Magnesium in PDB 1w79: Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39

All present enzymatic activity of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39:
3.4.16.4;

The structure of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39, PDB code: 1w79 was solved by E.Sauvage, R.Herman, S.Petrella, C.Duez, J.M.Frere, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.187, 93.369, 107.272, 90.00, 94.25, 90.00
R / Rfree (%)	21.4 / 24

The binding sites of Magnesium atom in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 (pdb code 1w79). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39, PDB code: 1w79:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:5.5 occ:1.00 OE1 A:GLU251 1.9 25.9 1.0 NE2 A:HIS247 2.0 28.6 1.0 O A:GLU188 2.2 18.4 1.0 CE1 A:HIS247 3.0 29.6 1.0 CD A:GLU251 3.0 24.5 1.0 CD2 A:HIS247 3.0 27.1 1.0 C A:GLU188 3.2 17.5 1.0 OE2 A:GLU251 3.4 22.5 1.0 CA A:GLY189 3.9 18.7 1.0 N A:GLY189 4.0 17.6 1.0 ND1 A:HIS247 4.1 29.4 1.0 CG A:HIS247 4.1 27.0 1.0 CB A:GLU188 4.2 20.1 1.0 CA A:GLU188 4.2 18.9 1.0 CG A:GLU251 4.2 26.1 1.0 O A:ALA186 4.3 18.9 1.0 N A:GLU188 4.5 19.0 1.0 C A:GLY189 4.5 21.1 1.0 O A:HOH2196 4.9 32.2 1.0 N A:TYR190 5.0 19.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg511 b:1.2 occ:1.00 ND1 A:HIS462 2.1 19.8 1.0 CE1 A:HIS462 2.9 16.8 1.0 CG A:HIS462 3.2 18.3 1.0 CG2 A:VAL406 3.4 18.2 1.0 CB A:HIS462 3.6 19.8 1.0 NE2 A:HIS462 4.1 16.4 1.0 CD2 A:HIS462 4.2 17.2 1.0 O A:ALA402 4.4 17.3 1.0 CA A:HIS462 4.4 21.9 1.0 O A:GLN463 4.7 21.0 1.0 N A:GLN463 4.9 21.9 1.0 CB A:VAL406 4.9 17.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg510 b:54.9 occ:1.00 MG D:MG511 2.5 51.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg511 b:51.6 occ:1.00 MG D:MG510 2.5 54.9 1.0

E.Sauvage, R.Herman, S.Petrella, C.Duez, F.Bouillenne, J.M.Frere, P.Charlier. Crystal Structure of the Actinomadura R39 Dd-Peptidase Reveals New Domains in Penicillin-Binding Proteins. J. Biol. Chem. V. 280 31249 2005.
ISSN: ISSN 0021-9258
PubMed: 15987687
DOI: 10.1074/JBC.M503271200