Magnesium in PDB 7vhv: Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase

All present enzymatic activity of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase:
6.2.1.54;

The structure of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase, PDB code: 7vhv was solved by B.J.Lee, I.-G.Lee, H.G.Im, H.J.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.91 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.468, 88.51, 130.85, 90, 91.67, 90
R / Rfree (%)	18.9 / 24

The binding sites of Magnesium atom in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase (pdb code 7vhv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase, PDB code: 7vhv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:44.8 occ:1.00 O1G D:ATP502 1.9 58.4 1.0 O2B D:ATP502 2.1 48.5 1.0 O D:HOH616 2.7 45.2 1.0 PG D:ATP502 3.2 57.3 1.0 PB D:ATP502 3.3 38.4 1.0 O3B D:ATP502 3.6 48.9 1.0 O3A D:ATP502 3.7 48.7 1.0 O2G D:ATP502 3.8 57.8 1.0 NH2 D:ARG379 3.8 56.4 1.0 CG2 D:THR144 3.8 53.6 1.0 O2A D:ATP502 4.0 45.5 1.0 OE1 D:GLU290 4.2 45.4 1.0 CB D:THR144 4.2 57.5 1.0 OE2 D:GLU290 4.3 51.6 1.0 O3G D:ATP502 4.4 50.3 1.0 PA D:ATP502 4.4 45.2 1.0 O1B D:ATP502 4.6 50.1 1.0 OG1 D:THR144 4.7 63.6 1.0 O5' D:ATP502 4.7 43.5 1.0 CD D:GLU290 4.7 46.2 1.0 C5' D:ATP502 4.8 43.0 1.0 OH D:TYR361 4.9 53.5 1.0 O3' D:ATP502 5.0 39.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:55.5 occ:1.00 O2B C:ATP502 2.3 49.0 1.0 O2G C:ATP502 2.4 60.0 1.0 O C:HOH625 2.4 53.3 1.0 O C:HOH613 3.0 51.0 1.0 OE1 C:GLU290 3.5 50.3 1.0 PB C:ATP502 3.6 46.2 1.0 OE2 C:GLU290 3.6 57.3 1.0 O2A C:ATP502 3.7 48.9 1.0 PG C:ATP502 3.8 64.3 1.0 O3A C:ATP502 3.9 47.6 1.0 CD C:GLU290 4.0 50.9 1.0 O3B C:ATP502 4.1 63.4 1.0 OH C:TYR361 4.2 43.3 1.0 PA C:ATP502 4.3 46.1 1.0 O1G C:ATP502 4.5 59.3 1.0 C5' C:ATP502 4.5 43.5 1.0 O5' C:ATP502 4.7 39.8 1.0 CB C:PRO288 4.7 44.5 1.0 O3' C:ATP502 4.7 47.4 1.0 O3G C:ATP502 4.9 70.6 1.0 O1B C:ATP502 4.9 48.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:38.8 occ:1.00 O A:HOH664 1.9 38.7 1.0 O1G A:ATP502 2.1 41.2 1.0 O A:HOH646 2.1 42.2 1.0 O A:HOH643 2.2 32.5 1.0 O2B A:ATP502 2.2 46.1 1.0 O A:HOH652 2.4 35.0 1.0 PG A:ATP502 3.2 51.5 1.0 PB A:ATP502 3.3 40.4 1.0 O3B A:ATP502 3.6 42.8 1.0 O2G A:ATP502 3.7 42.1 1.0 O3A A:ATP502 3.8 45.7 1.0 NH1 A:ARG379 4.0 34.1 1.0 OE2 A:GLU290 4.1 30.8 1.0 NZ A:LYS152 4.2 45.7 1.0 O A:HOH618 4.3 24.6 1.0 O2A A:ATP502 4.4 38.2 1.0 OE1 A:GLU290 4.4 31.3 1.0 O3G A:ATP502 4.5 48.3 1.0 CG2 A:THR144 4.5 47.5 1.0 PA A:ATP502 4.5 32.9 1.0 CE A:LYS152 4.6 40.9 1.0 O A:HOH620 4.6 37.5 1.0 O5' A:ATP502 4.6 36.9 1.0 O1B A:ATP502 4.7 41.3 1.0 CD A:GLU290 4.7 34.4 1.0 CB A:THR144 4.7 48.6 1.0 C5' A:ATP502 4.8 29.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of S. Aureus D-Alanine Alanyl Carrier Protein Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:49.9 occ:1.00 O B:HOH633 2.1 35.1 1.0 O2B B:ATP502 2.2 43.4 1.0 O B:HOH631 2.3 38.6 1.0 O B:HOH647 2.3 31.3 1.0 O1G B:ATP502 2.4 39.1 1.0 PG B:ATP502 3.2 52.7 1.0 O2G B:ATP502 3.3 46.3 1.0 O B:HOH700 3.3 35.5 1.0 PB B:ATP502 3.6 43.3 1.0 O B:HOH666 3.7 34.1 1.0 NH1 B:ARG379 3.7 45.7 1.0 O3B B:ATP502 3.9 43.1 1.0 O3A B:ATP502 4.3 47.9 1.0 O B:HOH601 4.3 25.8 1.0 OE1 B:GLU290 4.3 33.7 1.0 NZ B:LYS152 4.4 50.9 1.0 CE B:LYS152 4.6 46.5 1.0 O3G B:ATP502 4.6 49.5 1.0 O3' B:ATP502 4.7 38.2 1.0 O2A B:ATP502 4.7 32.6 1.0 O1B B:ATP502 4.8 40.2 1.0 OE2 B:GLU290 4.8 32.0 1.0 CZ B:ARG379 4.9 45.0 1.0 C5' B:ATP502 4.9 36.5 1.0 O5' B:ATP502 5.0 38.8 1.0 PA B:ATP502 5.0 36.9 1.0 CD B:GLU290 5.0 38.4 1.0 OH B:TYR361 5.0 33.2 1.0

I.G.Lee, C.Song, S.Yang, H.Jeon, J.Park, H.J.Yoon, H.Im, S.M.Kang, H.J.Eun, B.J.Lee. Structural and Functional Analysis of the D-Alanyl Carrier Protein Ligase Dlta From Staphylococcus Aureus MU50. Acta Crystallogr D Struct V. 78 424 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35362466
DOI: 10.1107/S2059798322000547