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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 8evx:

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

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ddla From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine, PDB code: 8evx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8evx

Go back to Magnesium Binding Sites List in 8evx
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg403

b:11.8
occ:0.91
 O10 A:DS0402 2.0 12.8 0.9
OD1 A:ASN301 2.1 15.6 1.0
O A:HOH606 2.1 12.8 1.0
O3B A:ADP401 2.1 12.0 1.0
OE2 A:GLU299 2.2 11.4 1.0
OE1 A:GLU299 2.2 12.1 1.0
CD A:GLU299 2.5 11.3 1.0
CG A:ASN301 3.1 16.2 1.0
P8 A:DS0402 3.2 15.8 0.9
PB A:ADP401 3.2 11.5 1.0
O1B A:ADP401 3.4 12.5 1.0
ND2 A:ASN301 3.4 12.7 1.0
O9 A:DS0402 3.4 10.3 0.9
MG A:MG404 3.6 10.5 1.0
K A:K405 3.8 12.4 0.8
NZ A:LYS134 4.0 11.8 1.0
CG A:GLU299 4.0 11.5 1.0
N6 A:DS0402 4.0 15.1 0.9
CA A:GLY177 4.0 11.6 1.0
O7 A:DS0402 4.0 13.6 0.9
O A:GLN176 4.1 14.3 1.0
O3A A:ADP401 4.2 12.9 1.0
O11 A:DS0402 4.3 13.3 0.9
O2B A:ADP401 4.3 13.9 1.0
O A:HOH612 4.4 17.6 1.0
CB A:ASN301 4.4 11.2 1.0
O2A A:ADP401 4.6 12.7 1.0
CE A:LYS134 4.6 11.2 1.0
O A:HOH626 4.7 15.5 1.0
N A:SER178 4.8 10.8 1.0
CB A:GLU299 4.8 13.4 1.0
OD2 A:ASP286 4.9 14.2 1.0
C4 A:DS0402 4.9 15.3 0.9
C3 A:DS0402 4.9 18.1 0.9
C A:GLY177 5.0 12.1 1.0
C A:GLN176 5.0 12.5 1.0
N A:GLY177 5.0 11.3 1.0

Magnesium binding site 2 out of 4 in 8evx

Go back to Magnesium Binding Sites List in 8evx
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg404

b:10.5
occ:0.96
 O9 A:DS0402 1.9 10.3 0.9
O2A A:ADP401 2.0 12.7 1.0
OE2 A:GLU299 2.0 11.4 1.0
O A:HOH620 2.1 12.6 1.0
O1B A:ADP401 2.1 12.5 1.0
OD2 A:ASP286 2.2 14.2 1.0
CD A:GLU299 3.2 11.3 1.0
P8 A:DS0402 3.2 15.8 0.9
PB A:ADP401 3.3 11.5 1.0
PA A:ADP401 3.3 13.0 1.0
CG A:ASP286 3.4 14.1 1.0
O10 A:DS0402 3.6 12.8 0.9
O3A A:ADP401 3.6 12.9 1.0
MG A:MG403 3.6 11.8 0.9
O3B A:ADP401 3.7 12.0 1.0
CG A:GLU299 3.8 11.5 1.0
NZ A:LYS244 3.9 14.1 1.0
O11 A:DS0402 3.9 13.3 0.9
ND2 A:ASN301 4.0 12.7 1.0
C5' A:ADP401 4.1 13.2 1.0
O A:HOH727 4.1 20.9 1.0
O5' A:ADP401 4.2 14.0 1.0
NH2 A:ARG284 4.2 13.0 1.0
CB A:ASP286 4.2 10.5 1.0
OE1 A:GLU299 4.2 12.1 1.0
OD1 A:ASP286 4.2 16.3 1.0
O7 A:DS0402 4.4 13.6 0.9
O3' A:ADP401 4.4 15.6 1.0
O1A A:ADP401 4.5 13.7 1.0
O2B A:ADP401 4.6 13.9 1.0
OD1 A:ASN301 4.7 15.6 1.0
C3' A:ADP401 4.8 12.4 1.0
CG A:ASN301 4.8 16.2 1.0
CE A:LYS244 4.9 13.4 1.0

Magnesium binding site 3 out of 4 in 8evx

Go back to Magnesium Binding Sites List in 8evx
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg403

b:12.0
occ:1.00
 O11 B:DS0402 2.0 12.1 0.9
O2B B:ADP401 2.0 11.9 1.0
O B:HOH618 2.1 13.2 1.0
OD1 B:ASN301 2.1 11.4 1.0
OE2 B:GLU299 2.2 10.2 1.0
OE1 B:GLU299 2.3 11.4 1.0
CD B:GLU299 2.5 11.1 1.0
CG B:ASN301 3.1 10.5 1.0
PB B:ADP401 3.2 12.9 1.0
P8 B:DS0402 3.2 14.2 0.9
O1B B:ADP401 3.3 14.2 1.0
O9 B:DS0402 3.5 12.6 0.9
ND2 B:ASN301 3.6 12.8 1.0
MG B:MG404 3.7 9.5 0.9
K B:K405 3.8 12.5 0.9
CA B:GLY177 4.0 13.8 1.0
CG B:GLU299 4.1 9.8 1.0
NZ B:LYS134 4.1 13.2 1.0
O7 B:DS0402 4.1 13.8 0.9
O3A B:ADP401 4.1 11.4 1.0
O B:GLN176 4.1 14.1 1.0
N6 B:DS0402 4.2 15.8 0.9
O B:HOH628 4.3 19.3 1.0
O3B B:ADP401 4.3 15.1 1.0
O10 B:DS0402 4.4 13.5 0.9
CB B:ASN301 4.5 9.3 1.0
CE B:LYS134 4.6 13.4 1.0
O2A B:ADP401 4.6 9.6 1.0
O B:HOH593 4.7 13.8 1.0
N B:SER178 4.7 12.7 1.0
OD2 B:ASP286 4.8 12.7 1.0
CB B:GLU299 4.9 9.5 1.0
C3 B:DS0402 4.9 14.8 0.9
C4 B:DS0402 4.9 15.6 0.9
C B:GLY177 4.9 12.7 1.0

Magnesium binding site 4 out of 4 in 8evx

Go back to Magnesium Binding Sites List in 8evx
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg404

b:9.5
occ:0.91
 OE2 B:GLU299 2.0 10.2 1.0
O9 B:DS0402 2.0 12.6 0.9
O2A B:ADP401 2.0 9.6 1.0
O B:HOH617 2.1 13.1 1.0
OD2 B:ASP286 2.1 12.7 1.0
O1B B:ADP401 2.1 14.2 1.0
CD B:GLU299 3.1 11.1 1.0
CG B:ASP286 3.3 13.5 1.0
PB B:ADP401 3.3 12.9 1.0
P8 B:DS0402 3.3 14.2 0.9
PA B:ADP401 3.3 12.8 1.0
O3A B:ADP401 3.6 11.4 1.0
O11 B:DS0402 3.6 12.1 0.9
MG B:MG403 3.7 12.0 1.0
CG B:GLU299 3.7 9.8 1.0
O2B B:ADP401 3.8 11.9 1.0
NZ B:LYS244 3.9 14.2 1.0
ND2 B:ASN301 4.0 12.8 1.0
O10 B:DS0402 4.0 13.5 0.9
CB B:ASP286 4.1 16.9 1.0
NH2 B:ARG284 4.1 14.4 1.0
OD1 B:ASP286 4.1 12.9 1.0
C5' B:ADP401 4.2 13.2 1.0
O B:HOH724 4.2 24.1 1.0
O5' B:ADP401 4.2 14.6 1.0
OE1 B:GLU299 4.2 11.4 1.0
O3' B:ADP401 4.4 14.4 1.0
O7 B:DS0402 4.5 13.8 0.9
O1A B:ADP401 4.5 12.0 1.0
O3B B:ADP401 4.6 15.1 1.0
OD1 B:ASN301 4.6 11.4 1.0
CG B:ASN301 4.8 10.5 1.0
C3' B:ADP401 4.8 13.2 1.0
CE B:LYS244 5.0 13.7 1.0

Reference:

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
Page generated: Thu Dec 28 09:01:32 2023

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