Magnesium in PDB 2vgj: Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin

All present enzymatic activity of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin:
3.4.16.4;

The structure of Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin, PDB code: 2vgj was solved by E.Sauvage, F.Kerff, R.Herman, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.03 / 2.4
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.030, 93.250, 108.160, 90.00, 94.21, 90.00
R / Rfree (%)	19.6 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin (pdb code 2vgj). 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 Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin, PDB code: 2vgj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


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 Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg611 b:38.8 occ:1.00 ND1 A:HIS462 3.0 38.4 1.0 CG2 A:VAL406 3.7 23.2 1.0 CE1 A:HIS462 3.7 37.7 1.0 CG A:HIS462 4.1 36.9 1.0 O A:GLU404 4.1 20.9 1.0 O A:ALA402 4.2 23.0 1.0 O A:GLN463 4.3 34.4 1.0 CB A:HIS462 4.4 36.2 1.0 CB A:VAL406 4.5 23.2 1.0 NE2 A:HIS462 4.9 37.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin


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 Actinomadura R39 Dd-Peptidase Complexed with A Peptidoglycan-Mimetic Cephalosporin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg611 b:17.5 occ:1.00 ND1 D:HIS462 2.5 41.9 1.0 CE1 D:HIS462 3.4 41.8 1.0 CG D:HIS462 3.5 42.3 1.0 CG2 D:VAL406 3.8 25.8 1.0 CB D:HIS462 3.8 42.6 1.0 O D:ALA402 4.4 27.4 1.0 NE2 D:HIS462 4.5 39.7 1.0 CA D:HIS462 4.6 42.9 1.0 CD2 D:HIS462 4.6 41.5 1.0 O D:GLN463 4.7 44.9 1.0 N D:GLN463 4.8 43.6 1.0 O D:GLU404 4.9 27.9 1.0

E.Sauvage, A.J.Powell, J.Heilemann, H.R.Josephin, P.Charlier, C.Davies, R.F.Pratt. Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: the Substrate Specificity Puzzle. J.Mol.Biol. V. 381 383 2008.
ISSN: ISSN 0022-2836
PubMed: 18602645
DOI: 10.1016/J.JMB.2008.06.012