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

Enzymatic activity of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala

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

Protein crystallography data

The structure of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala, PDB code: 8evy 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) 39.80 / 2.35
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.587, 198.892, 177.77, 90, 90, 90
R / Rfree (%) 21 / 24.8

Other elements in 8evy:

The structure of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala (pdb code 8evy). 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 Atp and D-Ala-D- Ala, PDB code: 8evy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8evy

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Magnesium binding site 1 out of 6 in the Ddlb 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 Ddlb 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:Mg403

b:34.2
occ:0.80
 O2G B:ATP405 1.9 46.7 1.0
OD2 B:ASP266 2.0 39.4 1.0
O2A B:ATP405 2.0 39.1 1.0
OE2 B:GLU279 2.1 32.7 1.0
O B:HOH541 2.1 37.9 1.0
O3B B:ATP405 2.4 41.8 1.0
PG B:ATP405 2.7 58.1 1.0
CG B:ASP266 3.2 45.5 1.0
CD B:GLU279 3.2 41.5 1.0
PA B:ATP405 3.3 40.0 1.0
PB B:ATP405 3.5 45.5 1.0
O3A B:ATP405 3.6 51.6 1.0
MG B:MG404 3.7 35.7 0.8
O3G B:ATP405 3.7 33.8 1.0
CG B:GLU279 3.8 35.5 1.0
O1G B:ATP405 3.8 40.8 1.0
NH1 B:ARG264 3.8 45.6 1.0
ND2 B:ASN281 3.9 42.1 1.0
CB B:ASP266 4.0 40.4 1.0
O1B B:ATP405 4.0 41.6 1.0
OD1 B:ASP266 4.1 45.7 1.0
O B:HOH570 4.1 44.6 1.0
NZ B:LYS224 4.2 38.3 1.0
OE1 B:GLU279 4.3 37.4 1.0
O5' B:ATP405 4.3 42.3 1.0
O1A B:ATP405 4.3 37.0 1.0
C5' B:ATP405 4.4 31.1 1.0
O3' B:ATP405 4.7 45.9 1.0
O2B B:ATP405 4.8 48.4 1.0
CG B:ASN281 4.8 44.0 1.0
OD1 B:ASN281 4.8 42.3 1.0
C3' B:ATP405 5.0 43.6 1.0

Magnesium binding site 2 out of 6 in 8evy

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Magnesium binding site 2 out of 6 in the Ddlb 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 Ddlb 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:Mg404

b:35.7
occ:0.75
 O3G B:ATP405 2.1 33.8 1.0
O B:HOH566 2.2 35.6 1.0
OD1 B:ASN281 2.2 42.3 1.0
OE2 B:GLU279 2.2 32.7 1.0
OE1 B:GLU279 2.4 37.4 1.0
O1B B:ATP405 2.4 41.6 1.0
CD B:GLU279 2.6 41.5 1.0
PG B:ATP405 3.0 58.1 1.0
O3B B:ATP405 3.1 41.8 1.0
CG B:ASN281 3.1 44.0 1.0
PB B:ATP405 3.2 45.5 1.0
O2G B:ATP405 3.3 46.7 1.0
ND2 B:ASN281 3.3 42.1 1.0
MG B:MG403 3.7 34.2 0.8
O B:HOH520 4.0 27.9 1.0
NZ B:LYS113 4.0 38.7 1.0
CG B:GLU279 4.1 35.5 1.0
O B:HOH553 4.1 36.2 1.0
CA B:GLY158 4.2 33.0 1.0
N B:DAL401 4.2 36.6 1.0
O2B B:ATP405 4.3 48.4 1.0
O B:GLU157 4.3 42.9 1.0
O1G B:ATP405 4.4 40.8 1.0
O3A B:ATP405 4.4 51.6 1.0
CB B:ASN281 4.5 39.2 1.0
O2A B:ATP405 4.6 39.1 1.0
O B:HOH536 4.7 38.7 1.0
CE B:LYS113 4.8 40.9 1.0
O B:HOH572 4.8 47.4 1.0
N B:SER159 4.8 33.6 1.0
OD2 B:ASP266 4.9 39.4 1.0
CB B:GLU279 4.9 34.8 1.0

Magnesium binding site 3 out of 6 in 8evy

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Magnesium binding site 3 out of 6 in the Ddlb 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 Ddlb 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:Mg404

b:37.9
occ:0.88
 O3G A:ATP406 2.1 39.0 0.9
OE2 A:GLU279 2.1 42.6 1.0
O A:HOH555 2.1 43.1 1.0
OD1 A:ASN281 2.2 43.3 1.0
O1B A:ATP406 2.2 48.1 0.9
OE1 A:GLU279 2.3 43.5 1.0
CD A:GLU279 2.5 42.2 1.0
O3B A:ATP406 3.1 45.3 0.9
PG A:ATP406 3.1 52.5 0.9
PB A:ATP406 3.1 39.5 0.9
CG A:ASN281 3.2 44.0 1.0
MG A:MG405 3.6 39.3 0.8
O2G A:ATP406 3.6 37.8 0.9
ND2 A:ASN281 3.6 41.0 1.0
O A:HOH521 3.8 29.1 1.0
O A:HOH544 3.9 38.8 1.0
NZ A:LYS113 3.9 41.1 1.0
CG A:GLU279 4.0 39.6 1.0
CA A:GLY158 4.1 38.2 1.0
O2B A:ATP406 4.1 39.2 0.9
O A:GLU157 4.2 42.6 1.0
N A:DAL401 4.2 42.9 1.0
O A:HOH545 4.3 39.9 1.0
O3A A:ATP406 4.4 38.9 0.9
O1G A:ATP406 4.4 43.3 0.9
CB A:ASN281 4.6 41.2 1.0
O A:HOH561 4.6 49.1 1.0
O2A A:ATP406 4.6 40.8 0.9
CE A:LYS113 4.7 44.7 1.0
N A:SER159 4.8 40.0 1.0
CB A:GLU279 4.9 45.2 1.0
OD2 A:ASP266 4.9 36.5 1.0

Magnesium binding site 4 out of 6 in 8evy

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Magnesium binding site 4 out of 6 in the Ddlb 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 Ddlb 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:Mg405

b:39.3
occ:0.82
 O2G A:ATP406 2.0 37.8 0.9
O2A A:ATP406 2.0 40.8 0.9
OD2 A:ASP266 2.0 36.5 1.0
OE2 A:GLU279 2.1 42.6 1.0
O3B A:ATP406 2.1 45.3 0.9
O A:HOH548 2.3 41.1 1.0
PG A:ATP406 2.6 52.5 0.9
CD A:GLU279 3.1 42.2 1.0
PA A:ATP406 3.2 34.6 0.9
PB A:ATP406 3.2 39.5 0.9
CG A:ASP266 3.3 44.9 1.0
O3A A:ATP406 3.4 38.9 0.9
O3G A:ATP406 3.5 39.0 0.9
MG A:MG404 3.6 37.9 0.9
CG A:GLU279 3.6 39.6 1.0
O1B A:ATP406 3.7 48.1 0.9
O1G A:ATP406 3.8 43.3 0.9
NH1 A:ARG264 3.9 35.8 1.0
ND2 A:ASN281 3.9 41.0 1.0
CB A:ASP266 4.1 39.9 1.0
OD1 A:ASP266 4.1 48.0 1.0
NZ A:LYS224 4.2 38.0 1.0
OE1 A:GLU279 4.2 43.5 1.0
O5' A:ATP406 4.2 44.7 0.9
O1A A:ATP406 4.3 42.4 0.9
C5' A:ATP406 4.3 33.8 0.9
O A:HOH573 4.4 38.8 1.0
O2B A:ATP406 4.5 39.2 0.9
OD1 A:ASN281 4.6 43.3 1.0
O3' A:ATP406 4.7 41.8 0.9
CG A:ASN281 4.7 44.0 1.0

Magnesium binding site 5 out of 6 in 8evy

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Magnesium binding site 5 out of 6 in the Ddlb 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 5 of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:40.2
occ:0.78
 OE2 C:GLU279 2.0 50.8 1.0
O3G C:ATP405 2.1 50.3 1.0
OD1 C:ASN281 2.1 49.2 1.0
O1B C:ATP405 2.3 49.3 1.0
OE1 C:GLU279 2.3 46.1 1.0
O C:HOH531 2.4 46.8 1.0
CD C:GLU279 2.5 47.0 1.0
O3B C:ATP405 3.0 47.5 1.0
PG C:ATP405 3.0 58.5 1.0
CG C:ASN281 3.1 45.9 1.0
PB C:ATP405 3.1 45.3 1.0
O2G C:ATP405 3.4 43.2 1.0
ND2 C:ASN281 3.5 49.4 1.0
MG C:MG404 3.6 39.3 0.8
CG C:GLU279 4.0 37.9 1.0
O C:HOH534 4.0 27.2 1.0
CA C:GLY158 4.0 42.7 1.0
NZ C:LYS113 4.1 42.2 1.0
O C:HOH513 4.2 47.6 1.0
O C:GLU157 4.2 39.6 1.0
O2B C:ATP405 4.2 48.6 1.0
N C:DAL401 4.3 46.6 1.0
O3A C:ATP405 4.3 46.2 1.0
O1G C:ATP405 4.3 58.5 1.0
CB C:ASN281 4.5 46.5 1.0
O2A C:ATP405 4.5 36.8 1.0
O C:HOH524 4.5 41.3 1.0
O C:HOH544 4.7 48.4 1.0
CE C:LYS113 4.7 45.2 1.0
N C:SER159 4.8 43.7 1.0
OD2 C:ASP266 4.8 43.4 1.0
CB C:GLU279 4.9 38.0 1.0
C C:GLY158 5.0 44.4 1.0
PA C:ATP405 5.0 49.4 1.0

Magnesium binding site 6 out of 6 in 8evy

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Magnesium binding site 6 out of 6 in the Ddlb 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 6 of Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:39.3
occ:0.81
 O2G C:ATP405 1.9 43.2 1.0
O2A C:ATP405 2.0 36.8 1.0
OD2 C:ASP266 2.0 43.4 1.0
OE2 C:GLU279 2.2 50.8 1.0
O3B C:ATP405 2.2 47.5 1.0
O C:HOH511 2.3 44.7 1.0
PG C:ATP405 2.6 58.5 1.0
CG C:ASP266 3.2 50.4 1.0
CD C:GLU279 3.2 47.0 1.0
PA C:ATP405 3.3 49.4 1.0
PB C:ATP405 3.4 45.3 1.0
O3A C:ATP405 3.6 46.2 1.0
O3G C:ATP405 3.6 50.3 1.0
MG C:MG403 3.6 40.2 0.8
O1G C:ATP405 3.7 58.5 1.0
NH1 C:ARG264 3.7 47.0 1.0
CG C:GLU279 3.7 37.9 1.0
ND2 C:ASN281 3.9 49.4 1.0
O1B C:ATP405 4.0 49.3 1.0
OD1 C:ASP266 4.1 49.3 1.0
CB C:ASP266 4.1 43.8 1.0
NZ C:LYS224 4.2 53.3 1.0
O5' C:ATP405 4.2 46.1 1.0
OE1 C:GLU279 4.3 46.1 1.0
O1A C:ATP405 4.3 38.0 1.0
C5' C:ATP405 4.4 40.5 1.0
O3' C:ATP405 4.6 48.7 1.0
OD1 C:ASN281 4.6 49.2 1.0
O2B C:ATP405 4.7 48.6 1.0
CG C:ASN281 4.7 45.9 1.0
CZ C:ARG264 5.0 47.1 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 01:21:29 2024

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