa ᴅ-Alanine-ᴅ-Alanine Ligase Isoforms As Prospective Antibiotic Targets. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37581574
DOI: 10.1111/FEBS.16932