Sodium 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:

Magnesium (Mg) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Ddlb From Pseudomonas Aeruginosa PAO1 in Complex with Atp and D-Ala-D- Ala, PDB code: 8evy:

Sodium binding site 1 out of 1 in 8evy

Go back to Sodium Binding Sites List in 8evy
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
A:Na403

b:46.7
occ:0.78
 O A:HOH575 2.3 49.9 1.0
O A:THR214 2.4 46.7 1.0
O A:HIS216 2.4 48.7 1.0
O A:HOH525 2.5 49.0 1.0
O A:HOH572 2.5 43.7 1.0
C A:THR214 3.4 45.7 1.0
CG2 A:THR214 3.5 39.1 1.0
C A:HIS216 3.6 48.0 1.0
N A:THR214 3.9 41.7 1.0
C A:PRO215 4.1 47.8 1.0
N A:HIS216 4.1 41.9 1.0
CA A:THR214 4.1 44.9 1.0
O A:THR217 4.2 43.9 1.0
O A:HOH514 4.2 42.5 1.0
C A:THR217 4.2 48.3 1.0
O A:PRO215 4.3 47.5 1.0
CB A:THR214 4.4 41.8 1.0
N A:PRO215 4.4 52.2 1.0
CA A:HIS216 4.5 47.1 1.0
N A:PHE218 4.5 42.8 1.0
N A:THR217 4.5 38.9 1.0
CA A:PRO215 4.6 51.4 1.0
CA A:THR217 4.6 47.2 1.0
O A:HOH538 4.7 50.0 1.0
CA A:PHE218 4.7 52.8 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: Wed Oct 9 11:44:01 2024

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