Magnesium in PDB 3vmt: Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog

The structure of Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog, PDB code: 3vmt was solved by C.Y.Huang, H.W.Shih, L.Y.Lin, Y.W.Tien, T.J.R.Cheng, W.C.Cheng, C.H.Wong, C.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.08 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.493, 67.429, 152.186, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog (pdb code 3vmt). 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 Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog, PDB code: 3vmt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog


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 Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:90.7 occ:1.00 O A:SER98 2.4 65.8 1.0 OE1 A:GLU102 2.4 82.5 1.0 OA2 A:LHI301 2.7 0.9 1.0 OA9 A:LHI301 2.8 76.1 1.0 NZ A:LYS248 3.3 66.8 1.0 CD A:GLU102 3.4 72.3 1.0 CD A:LYS248 3.5 52.1 1.0 C12 A:LHI301 3.5 0.9 1.0 C A:SER98 3.6 52.6 1.0 C11 A:LHI301 3.7 1.0 1.0 C13 A:LHI301 3.8 79.6 1.0 CG A:GLU102 3.8 58.0 1.0 CE A:LYS248 3.9 56.3 1.0 C8 A:LHI301 3.9 99.3 1.0 C10 A:LHI301 4.0 96.3 1.0 O A:MET99 4.1 56.8 1.0 CB A:GLU102 4.2 45.8 1.0 OE1 A:GLN252 4.2 65.0 1.0 C9 A:LHI301 4.2 0.5 1.0 C A:MET99 4.3 55.8 1.0 CA A:MET99 4.3 49.1 1.0 N A:MET99 4.4 51.2 1.0 OE2 A:GLU102 4.5 75.5 1.0 O A:HOH401 4.5 87.9 1.0 CA A:SER98 4.6 48.8 1.0 OB3 A:LHI301 4.6 1.0 1.0 CG A:LYS248 4.7 58.4 1.0 N A:GLU102 4.9 46.2 1.0 OA3 A:LHI301 5.0 0.8 1.0 N A:GLU100 5.0 57.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog


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 Staphylococcus Aureus Membrane-Bound Transglycosylase in Complex with A Lipid II Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:88.8 occ:1.00 OG1 A:THR115 2.3 0.0 1.0 OE1 A:GLN136 2.4 76.2 1.0 O A:GLY131 3.0 78.1 1.0 CD A:GLN136 3.3 71.7 1.0 N A:ASP111 3.4 81.8 1.0 O A:ASP111 3.6 68.4 1.0 NE2 A:GLN136 3.6 77.2 1.0 CB A:THR115 3.8 0.1 1.0 N A:THR133 3.8 49.7 1.0 CD1 A:PHE110 4.0 0.3 1.0 C A:GLY131 4.1 76.8 1.0 CA A:PHE110 4.1 75.8 1.0 CA A:ASP111 4.2 75.6 1.0 CA1 A:LHI301 4.2 97.2 1.0 C A:PHE110 4.2 76.4 1.0 C A:ASP111 4.2 79.6 1.0 CA A:SER132 4.3 66.9 1.0 CB A:THR133 4.3 59.7 1.0 CB A:ASP111 4.3 75.3 1.0 CE1 A:PHE110 4.4 0.5 1.0 CG2 A:THR115 4.5 0.6 1.0 CG A:PHE110 4.5 94.5 1.0 C A:SER132 4.5 68.9 1.0 O A:GLY109 4.6 68.8 1.0 CA A:THR115 4.6 0.6 1.0 CA A:THR133 4.7 55.0 1.0 N A:SER132 4.7 59.8 1.0 CG A:GLN136 4.7 60.6 1.0 N A:THR115 4.8 97.0 1.0 CG2 A:THR133 4.8 45.8 1.0 CB A:PHE110 4.9 74.4 1.0

C.Y.Huang, H.W.Shih, L.Y.Lin, Y.W.Tien, T.J.R.Cheng, W.C.Cheng, C.H.Wong, C.Ma. Crystal Structure of Staphylococcus Aureus Transglycosylase in Complex with A Lipid II Analog and Elucidation of Peptidoglycan Synthesis Mechanism Proc.Natl.Acad.Sci.Usa V. 109 6496 2012.
ISSN: ISSN 0027-8424
PubMed: 22493270
DOI: 10.1073/PNAS.1203900109