Magnesium in PDB 2dln: Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution

All present enzymatic activity of Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution:
6.3.2.4;

The structure of Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution, PDB code: 2dln was solved by J.R.Knox, P.C.Moews, C.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.300, 51.400, 51.200, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution (pdb code 2dln). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution, PDB code: 2dln:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg330 b:6.1 occ:1.00 O4P A:PHY320 1.9 11.3 1.0 OD2 A:ASP257 2.0 6.9 1.0 O2A A:ADP310 2.4 5.3 1.0 O3B A:ADP310 2.6 5.5 1.0 OE2 A:GLU270 2.7 4.7 1.0 CG A:ASP257 3.0 6.8 1.0 P2 A:PHY320 3.3 11.4 1.0 PA A:ADP310 3.5 5.2 1.0 NZ A:LYS215 3.5 5.2 1.0 O3' A:ADP310 3.8 3.0 1.0 CD A:GLU270 3.8 4.8 1.0 PB A:ADP310 3.8 4.5 1.0 OD1 A:ASP257 3.8 6.9 1.0 O5' A:ADP310 3.8 4.2 1.0 O3A A:ADP310 3.9 4.5 1.0 CB A:ASP257 3.9 6.5 1.0 O5P A:PHY320 3.9 11.1 1.0 O A:HOH410 4.1 12.8 1.0 MG A:MG331 4.2 5.9 1.0 O3P A:PHY320 4.2 11.2 1.0 O2B A:ADP310 4.2 4.1 1.0 C5' A:ADP310 4.3 3.7 1.0 CG A:GLU270 4.3 4.9 1.0 ND2 A:ASN272 4.3 5.1 1.0 O2P A:PHY320 4.3 10.9 1.0 O A:HOH637 4.4 15.1 1.0 NH2 A:ARG255 4.5 5.3 1.0 C3' A:ADP310 4.5 3.2 1.0 CE A:LYS215 4.5 5.3 1.0 O1A A:ADP310 4.8 4.5 1.0 OE1 A:GLU270 4.9 5.1 1.0 O1B A:ADP310 4.9 4.2 1.0 C4' A:ADP310 4.9 3.3 1.0

Magnesium binding site 2 out of 2 in the Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg331 b:5.9 occ:1.00 O A:HOH400 1.9 11.6 1.0 OE2 A:GLU270 1.9 4.7 1.0 OE1 A:GLU270 2.1 5.1 1.0 OD1 A:ASN272 2.1 5.8 1.0 CD A:GLU270 2.3 4.8 1.0 O2B A:ADP310 2.3 4.1 1.0 O5P A:PHY320 2.3 11.1 1.0 CG A:ASN272 3.2 5.5 1.0 PB A:ADP310 3.5 4.5 1.0 O A:HOH401 3.5 14.0 1.0 P2 A:PHY320 3.5 11.4 1.0 O3B A:ADP310 3.6 5.5 1.0 ND2 A:ASN272 3.6 5.1 1.0 CG A:GLU270 3.8 4.9 1.0 O4P A:PHY320 3.8 11.3 1.0 NZ A:LYS97 4.1 2.4 1.0 CA A:GLY149 4.1 2.0 1.0 MG A:MG330 4.2 6.1 1.0 O A:GLU148 4.2 3.1 1.0 O A:HOH430 4.2 20.9 1.0 O2A A:ADP310 4.3 5.3 1.0 O3A A:ADP310 4.3 4.5 1.0 O2P A:PHY320 4.4 10.9 1.0 CB A:ASN272 4.5 5.2 1.0 OD2 A:ASP257 4.5 6.9 1.0 CE A:LYS97 4.6 2.8 1.0 CB A:GLU270 4.6 5.4 1.0 O A:HOH416 4.6 4.5 1.0 O1B A:ADP310 4.6 4.2 1.0 O3P A:PHY320 4.6 11.2 1.0 N1 A:PHY320 4.7 10.3 1.0 O A:ALA271 4.8 5.4 1.0 PA A:ADP310 5.0 5.2 1.0

C.Fan, P.C.Moews, C.T.Walsh, J.R.Knox. Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 A Resolution. Science V. 266 439 1994.
ISSN: ISSN 0036-8075
PubMed: 7939684