Magnesium in PDB 8evw: Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala

All present enzymatic activity of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala:
6.3.2.4;

The structure of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala, PDB code: 8evw 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)	39.16 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.273, 123.615, 53.582, 90, 109.12, 90
R / Rfree (%)	16 / 18.1

The binding sites of Magnesium atom in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala (pdb code 8evw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala, PDB code: 8evw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:10.1 occ:1.00 O1G A:ATP601 2.1 9.6 1.0 OD1 A:ASN301 2.2 11.6 1.0 O A:HOH791 2.2 12.7 1.0 O2B A:ATP601 2.2 8.6 1.0 OE1 A:GLU299 2.3 19.9 1.0 OE2 A:GLU299 2.4 9.3 1.0 CD A:GLU299 2.7 10.4 1.0 PG A:ATP601 3.2 8.4 1.0 CG A:ASN301 3.2 9.0 1.0 PB A:ATP601 3.3 8.6 1.0 O3B A:ATP601 3.4 9.8 1.0 ND2 A:ASN301 3.6 13.1 1.0 O3G A:ATP601 3.6 10.4 1.0 O A:HOH1016 3.7 15.5 1.0 MG A:MG605 4.0 9.6 1.0 NZ A:LYS134 4.0 9.4 1.0 O A:GLN176 4.1 9.4 1.0 O A:HOH704 4.1 8.6 1.0 CG A:GLU299 4.1 15.0 1.0 N A:DAL602 4.2 9.0 1.0 CA A:GLY177 4.2 8.6 1.0 O3A A:ATP601 4.3 10.4 1.0 O A:HOH797 4.3 10.9 1.0 O1B A:ATP601 4.4 10.4 1.0 O2G A:ATP601 4.5 9.3 1.0 O A:HOH880 4.5 15.2 1.0 CB A:ASN301 4.5 10.7 1.0 CE A:LYS134 4.6 9.8 1.0 O A:HOH782 4.7 11.7 1.0 O1A A:ATP601 4.8 9.7 1.0 CB A:GLU299 5.0 13.7 1.0

Magnesium binding site 2 out of 4 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:9.6 occ:1.00 OD2 A:ASP286 2.0 13.2 1.0 O1A A:ATP601 2.1 9.7 1.0 OE2 A:GLU299 2.2 9.3 1.0 O3G A:ATP601 2.2 10.4 1.0 O A:HOH771 2.2 11.3 1.0 O3B A:ATP601 2.6 9.8 1.0 PG A:ATP601 3.0 8.4 1.0 CG A:ASP286 3.2 11.5 1.0 CD A:GLU299 3.2 10.4 1.0 PA A:ATP601 3.4 9.3 1.0 O3A A:ATP601 3.7 10.4 1.0 PB A:ATP601 3.7 8.6 1.0 CG A:GLU299 3.7 15.0 1.0 NH1 A:ARG284 3.8 10.6 1.0 O1G A:ATP601 3.9 9.6 1.0 CB A:ASP286 3.9 10.0 1.0 ND2 A:ASN301 4.0 13.1 1.0 MG A:MG604 4.0 10.1 1.0 O2B A:ATP601 4.1 8.6 1.0 O2G A:ATP601 4.1 9.3 1.0 OD1 A:ASP286 4.2 11.6 1.0 OE1 A:GLU299 4.2 19.9 1.0 NZ A:LYS244 4.3 9.7 1.0 O5' A:ATP601 4.3 9.5 1.0 O3' A:ATP601 4.4 11.2 1.0 C5' A:ATP601 4.4 8.9 1.0 O2A A:ATP601 4.4 10.0 1.0 OD1 A:ASN301 4.9 11.6 1.0 C3' A:ATP601 4.9 9.6 1.0 CG A:ASN301 4.9 9.0 1.0 O1B A:ATP601 5.0 10.4 1.0

Magnesium binding site 3 out of 4 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:10.5 occ:1.00 O1G B:ATP601 2.2 9.7 1.0 OD1 B:ASN301 2.2 12.5 1.0 O B:HOH814 2.3 12.4 1.0 O2B B:ATP601 2.3 9.1 1.0 OE1 B:GLU299 2.3 11.3 1.0 OE2 B:GLU299 2.4 9.6 1.0 CD B:GLU299 2.7 9.2 1.0 PG B:ATP601 3.2 8.6 1.0 CG B:ASN301 3.2 9.2 1.0 PB B:ATP601 3.3 8.7 1.0 O3B B:ATP601 3.4 9.7 1.0 ND2 B:ASN301 3.6 12.2 1.0 O3G B:ATP601 3.6 10.9 1.0 MG B:MG605 4.0 9.5 1.0 NZ B:LYS134 4.1 9.3 1.0 O B:GLN176 4.1 10.8 1.0 N B:DAL602 4.2 9.2 1.0 CG B:GLU299 4.2 11.1 1.0 CA B:GLY177 4.3 8.8 1.0 O B:HOH800 4.4 11.1 1.0 O3A B:ATP601 4.4 12.6 1.0 O1B B:ATP601 4.4 10.8 1.0 O2G B:ATP601 4.5 9.9 1.0 CB B:ASN301 4.5 10.6 1.0 CE B:LYS134 4.6 10.1 1.0 O B:HOH841 4.7 12.0 1.0 O B:HOH887 4.7 16.1 1.0 O1A B:ATP601 4.8 10.1 1.0

Magnesium binding site 4 out of 4 in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:9.5 occ:1.00 OD2 B:ASP286 2.0 12.7 1.0 O1A B:ATP601 2.0 10.1 1.0 O3G B:ATP601 2.1 10.9 1.0 OE2 B:GLU299 2.1 9.6 1.0 O B:HOH807 2.2 11.3 1.0 O3B B:ATP601 2.6 9.7 1.0 PG B:ATP601 3.0 8.6 1.0 CG B:ASP286 3.2 11.0 1.0 CD B:GLU299 3.2 9.2 1.0 PA B:ATP601 3.3 8.9 1.0 PB B:ATP601 3.7 8.7 1.0 O3A B:ATP601 3.7 12.6 1.0 CG B:GLU299 3.7 11.1 1.0 O1G B:ATP601 3.9 9.7 1.0 NH1 B:ARG284 3.9 11.0 1.0 CB B:ASP286 3.9 10.0 1.0 O B:HOH1006 3.9 20.5 1.0 MG B:MG604 4.0 10.5 1.0 ND2 B:ASN301 4.0 12.2 1.0 O2B B:ATP601 4.1 9.1 1.0 O2G B:ATP601 4.1 9.9 1.0 OD1 B:ASP286 4.2 10.8 1.0 OE1 B:GLU299 4.3 11.3 1.0 O5' B:ATP601 4.3 10.0 1.0 C5' B:ATP601 4.4 9.0 1.0 NZ B:LYS244 4.4 11.3 1.0 O2A B:ATP601 4.4 10.8 1.0 O3' B:ATP601 4.4 10.5 1.0 OD1 B:ASN301 4.9 12.5 1.0 CG B:ASN301 4.9 9.2 1.0 C3' B:ATP601 4.9 9.9 1.0 O1B B:ATP601 5.0 10.8 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