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

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

The structure of Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Pi, PDB code: 3wnz 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)	17.42 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.581, 90.581, 252.654, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Subtilis Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Pi (pdb code 3wnz). 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-Pi, PDB code: 3wnz:
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-Pi


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-Pi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.8 occ:1.00 O1 A:PO4504 1.9 42.1 1.0 OE1 A:GLU324 1.9 32.6 1.0 OE1 A:GLU311 2.1 42.3 1.0 O1A A:ADP501 2.2 34.8 1.0 O3B A:ADP501 2.3 38.1 1.0 O A:HOH1001 2.3 36.3 1.0 CD A:GLU311 2.9 41.0 1.0 CD A:GLU324 2.9 34.7 1.0 OE2 A:GLU311 3.1 44.9 1.0 P A:PO4504 3.2 41.9 1.0 PB A:ADP501 3.3 41.4 1.0 MG A:MG503 3.4 37.3 1.0 PA A:ADP501 3.4 40.5 1.0 O2 A:PO4504 3.5 36.7 1.0 CG A:GLU324 3.5 34.3 1.0 O2B A:ADP501 3.6 40.8 1.0 O3A A:ADP501 3.7 42.6 1.0 O A:HOH1150 3.8 43.5 1.0 OE2 A:GLU324 3.9 40.0 1.0 O A:HOH1266 3.9 39.0 1.0 O3 A:PO4504 4.0 45.0 1.0 O A:HOH1204 4.1 37.4 1.0 C5' A:ADP501 4.2 44.6 1.0 O4 A:PO4504 4.2 34.5 1.0 O3' A:ADP501 4.3 38.0 1.0 O5' A:ADP501 4.3 42.5 1.0 O A:HOH1002 4.3 37.6 1.0 CG A:GLU311 4.4 39.3 1.0 O2A A:ADP501 4.6 36.1 1.0 O1B A:ADP501 4.6 44.1 1.0 C3' A:ADP501 4.7 37.5 1.0 CB A:GLU311 4.9 37.5 1.0 CB A:GLU324 5.0 34.6 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-Pi


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-Pi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:37.3 occ:1.00 O2 A:PO4504 1.8 36.7 1.0 O2B A:ADP501 1.9 40.8 1.0 O A:HOH1002 1.9 37.6 1.0 OE1 A:GLU324 2.2 32.6 1.0 OE2 A:GLU324 2.4 40.0 1.0 O A:HOH1248 2.4 32.1 1.0 CD A:GLU324 2.6 34.7 1.0 PB A:ADP501 3.1 41.4 1.0 P A:PO4504 3.2 41.9 1.0 O3B A:ADP501 3.4 38.1 1.0 MG A:MG502 3.4 39.8 1.0 O1 A:PO4504 3.5 42.1 1.0 O3A A:ADP501 3.9 42.6 1.0 NZ A:LYS138 4.0 45.5 1.0 NH2 A:ARG328 4.0 41.0 1.0 O3 A:PO4504 4.0 45.0 1.0 O A:HOH1204 4.0 37.4 1.0 CG A:GLU324 4.1 34.3 1.0 O4 A:PO4504 4.2 34.5 1.0 CA A:ALA183 4.2 48.0 1.0 O A:HOH1250 4.2 32.9 1.0 O1A A:ADP501 4.3 34.8 1.0 O1B A:ADP501 4.4 44.1 1.0 O A:LEU182 4.4 44.5 1.0 CB A:ALA183 4.4 47.2 1.0 O A:HOH1249 4.4 44.0 1.0 OE2 A:GLU109 4.6 42.3 1.0 OE1 A:GLU311 4.7 42.3 1.0 CE A:LYS138 4.7 44.8 1.0 PA A:ADP501 4.8 40.5 1.0 N A:SER184 4.9 47.7 1.0 CB A:GLU324 4.9 34.6 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