Magnesium in PDB 3wdl: Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp

All present enzymatic activity of Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp:
6.3.2.36;

The structure of Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp, PDB code: 3wdl was solved by A.Kishimoto, A.Kita, T.Ishibashi, H.Tomita, Y.Yokooji, T.Imanaka, H.Atomi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.36 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.655, 80.071, 83.998, 90.00, 110.43, 90.00
R / Rfree (%)	22.7 / 28.2

The binding sites of Magnesium atom in the Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp (pdb code 3wdl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp, PDB code: 3wdl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp


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 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:22.2 occ:1.00 OD1 B:ASP163 2.0 24.1 1.0 O1B B:ATP901 2.1 27.2 1.0 O B:HOH1025 2.2 20.1 1.0 O B:HOH1032 2.3 32.3 1.0 O2A B:ATP901 2.3 45.6 1.0 O2G B:ATP901 2.4 28.9 1.0 CG B:ASP163 3.2 25.2 1.0 PA B:ATP901 3.3 53.2 1.0 PB B:ATP901 3.4 29.7 1.0 O1A B:ATP901 3.6 51.6 1.0 PG B:ATP901 3.6 28.7 1.0 NH1 A:ARG17 3.8 25.0 1.0 O B:HOH1019 3.8 21.9 1.0 O3A B:ATP901 3.8 40.1 1.0 O3B B:ATP901 3.9 36.2 1.0 CB B:ASP163 4.0 21.9 1.0 O1G B:ATP901 4.1 35.4 1.0 CA B:ASP163 4.2 19.9 1.0 OD2 B:ASP163 4.2 26.5 1.0 NH1 B:ARG187 4.2 17.7 1.0 N B:GLY164 4.5 20.7 1.0 O2B B:ATP901 4.7 32.7 1.0 O5' B:ATP901 4.7 49.7 1.0 CD2 A:LEU14 4.9 26.8 1.0 O B:HOH1035 4.9 17.8 1.0 C B:ASP163 4.9 20.3 1.0 CZ A:ARG17 4.9 24.9 1.0 O3G B:ATP901 4.9 33.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp


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 4-Phosphopantoate-Beta-Alanine Ligase Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:39.4 occ:1.00 O1B D:ATP301 1.9 37.0 1.0 O D:HOH407 2.0 39.6 1.0 OD1 D:ASP163 2.2 37.7 1.0 O2G D:ATP301 2.3 38.9 1.0 O D:HOH408 2.5 43.3 1.0 O1A D:ATP301 2.7 50.7 1.0 PB D:ATP301 3.1 37.4 1.0 O3A D:ATP301 3.3 46.6 1.0 CG D:ASP163 3.4 38.1 1.0 PA D:ATP301 3.4 54.9 1.0 PG D:ATP301 3.4 35.3 1.0 O3B D:ATP301 3.7 40.8 1.0 O1G D:ATP301 3.7 44.3 1.0 O D:HOH405 3.9 22.0 1.0 O2A D:ATP301 4.0 50.7 1.0 NH1 C:ARG17 4.0 25.8 1.0 N D:GLY164 4.1 38.2 1.0 CB D:ASP163 4.1 38.3 1.0 CA D:ASP163 4.1 39.0 1.0 OD2 D:ASP163 4.3 38.9 1.0 O2B D:ATP301 4.4 45.2 1.0 NH2 D:ARG187 4.4 45.0 1.0 C D:ASP163 4.6 38.8 1.0 O3G D:ATP301 4.8 39.3 1.0 CD1 C:LEU14 4.8 36.4 1.0 O5' D:ATP301 4.9 54.3 1.0 O C:HOH420 5.0 24.3 1.0

A.Kishimoto, A.Kita, T.Ishibashi, H.Tomita, Y.Yokooji, T.Imanaka, H.Atomi, K.Miki. Crystal Structure of Phosphopantothenate Synthetase From Thermococcus Kodakarensis Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 24638914
DOI: 10.1002/PROT.24546