Magnesium in PDB 5gjn: Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group

All present enzymatic activity of Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group:
4.1.1.18;

The structure of Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group, PDB code: 5gjn was solved by H.-Y.Sagong, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.966, 105.966, 73.634, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

The binding sites of Magnesium atom in the Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group (pdb code 5gjn). 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 Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group, PDB code: 5gjn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:29.8 occ:1.00 N A:ASP249 3.1 36.2 1.0 OG1 A:THR250 3.2 36.5 1.0 NH1 A:ARG198 3.4 36.4 1.0 N A:THR250 3.6 34.5 1.0 N A:PRO248 3.6 35.8 1.0 CA A:PHE247 3.6 30.4 1.0 CD A:PRO248 3.6 36.4 1.0 O A:HOH608 3.6 44.6 1.0 C A:PHE247 3.7 33.6 1.0 CA A:ASP249 3.7 39.4 1.0 C A:ASP249 3.8 41.4 1.0 CB A:ASP249 3.9 46.3 1.0 CG A:PRO248 4.0 39.1 1.0 CB A:THR250 4.0 32.4 1.0 C A:PRO248 4.2 35.6 1.0 O A:LEU246 4.3 34.1 1.0 CB A:PHE247 4.3 31.9 1.0 O A:PHE247 4.3 29.9 1.0 CA A:THR250 4.4 35.1 1.0 CA A:PRO248 4.4 37.9 1.0 O A:HOH549 4.4 44.9 1.0 CD1 A:PHE247 4.5 31.9 1.0 CZ A:ARG198 4.5 35.1 1.0 O A:ASP249 4.6 40.6 1.0 CG A:ASP249 4.7 47.0 1.0 O A:HOH666 4.7 57.4 1.0 N A:PHE247 4.7 31.7 1.0 OD2 A:ASP249 4.7 51.5 1.0 NH2 A:ARG198 4.7 34.5 1.0 CB A:PRO248 4.8 39.4 1.0 CG A:PHE247 4.8 29.2 1.0 C A:LEU246 4.9 33.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Strcuture of Lysine Decarboxylase From Selenomonas Ruminantium in P43212 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:28.6 occ:1.00 O A:HOH527 3.1 39.9 1.0 N A:GLY257 3.2 35.4 1.0 N A:TYR259 3.3 36.2 1.0 N A:GLY219 3.3 45.9 1.0 C3 A:GOL401 3.4 52.6 1.0 N A:PHE220 3.5 39.6 1.0 CB A:TYR259 3.5 36.4 1.0 O2 A:GOL401 3.6 37.9 1.0 N A:ARG258 3.6 32.7 1.0 C1 A:GOL401 3.7 66.9 1.0 CA A:GLY219 3.7 45.5 1.0 C2 A:GOL401 3.8 59.4 1.0 CA A:PRO256 3.8 33.1 1.0 C A:PRO256 4.0 33.5 1.0 CA A:TYR259 4.0 32.8 1.0 C A:GLY257 4.1 32.1 1.0 C A:GLY219 4.1 43.5 1.0 CA A:GLY257 4.1 36.0 1.0 CD2 A:PHE220 4.1 41.0 1.0 CB A:ARG258 4.1 35.2 1.0 CA A:ARG258 4.2 33.0 1.0 C A:ARG258 4.2 35.5 1.0 C A:GLY218 4.4 39.4 1.0 CB A:PHE220 4.4 40.7 1.0 CA A:PHE220 4.4 40.2 1.0 CB A:PRO256 4.4 34.4 1.0 O3 A:GOL401 4.5 50.5 1.0 O A:PHE220 4.5 39.5 1.0 CA A:GLY218 4.6 41.0 1.0 CG A:PHE220 4.8 39.4 1.0 O A:GLU255 4.8 34.8 1.0 O A:GLY257 4.9 34.7 1.0 CG A:TYR259 4.9 34.6 1.0 O1 A:GOL401 4.9 54.0 1.0 C A:PHE220 4.9 39.0 1.0

H.-Y.Sagong, H.F.Son, S.Kim, Y.-H.Kim, I.-K.Kim, K.-J.Kim. Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase From Selenomonas Ruminantium Plos One V. 11 66667 2016.
ISSN: ESSN 1932-6203
PubMed: 27861532
DOI: 10.1371/JOURNAL.PONE.0166667