Magnesium in PDB 7u9k: Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+

All present enzymatic activity of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+:
6.3.2.4;

The structure of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+, PDB code: 7u9k was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.68 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.447, 70.058, 91.598, 90, 102.58, 90
R / Rfree (%)	24 / 27.7

The structure of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ (pdb code 7u9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+, PDB code: 7u9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:28.9 occ:0.88 O1A A:ADP403 2.1 29.8 1.0 O A:HOH609 2.1 31.0 1.0 O1B A:ADP403 2.1 36.0 1.0 OE2 A:GLU306 2.1 27.7 1.0 O A:HOH586 2.2 29.6 1.0 O A:HOH543 2.4 23.5 1.0 PB A:ADP403 3.0 45.1 1.0 O2B A:ADP403 3.2 46.2 1.0 PA A:ADP403 3.3 30.0 1.0 CD A:GLU306 3.4 30.0 1.0 O3A A:ADP403 3.4 38.2 1.0 O A:HOH538 4.0 33.7 1.0 CG A:GLU306 4.2 26.8 1.0 O A:HOH653 4.2 39.0 1.0 OE1 A:GLU306 4.2 27.1 1.0 O5' A:ADP403 4.3 23.8 1.0 O2A A:ADP403 4.4 28.8 1.0 C5' A:ADP403 4.4 28.2 1.0 ND2 A:ASN305 4.4 27.4 1.0 OD2 A:ASP293 4.4 21.4 1.0 O3B A:ADP403 4.4 44.9 1.0 OD1 A:ASN308 4.5 30.1 1.0

Magnesium binding site 2 out of 2 in the Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:19.6 occ:1.00 O2G B:ATP405 2.0 30.5 1.0 O B:HOH535 2.0 16.1 1.0 OD1 B:ASN308 2.1 18.6 1.0 OE2 B:GLU306 2.1 20.8 1.0 O2B B:ATP405 2.2 26.2 1.0 OE1 B:GLU306 2.5 20.3 1.0 CD B:GLU306 2.6 17.3 1.0 PG B:ATP405 3.1 22.9 1.0 CG B:ASN308 3.2 24.7 1.0 PB B:ATP405 3.2 20.8 1.0 O3B B:ATP405 3.3 19.4 1.0 ND2 B:ASN308 3.6 29.5 1.0 O3G B:ATP405 3.7 21.9 1.0 K B:K402 3.8 23.9 0.9 O1B B:ATP405 4.0 29.5 1.0 CG B:GLU306 4.1 21.8 1.0 NZ B:LYS130 4.2 22.1 1.0 O B:LEU181 4.3 22.1 1.0 CA B:GLY182 4.3 23.0 1.0 O B:HOH507 4.3 25.8 1.0 O B:HOH553 4.3 20.4 1.0 N F:DAL1 4.4 26.3 1.0 O1G B:ATP405 4.4 32.2 1.0 O2A B:ATP405 4.5 36.5 1.0 CB B:ASN308 4.5 20.9 1.0 O3A B:ATP405 4.6 29.4 1.0 K B:K401 4.6 30.0 0.9 CE B:LYS130 4.7 26.7 1.0 O B:THR307 4.9 19.3 1.0

J.L.Pederick, J.B.Bruning. Staphylococcus Aureus D-Alanine-D-Alanine Ligase in Complex with Atp, D-Ala-D-Ala, MG2+ and K+ To Be Published.