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

Enzymatic activity of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine

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

Protein crystallography data

The structure of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine, PDB code: 8evz 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) 39.66 / 2.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.664, 199.046, 177.084, 90, 90, 90
R / Rfree (%) 20.4 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine (pdb code 8evz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine, PDB code: 8evz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8evz

Go back to Magnesium Binding Sites List in 8evz
Magnesium binding site 1 out of 6 in the Ddlb 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 Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:36.4
occ:1.00
 O11 A:DS0404 1.9 35.9 0.9
O2B A:ADP403 2.0 31.2 0.9
O2A A:ADP403 2.0 33.7 0.9
OE2 A:GLU279 2.1 35.6 1.0
OD2 A:ASP266 2.2 33.9 1.0
O A:HOH550 2.3 34.3 1.0
PB A:ADP403 3.1 27.3 0.9
P8 A:DS0404 3.1 36.9 0.9
CD A:GLU279 3.1 43.0 1.0
O10 A:DS0404 3.3 30.4 0.9
PA A:ADP403 3.3 31.3 0.9
CG A:ASP266 3.4 40.6 1.0
O3B A:ADP403 3.4 37.0 0.9
MG A:MG402 3.5 39.5 1.0
O3A A:ADP403 3.6 29.9 0.9
CG A:GLU279 3.7 33.2 1.0
O9 A:DS0404 3.8 34.0 0.9
NZ A:LYS224 3.8 35.1 1.0
NH2 A:ARG264 3.9 32.7 1.0
C5' A:ADP403 4.0 30.7 0.9
ND2 A:ASN281 4.1 38.8 1.0
OE1 A:GLU279 4.1 43.6 1.0
O5' A:ADP403 4.2 37.7 0.9
OD1 A:ASP266 4.2 39.2 1.0
O A:HOH587 4.3 36.5 1.0
CB A:ASP266 4.3 32.3 1.0
O7 A:DS0404 4.4 42.3 0.9
O1B A:ADP403 4.4 33.3 0.9
OD1 A:ASN281 4.4 38.7 1.0
O1A A:ADP403 4.5 35.6 0.9
O3' A:ADP403 4.7 39.3 0.9
CG A:ASN281 4.7 40.1 1.0
CE A:LYS224 4.9 43.7 1.0
C3' A:ADP403 5.0 32.5 0.9

Magnesium binding site 2 out of 6 in 8evz

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Magnesium binding site 2 out of 6 in the Ddlb 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 Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:39.5
occ:0.96
 O10 A:DS0404 1.9 30.4 0.9
OD1 A:ASN281 2.0 38.7 1.0
O A:HOH555 2.1 36.8 1.0
O3B A:ADP403 2.1 37.0 0.9
OE2 A:GLU279 2.2 35.6 1.0
OE1 A:GLU279 2.4 43.6 1.0
CD A:GLU279 2.6 43.0 1.0
CG A:ASN281 3.1 40.1 1.0
P8 A:DS0404 3.2 36.9 0.9
PB A:ADP403 3.3 27.3 0.9
O2B A:ADP403 3.5 31.2 0.9
MG A:MG401 3.5 36.4 1.0
O11 A:DS0404 3.5 35.9 0.9
ND2 A:ASN281 3.6 38.8 1.0
N6 A:DS0404 3.7 41.0 0.9
CA A:GLY158 3.9 39.7 1.0
O A:HOH508 3.9 36.4 1.0
O7 A:DS0404 4.1 42.3 0.9
O A:HOH551 4.1 34.0 1.0
NZ A:LYS113 4.1 37.9 1.0
CG A:GLU279 4.1 33.2 1.0
O A:GLU157 4.2 40.5 1.0
O9 A:DS0404 4.2 34.0 0.9
O1B A:ADP403 4.3 33.3 0.9
CB A:ASN281 4.4 42.3 1.0
O3A A:ADP403 4.4 29.9 0.9
C4 A:DS0404 4.5 36.5 0.9
O2A A:ADP403 4.6 33.7 0.9
C3 A:DS0404 4.6 42.8 0.9
N A:SER159 4.6 39.4 1.0
O A:HOH560 4.7 42.3 1.0
O A:HOH588 4.7 48.6 1.0
OD2 A:ASP266 4.8 33.9 1.0
C A:GLY158 4.8 38.8 1.0
N A:GLY158 4.9 39.6 1.0
CB A:GLU279 5.0 41.6 1.0
C A:GLU157 5.0 43.5 1.0
CE A:LYS113 5.0 39.7 1.0

Magnesium binding site 3 out of 6 in 8evz

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Magnesium binding site 3 out of 6 in the Ddlb 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 Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:38.4
occ:0.95
 O11 B:DS0404 1.9 26.8 0.9
O1B B:ADP403 2.1 36.5 0.9
O B:HOH546 2.1 34.9 1.0
OD1 B:ASN281 2.2 40.6 1.0
OE1 B:GLU279 2.4 35.0 1.0
OE2 B:GLU279 2.4 32.8 1.0
CD B:GLU279 2.7 42.2 1.0
P8 B:DS0404 3.2 35.5 0.9
PB B:ADP403 3.3 34.0 0.9
CG B:ASN281 3.3 47.0 1.0
O9 B:DS0404 3.5 37.7 0.9
O3B B:ADP403 3.5 31.7 0.9
N6 B:DS0404 3.8 35.5 0.9
CA B:GLY158 3.8 26.8 1.0
MG B:MG402 3.8 36.9 0.8
ND2 B:ASN281 3.8 38.8 1.0
O B:HOH531 4.0 36.4 1.0
O B:GLU157 4.1 36.8 1.0
O B:HOH539 4.1 37.5 1.0
NZ B:LYS113 4.1 35.4 1.0
O7 B:DS0404 4.1 40.4 0.9
CG B:GLU279 4.2 31.3 1.0
O2B B:ADP403 4.2 36.3 0.9
O10 B:DS0404 4.3 37.1 0.9
O3A B:ADP403 4.4 38.2 0.9
N B:SER159 4.5 30.2 1.0
C4 B:DS0404 4.5 39.8 0.9
CB B:ASN281 4.6 36.5 1.0
O B:HOH552 4.6 34.1 1.0
O B:HOH594 4.7 47.1 1.0
C3 B:DS0404 4.7 37.2 0.9
C B:GLY158 4.7 34.9 1.0
O1A B:ADP403 4.8 34.9 0.9
N B:GLY158 4.8 31.5 1.0
C B:GLU157 4.9 34.6 1.0
CE B:LYS113 4.9 37.2 1.0

Magnesium binding site 4 out of 6 in 8evz

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Magnesium binding site 4 out of 6 in the Ddlb 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 Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:36.9
occ:0.83
 O9 B:DS0404 2.0 37.7 0.9
OE2 B:GLU279 2.0 32.8 1.0
OD2 B:ASP266 2.0 39.9 1.0
O1A B:ADP403 2.0 34.9 0.9
O B:HOH547 2.1 32.0 1.0
O3B B:ADP403 2.3 31.7 0.9
CD B:GLU279 3.1 42.2 1.0
P8 B:DS0404 3.2 35.5 0.9
CG B:ASP266 3.3 46.2 1.0
PB B:ADP403 3.3 34.0 0.9
PA B:ADP403 3.4 38.1 0.9
O11 B:DS0404 3.6 26.8 0.9
O1B B:ADP403 3.6 36.5 0.9
CG B:GLU279 3.7 31.3 1.0
O3A B:ADP403 3.7 38.2 0.9
O10 B:DS0404 3.8 37.1 0.9
MG B:MG401 3.8 38.4 0.9
NZ B:LYS224 3.9 31.2 1.0
NH2 B:ARG264 3.9 36.1 1.0
C5' B:ADP403 4.1 27.5 0.9
ND2 B:ASN281 4.1 38.8 1.0
OD1 B:ASP266 4.1 40.9 1.0
CB B:ASP266 4.2 39.4 1.0
OE1 B:GLU279 4.2 35.0 1.0
O5' B:ADP403 4.2 40.2 0.9
O3' B:ADP403 4.5 40.0 0.9
O2A B:ADP403 4.5 32.1 0.9
O7 B:DS0404 4.5 40.4 0.9
OD1 B:ASN281 4.6 40.6 1.0
O2B B:ADP403 4.7 36.3 0.9
CG B:ASN281 4.8 47.0 1.0
C3' B:ADP403 4.8 37.4 0.9
CE B:LYS224 4.8 39.6 1.0
C4' B:ADP403 5.0 37.6 0.9

Magnesium binding site 5 out of 6 in 8evz

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Magnesium binding site 5 out of 6 in the Ddlb 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 5 of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:47.9
occ:1.00
 O11 C:DS0404 1.9 45.3 0.9
O1B C:ADP403 2.0 48.8 1.0
OE2 C:GLU279 2.1 53.6 1.0
OD1 C:ASN281 2.1 46.2 1.0
OE1 C:GLU279 2.3 41.2 1.0
O C:HOH545 2.4 44.8 1.0
CD C:GLU279 2.5 47.4 1.0
CG C:ASN281 3.1 46.1 1.0
PB C:ADP403 3.2 41.5 1.0
P8 C:DS0404 3.2 44.3 0.9
MG C:MG402 3.4 42.3 1.0
O2B C:ADP403 3.4 40.7 1.0
ND2 C:ASN281 3.5 49.6 1.0
O9 C:DS0404 3.6 44.4 0.9
O7 C:DS0404 3.8 45.1 0.9
CA C:GLY158 3.8 43.3 1.0
N6 C:DS0404 3.9 44.3 0.9
O3A C:ADP403 4.0 39.2 1.0
CG C:GLU279 4.0 37.3 1.0
NZ C:LYS113 4.1 37.2 1.0
O C:GLU157 4.1 36.4 1.0
O C:HOH539 4.3 33.2 1.0
O C:HOH522 4.3 44.2 1.0
O3B C:ADP403 4.4 42.0 1.0
O10 C:DS0404 4.4 46.8 0.9
N C:SER159 4.4 48.2 1.0
CB C:ASN281 4.5 42.7 1.0
C3 C:DS0404 4.6 47.1 0.9
C4 C:DS0404 4.6 41.1 0.9
O1A C:ADP403 4.7 39.9 1.0
C C:GLY158 4.7 44.9 1.0
OD2 C:ASP266 4.7 44.3 1.0
CE C:LYS113 4.8 42.3 1.0
N C:GLY158 4.9 39.3 1.0
CB C:GLU279 4.9 40.6 1.0
C C:GLU157 4.9 44.2 1.0

Magnesium binding site 6 out of 6 in 8evz

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Magnesium binding site 6 out of 6 in the Ddlb 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 6 of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Adp and Phosphorylated D-Cycloserine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:42.3
occ:1.00
 OE2 C:GLU279 1.9 53.6 1.0
O9 C:DS0404 2.0 44.4 0.9
O2B C:ADP403 2.1 40.7 1.0
OD2 C:ASP266 2.1 44.3 1.0
O1A C:ADP403 2.2 39.9 1.0
O C:HOH516 2.4 44.8 1.0
CD C:GLU279 3.0 47.4 1.0
P8 C:DS0404 3.1 44.3 0.9
PB C:ADP403 3.1 41.5 1.0
O11 C:DS0404 3.1 45.3 0.9
CG C:ASP266 3.4 51.2 1.0
PA C:ADP403 3.4 39.6 1.0
MG C:MG401 3.4 47.9 1.0
O3A C:ADP403 3.4 39.2 1.0
O1B C:ADP403 3.5 48.8 1.0
CG C:GLU279 3.6 37.3 1.0
NH2 C:ARG264 3.8 44.5 1.0
ND2 C:ASN281 3.9 49.6 1.0
OE1 C:GLU279 4.0 41.2 1.0
O10 C:DS0404 4.0 46.8 0.9
NZ C:LYS224 4.1 51.0 1.0
C5' C:ADP403 4.1 39.9 1.0
OD1 C:ASP266 4.2 45.0 1.0
O5' C:ADP403 4.3 43.9 1.0
O7 C:DS0404 4.3 45.1 0.9
CB C:ASP266 4.3 44.0 1.0
OD1 C:ASN281 4.4 46.2 1.0
O3B C:ADP403 4.5 42.0 1.0
CG C:ASN281 4.6 46.1 1.0
O2A C:ADP403 4.6 34.7 1.0
O3' C:ADP403 4.6 46.1 1.0
C3' C:ADP403 4.9 49.5 1.0
CB C:GLU279 5.0 40.6 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 09:01:33 2023

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