Magnesium in PDB 3wo1: Crystal Structure of TRP332ALA Mutant Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala

All present enzymatic activity of Crystal Structure of TRP332ALA Mutant Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala:
6.3.2.28;

The structure of Crystal Structure of TRP332ALA Mutant Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala, PDB code: 3wo1 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)	19.74 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.129, 91.129, 258.757, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 26.1

The binding sites of Magnesium atom in the Crystal Structure of TRP332ALA Mutant Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala (pdb code 3wo1). 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 TRP332ALA Mutant Ywfe, An L-Amino Acid Ligase, with Bound Adp-Mg-Ala, PDB code: 3wo1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of TRP332ALA Mutant 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 TRP332ALA Mutant 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:89.9 occ:1.00 O1A A:ADP501 2.0 0.3 1.0 O3B A:ADP501 2.3 0.2 1.0 O A:HOH1084 2.5 49.1 1.0 OE1 A:GLU311 2.5 57.0 1.0 OE2 A:GLU324 2.6 66.0 1.0 MG A:MG503 2.9 86.1 1.0 O A:HOH1021 3.0 53.9 1.0 PB A:ADP501 3.3 0.2 1.0 PA A:ADP501 3.3 0.1 1.0 O A:HOH1085 3.4 61.8 1.0 O2B A:ADP501 3.5 0.8 1.0 CD A:GLU311 3.6 56.8 1.0 O3A A:ADP501 3.8 0.3 1.0 CD A:GLU324 3.8 64.1 1.0 O A:HOH1086 3.8 67.0 1.0 O5' A:ADP501 4.2 0.1 1.0 OE2 A:GLU311 4.2 56.3 1.0 C5' A:ADP501 4.4 0.1 1.0 CB A:GLU324 4.5 56.9 1.0 O2A A:ADP501 4.5 0.4 1.0 OE1 A:GLU324 4.6 61.1 1.0 O1B A:ADP501 4.6 0.5 1.0 CG A:GLU324 4.7 67.9 1.0 O3' A:ADP501 4.7 84.3 1.0 CG A:GLU311 4.7 54.5 1.0 N A:ALA504 4.9 62.0 1.0 O A:ALA504 4.9 47.3 1.0 C3' A:ADP501 5.0 92.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of TRP332ALA Mutant 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 TRP332ALA Mutant 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:86.1 occ:1.00 O A:HOH1086 2.2 67.0 1.0 O A:HOH1021 2.4 53.9 1.0 O2B A:ADP501 2.5 0.8 1.0 O3B A:ADP501 2.8 0.2 1.0 MG A:MG502 2.9 89.9 1.0 PB A:ADP501 3.1 0.2 1.0 OE2 A:GLU324 3.2 66.0 1.0 O A:HOH1024 3.2 80.0 1.0 OE2 A:GLU109 3.7 79.6 1.0 O1B A:ADP501 4.1 0.5 1.0 O A:HOH1084 4.1 49.1 1.0 O1A A:ADP501 4.1 0.3 1.0 CD A:GLU324 4.1 64.1 1.0 NH2 A:ARG328 4.2 52.4 1.0 O A:HOH1085 4.3 61.8 1.0 O A:ALA504 4.3 47.3 1.0 CB A:ALA183 4.4 0.2 1.0 OE1 A:GLU324 4.4 61.1 1.0 O3A A:ADP501 4.4 0.3 1.0 OE1 A:GLU109 4.4 76.5 1.0 CD A:GLU109 4.5 73.0 1.0 CA A:ALA183 4.5 0.2 1.0 N A:SER184 4.6 0.2 1.0 PA A:ADP501 4.9 0.1 1.0 O A:LEU182 5.0 0.6 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