Magnesium in PDB 3vmm: Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis:
6.3.2.28;

The structure of Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis, PDB code: 3vmm was solved by Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	130.787, 130.787, 147.742, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.9

The binding sites of Magnesium atom in the Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis (pdb code 3vmm). 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 Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis, PDB code: 3vmm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis


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 Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.0 occ:1.00 OE2 A:GLU324 2.0 40.4 1.0 O1B A:ADP503 2.0 36.1 1.0 O5P A:P0D504 2.0 31.9 1.0 OE1 A:GLU311 2.1 36.0 1.0 O1A A:ADP503 2.2 34.5 1.0 O A:HOH719 2.3 33.9 1.0 P2 A:P0D504 3.0 32.2 1.0 CD A:GLU324 3.0 40.3 1.0 CD A:GLU311 3.1 35.4 1.0 O3P A:P0D504 3.1 34.3 1.0 PB A:ADP503 3.2 36.8 1.0 OE1 A:GLU324 3.4 40.3 1.0 OE2 A:GLU311 3.4 36.2 1.0 PA A:ADP503 3.4 36.4 1.0 O3B A:ADP503 3.6 36.5 1.0 O3A A:ADP503 3.6 38.1 1.0 O4P A:P0D504 3.8 32.8 1.0 O A:HOH658 4.1 40.0 1.0 C5' A:ADP503 4.2 34.9 1.0 N1 A:P0D504 4.2 27.1 1.0 O2P A:P0D504 4.3 31.1 1.0 O5' A:ADP503 4.3 36.7 1.0 CG A:GLU324 4.4 40.3 1.0 CG A:GLU311 4.4 33.8 1.0 O3' A:ADP503 4.4 32.1 1.0 O2B A:ADP503 4.5 35.4 1.0 CB A:GLU324 4.6 39.0 1.0 O2A A:ADP503 4.6 37.0 1.0 O A:HOH721 4.7 29.6 1.0 C3' A:ADP503 4.8 34.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis


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 Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.7 occ:1.00 OE1 A:GLU324 2.4 40.3 1.0 O A:HOH721 2.5 29.6 1.0 O3B A:ADP503 2.6 36.5 1.0 OE2 A:GLU109 2.7 38.9 1.0 O3P A:P0D504 2.8 34.3 1.0 O A:LEU182 2.9 38.2 1.0 NZ A:LYS138 3.5 46.9 1.0 CD A:GLU109 3.5 39.0 1.0 O A:HOH720 3.5 36.2 1.0 O A:HOH669 3.6 43.5 1.0 CD A:GLU324 3.6 40.3 1.0 CB A:ALA183 3.6 33.4 1.0 CA A:ALA183 3.7 34.4 1.0 C A:LEU182 3.9 37.9 1.0 CG A:GLU109 4.0 37.9 1.0 PB A:ADP503 4.1 36.8 1.0 NH2 A:ARG328 4.1 33.9 1.0 N A:ALA183 4.3 36.4 1.0 OE1 A:GLU109 4.3 37.6 1.0 P2 A:P0D504 4.3 32.2 1.0 OE2 A:GLU324 4.5 40.4 1.0 CG A:GLU324 4.5 40.3 1.0 NH1 A:ARG136 4.5 42.2 1.0 CE A:LYS138 4.7 48.2 1.0 O1B A:ADP503 4.8 36.1 1.0 O3A A:ADP503 4.9 38.1 1.0 O2B A:ADP503 5.0 35.4 1.0

Y.Shomura, E.Hinokuchi, H.Ikeda, A.Senoo, Y.Takahashi, J.Saito, H.Komori, N.Shibata, Y.Yonetani, Y.Higuchi. Structural and Enzymatic Characterization of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis Protein Sci. 2012.
ISSN: ESSN 1469-896X
PubMed: 22407814
DOI: 10.1002/PRO.2058