Magnesium in PDB 1e4e: D-Alanyl-D-Lacate Ligase

All present enzymatic activity of D-Alanyl-D-Lacate Ligase:
6.1.2.1;

The structure of D-Alanyl-D-Lacate Ligase, PDB code: 1e4e was solved by D.I.Roper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	123.204, 225.359, 72.439, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 25.7

The binding sites of Magnesium atom in the D-Alanyl-D-Lacate Ligase (pdb code 1e4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the D-Alanyl-D-Lacate Ligase, PDB code: 1e4e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the D-Alanyl-D-Lacate Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D-Alanyl-D-Lacate Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg360 b:46.0 occ:1.00 ND2 A:ASN307 2.0 36.5 1.0 O1B A:ADP350 2.1 46.2 1.0 O A:HOH2095 2.1 41.0 1.0 OE2 A:GLU305 2.3 48.9 1.0 OE1 A:GLU305 2.4 62.0 1.0 CD A:GLU305 2.7 57.0 1.0 CG A:ASN307 3.1 43.7 1.0 P2 A:PHY355 3.2 41.1 1.0 PB A:ADP350 3.3 45.8 1.0 O4P A:PHY355 3.3 44.1 1.0 O2B A:ADP350 3.4 44.9 1.0 OD1 A:ASN307 3.5 47.7 1.0 MG A:MG365 3.7 42.0 1.0 CA A:GLY176 3.8 43.2 1.0 O A:HOH2153 4.0 40.6 1.0 N1 A:PHY355 4.0 38.8 1.0 O2P A:PHY355 4.0 40.2 1.0 NZ A:LYS133 4.0 38.6 1.0 O A:SER175 4.1 43.8 1.0 O3A A:ADP350 4.2 48.5 1.0 O3B A:ADP350 4.2 45.0 1.0 O A:HOH2059 4.3 39.2 1.0 O3P A:PHY355 4.3 41.3 1.0 CG A:GLU305 4.3 50.9 1.0 CB A:ASN307 4.4 46.6 1.0 N A:SER177 4.4 43.0 1.0 CE A:LYS133 4.6 36.6 1.0 C A:GLY176 4.7 44.2 1.0 O A:HOH2078 4.7 45.9 1.0 N A:GLY176 4.8 43.7 1.0 O2A A:ADP350 4.9 46.8 1.0 C A:SER175 4.9 43.6 1.0

Magnesium binding site 2 out of 4 in the D-Alanyl-D-Lacate Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D-Alanyl-D-Lacate Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg365 b:42.0 occ:1.00 O4P A:PHY355 1.9 44.1 1.0 O2B A:ADP350 2.0 44.9 1.0 O A:HOH2151 2.2 38.1 1.0 O A:HOH2167 2.2 44.1 1.0 O2A A:ADP350 2.3 46.8 1.0 OE2 A:GLU305 2.3 48.9 1.0 P2 A:PHY355 3.1 41.1 1.0 CD A:GLU305 3.2 57.0 1.0 PB A:ADP350 3.3 45.8 1.0 PA A:ADP350 3.4 47.5 1.0 O A:HOH2168 3.4 40.1 1.0 O3A A:ADP350 3.7 48.5 1.0 MG A:MG360 3.7 46.0 1.0 OD2 A:ASP292 3.8 47.6 1.0 O1B A:ADP350 3.8 46.2 1.0 O3P A:PHY355 3.8 41.3 1.0 CG A:GLU305 3.9 50.9 1.0 O A:HOH2097 4.0 48.7 1.0 ND2 A:ASN304 4.1 43.3 1.0 OE1 A:GLU305 4.2 62.0 1.0 OD1 A:ASN307 4.2 47.7 1.0 C5' A:ADP350 4.2 46.1 1.0 O3' A:ADP350 4.3 46.2 1.0 O5' A:ADP350 4.3 50.5 1.0 O2P A:PHY355 4.4 40.2 1.0 NH2 A:ARG290 4.5 46.2 1.0 O3B A:ADP350 4.5 45.0 1.0 O1A A:ADP350 4.6 51.7 1.0 ND2 A:ASN307 4.8 36.5 1.0 C3' A:ADP350 4.8 48.2 1.0 O A:HOH2111 4.9 56.4 1.0 CG A:ASN307 4.9 43.7 1.0 CG A:ASP292 4.9 43.9 1.0

Magnesium binding site 3 out of 4 in the D-Alanyl-D-Lacate Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D-Alanyl-D-Lacate Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg360 b:42.2 occ:1.00 ND2 B:ASN307 2.1 39.3 1.0 O1B B:ADP350 2.1 39.0 1.0 OE1 B:GLU305 2.2 47.4 1.0 O B:HOH2094 2.3 38.4 1.0 OE2 B:GLU305 2.4 37.4 1.0 CD B:GLU305 2.7 43.4 1.0 CG B:ASN307 3.0 41.9 1.0 OD1 B:ASN307 3.2 40.5 1.0 P2 B:PHY355 3.2 38.8 1.0 PB B:ADP350 3.4 40.9 1.0 CA B:GLY176 3.6 41.4 1.0 O2B B:ADP350 3.7 33.1 1.0 O4P B:PHY355 3.8 35.9 1.0 O B:HOH2153 3.9 48.4 1.0 N1 B:PHY355 3.9 36.1 1.0 MG B:MG365 4.0 38.8 1.0 NZ B:LYS133 4.0 32.5 1.0 O2P B:PHY355 4.0 38.7 1.0 O B:HOH2055 4.1 38.8 1.0 O B:SER175 4.2 41.2 1.0 CG B:GLU305 4.2 41.1 1.0 O3P B:PHY355 4.3 39.5 1.0 O3B B:ADP350 4.4 42.3 1.0 CB B:ASN307 4.4 43.7 1.0 N B:SER177 4.5 42.2 1.0 O3A B:ADP350 4.5 44.9 1.0 O B:HOH2072 4.6 39.7 1.0 C B:GLY176 4.6 41.2 1.0 N B:GLY176 4.7 43.0 1.0 CE B:LYS133 4.8 38.6 1.0 C B:SER175 4.9 42.2 1.0 O B:HOH2054 4.9 38.9 1.0

Magnesium binding site 4 out of 4 in the D-Alanyl-D-Lacate Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D-Alanyl-D-Lacate Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg365 b:38.8 occ:1.00 O B:HOH2150 1.9 47.4 1.0 O2A B:ADP350 2.1 45.8 1.0 O2B B:ADP350 2.1 33.1 1.0 O B:HOH2171 2.2 32.2 1.0 OE2 B:GLU305 2.2 37.4 1.0 O4P B:PHY355 2.4 35.9 1.0 CD B:GLU305 3.1 43.4 1.0 PA B:ADP350 3.3 44.9 1.0 PB B:ADP350 3.3 40.9 1.0 P2 B:PHY355 3.4 38.8 1.0 O1B B:ADP350 3.6 39.0 1.0 O3A B:ADP350 3.7 44.9 1.0 CG B:GLU305 3.7 41.1 1.0 O B:HOH2160 3.9 37.8 1.0 C5' B:ADP350 3.9 47.4 1.0 OD2 B:ASP292 3.9 46.3 1.0 OE1 B:GLU305 4.0 47.4 1.0 MG B:MG360 4.0 42.2 1.0 O B:HOH2096 4.0 46.5 1.0 O3P B:PHY355 4.1 39.5 1.0 ND2 B:ASN304 4.1 38.2 1.0 O3' B:ADP350 4.1 44.8 1.0 O5' B:ADP350 4.1 50.2 1.0 OD1 B:ASN307 4.2 40.5 1.0 O1A B:ADP350 4.4 50.6 1.0 C3' B:ADP350 4.6 43.6 1.0 O3B B:ADP350 4.7 42.3 1.0 O2P B:PHY355 4.7 38.7 1.0 O B:HOH2111 4.8 50.9 1.0 NH2 B:ARG290 4.8 38.1 1.0 OD1 B:ASN304 4.9 39.7 1.0 C4' B:ADP350 4.9 45.2 1.0 CG B:ASN304 5.0 39.5 1.0

D.I.Roper, T.Huyton, A.Vagin, G.Dodson. The Molecular Basis of Vancomycin Resistance in Clinically Relevant Enterococci: Crystal Structure of D-Alanyl-D-Lactate Ligase (Vana). Proc. Natl. Acad. Sci. V. 97 8921 2000U.S.A..
ISSN: ISSN 0027-8424
PubMed: 10908650
DOI: 10.1073/PNAS.150116497