Atomistry » Magnesium » PDB 8ely-8ezi » 8evx
Atomistry »
  Magnesium »
    PDB 8ely-8ezi »
      8evx »

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: Fri Oct 4 01:21:11 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy