Magnesium in PDB 7r8q: Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+

The structure of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+, PDB code: 7r8q 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)	36.89 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.868, 82.812, 107.782, 90, 131.06, 90
R / Rfree (%)	19.1 / 22

The structure of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

The binding sites of Magnesium atom in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ (pdb code 7r8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+, PDB code: 7r8q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:32.2 occ:0.93 O1A A:ADP402 2.0 27.6 1.0 O2B A:ADP402 2.0 27.5 1.0 OD2 A:ASP288 2.0 31.0 1.0 OD2 A:ASP301 2.1 29.5 1.0 O2 A:CIT401 2.1 26.2 1.0 O A:HOH590 2.1 26.2 1.0 CG A:ASP288 3.1 32.8 1.0 CG A:ASP301 3.1 30.9 1.0 NA A:NA404 3.2 32.3 1.0 C1 A:CIT401 3.2 32.2 1.0 PB A:ADP402 3.3 28.7 1.0 PA A:ADP402 3.3 31.1 1.0 CB A:ASP301 3.6 33.5 1.0 O3A A:ADP402 3.7 31.8 1.0 OD1 A:ASP288 3.7 32.1 1.0 O7 A:CIT401 3.8 31.3 1.0 O1 A:CIT401 3.8 33.2 1.0 O3B A:ADP402 4.0 32.5 1.0 OE1 A:GLN244 4.0 34.8 1.0 OD1 A:ASP301 4.2 30.2 1.0 CB A:ASP288 4.2 30.1 1.0 C5' A:ADP402 4.2 28.8 1.0 C2 A:CIT401 4.2 28.9 1.0 ND2 A:ASN303 4.2 29.8 1.0 O A:HOH595 4.3 25.8 1.0 O5' A:ADP402 4.3 32.9 1.0 O3' A:ADP402 4.4 28.7 1.0 O2A A:ADP402 4.4 32.0 1.0 NE2 A:GLN244 4.4 29.4 1.0 C3 A:CIT401 4.5 33.9 1.0 O1B A:ADP402 4.5 34.7 1.0 O6 A:CIT401 4.6 35.0 1.0 C6 A:CIT401 4.6 34.9 1.0 CD A:GLN244 4.6 32.7 1.0 OD1 A:ASN303 4.7 28.1 1.0 C3' A:ADP402 4.7 28.3 1.0 CG A:ASN303 5.0 28.5 1.0

Magnesium binding site 2 out of 2 in the Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Closed Form of SAOUHSC_02373 in Complex with Adp, Citrate, MG2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:27.1 occ:0.84 OD2 B:ASP288 1.9 30.7 1.0 O2A B:ADP402 2.0 31.5 1.0 OD2 B:ASP301 2.1 30.2 1.0 O3B B:ADP402 2.1 27.1 1.0 O B:HOH512 2.1 28.4 1.0 O1 B:CIT401 2.2 29.4 1.0 CG B:ASP288 3.0 34.9 1.0 CG B:ASP301 3.1 32.3 1.0 NA B:NA407 3.1 30.3 0.9 C1 B:CIT401 3.2 31.5 1.0 PA B:ADP402 3.4 33.8 1.0 PB B:ADP402 3.4 33.1 1.0 CB B:ASP301 3.6 31.6 1.0 OD1 B:ASP288 3.7 30.2 1.0 O2 B:CIT401 3.7 26.4 1.0 O3A B:ADP402 3.7 34.8 1.0 O7 B:CIT401 3.8 32.7 1.0 OE1 B:GLN244 4.0 38.4 1.0 CB B:ASP288 4.1 29.3 1.0 O1B B:ADP402 4.1 35.5 1.0 ND2 B:ASN303 4.2 28.7 1.0 OD1 B:ASP301 4.2 31.5 1.0 NE2 B:GLN244 4.3 31.6 1.0 C5' B:ADP402 4.3 30.2 1.0 O B:HOH636 4.3 32.0 1.0 C2 B:CIT401 4.4 29.7 1.0 O5' B:ADP402 4.4 35.5 1.0 O3' B:ADP402 4.4 30.7 1.0 O1A B:ADP402 4.4 33.5 1.0 C3 B:CIT401 4.5 31.1 1.0 CD B:GLN244 4.6 36.5 1.0 O2B B:ADP402 4.6 37.1 1.0 C6 B:CIT401 4.7 33.1 1.0 C3' B:ADP402 4.7 32.2 1.0 O5 B:CIT401 4.7 31.1 1.0 OD1 B:ASN303 4.8 32.2 1.0 CG B:ASN303 5.0 31.6 1.0

J.L.Pederick, A.J.Horsfall, B.Jovcevski, J.Klose, A.D.Abell, T.L.Pukala, J.B.Bruning. Discovery of An ʟ-Amino Acid Ligase Implicated in Staphylococcal Sulfur Amino Acid Metabolism. J.Biol.Chem. V. 298 02392 2022.
ISSN: ESSN 1083-351X
PubMed: 35988643
DOI: 10.1016/J.JBC.2022.102392