Magnesium in PDB 3wo0: Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala

All present enzymatic activity of Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala:
6.3.2.28;

The structure of Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala, PDB code: 3wo0 was solved by T.Tsuda, S.Kojima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.017, 90.017, 249.795, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala (pdb code 3wo0). 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 Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala, PDB code: 3wo0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala


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 Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.8 occ:1.00 OE2 A:GLU324 1.9 31.5 1.0 O1A A:ADP501 2.0 45.2 1.0 O A:HOH1001 2.0 39.5 1.0 OE1 A:GLU311 2.2 32.3 1.0 O A:HOH1032 2.3 37.2 1.0 O3B A:ADP501 2.3 39.5 1.0 CD A:GLU324 3.0 35.3 1.0 CD A:GLU311 3.1 28.3 1.0 PA A:ADP501 3.2 43.2 1.0 MG A:MG503 3.2 34.5 1.0 PB A:ADP501 3.3 38.2 1.0 O A:HOH1029 3.4 37.4 1.0 OE2 A:GLU311 3.4 31.2 1.0 O2B A:ADP501 3.5 38.0 1.0 O3A A:ADP501 3.6 45.7 1.0 CG A:GLU324 3.6 33.4 1.0 O A:HOH1202 3.7 41.5 1.0 O A:HOH1033 3.8 30.3 1.0 OE1 A:GLU324 4.0 35.6 1.0 O A:HOH1031 4.2 36.1 1.0 O5' A:ADP501 4.3 42.1 1.0 C5' A:ADP501 4.3 45.3 1.0 O2A A:ADP501 4.3 37.8 1.0 N A:ALA504 4.3 29.9 1.0 O3' A:ADP501 4.4 42.5 1.0 O A:HOH1030 4.4 43.7 1.0 CG A:GLU311 4.5 26.9 1.0 O1B A:ADP501 4.6 38.4 1.0 C3' A:ADP501 4.7 45.6 1.0 O A:ALA504 4.9 32.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala


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 Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:34.5 occ:1.00 O A:HOH1029 1.9 37.4 1.0 O2B A:ADP501 1.9 38.0 1.0 OE2 A:GLU324 2.0 31.5 1.0 O A:HOH1030 2.0 43.7 1.0 OE1 A:GLU324 2.3 35.6 1.0 O A:HOH1200 2.3 41.5 1.0 CD A:GLU324 2.5 35.3 1.0 PB A:ADP501 3.1 38.2 1.0 MG A:MG502 3.2 45.8 1.0 O A:HOH1001 3.4 39.5 1.0 O3B A:ADP501 3.4 39.5 1.0 NZ A:LYS138 3.7 52.5 1.0 O3A A:ADP501 3.9 45.7 1.0 CG A:GLU324 4.0 33.4 1.0 O A:HOH1202 4.0 41.5 1.0 O1A A:ADP501 4.2 45.2 1.0 O A:HOH1189 4.3 32.2 1.0 CA A:ALA183 4.4 54.0 1.0 O A:HOH1031 4.4 36.1 1.0 O1B A:ADP501 4.4 38.4 1.0 O A:LEU182 4.4 44.6 1.0 CB A:ALA183 4.5 50.4 1.0 O A:HOH1127 4.5 44.3 1.0 NH2 A:ARG328 4.5 32.6 1.0 CE A:LYS138 4.6 51.9 1.0 PA A:ADP501 4.6 43.2 1.0 OE1 A:GLU109 4.6 51.1 1.0 OE1 A:GLU311 4.7 32.3 1.0 CB A:GLU324 4.9 35.6 1.0 O A:ALA504 5.0 32.0 1.0

T.Tsuda, M.Asami, Y.Koguchi, S.Kojima. Single Mutation Alters the Substrate Specificity of L-Amino Acid Ligase Biochemistry V. 53 2650 2014.
ISSN: ISSN 0006-2960
PubMed: 24702628
DOI: 10.1021/BI500292B