Magnesium in PDB 1w8y: Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39.

All present enzymatic activity of Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39.:
3.4.16.4;

The structure of Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39., PDB code: 1w8y 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)	19.94 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.490, 94.360, 107.200, 90.00, 94.58, 90.00
R / Rfree (%)	22 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39. (pdb code 1w8y). 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 Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39., PDB code: 1w8y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase 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 Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:28.0 occ:1.00 OE1 A:GLU251 2.0 49.3 1.0 O A:GLU188 2.0 47.2 1.0 NE2 A:HIS247 2.1 59.2 1.0 CD A:GLU251 2.6 51.0 1.0 OE2 A:GLU251 2.8 47.7 1.0 CD2 A:HIS247 3.0 59.2 1.0 C A:GLU188 3.2 49.5 1.0 CE1 A:HIS247 3.2 59.8 1.0 O A:ALA186 3.7 48.3 1.0 CG A:GLU251 4.0 52.9 1.0 CA A:GLU188 4.0 49.9 1.0 CB A:GLU188 4.0 51.2 1.0 N A:GLU188 4.2 51.1 1.0 CG A:HIS247 4.2 59.2 1.0 N A:GLY189 4.2 49.1 1.0 ND1 A:HIS247 4.3 59.5 1.0 CA A:GLY189 4.4 51.3 1.0 C A:ALA186 4.8 47.4 1.0 N A:TYR190 4.9 53.4 1.0 C A:GLY189 4.9 53.0 1.0 C A:ALA187 5.0 51.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase 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 Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg511 b:24.1 occ:1.00 ND1 A:HIS462 2.2 54.6 1.0 CE1 A:HIS462 2.8 53.6 1.0 CG A:HIS462 3.3 54.8 1.0 CG2 A:VAL406 3.5 41.9 1.0 CB A:HIS462 3.9 54.7 1.0 NE2 A:HIS462 4.0 51.4 1.0 CD2 A:HIS462 4.2 52.9 1.0 O A:ALA402 4.3 41.9 1.0 O A:GLU404 4.6 43.9 1.0 CA A:HIS462 4.7 57.1 1.0 O A:GLN463 4.8 60.4 1.0 N A:GLN463 4.9 59.9 1.0 CB A:VAL406 5.0 41.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase 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 Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg510 b:21.3 occ:1.00 OE2 D:GLU251 1.9 39.5 1.0 NE2 D:HIS247 1.9 49.9 1.0 O D:GLU188 2.1 32.6 1.0 CD D:GLU251 2.8 41.0 1.0 CD2 D:HIS247 2.8 50.0 1.0 CE1 D:HIS247 2.9 50.9 1.0 OE1 D:GLU251 3.2 41.5 1.0 C D:GLU188 3.3 34.4 1.0 CA D:GLY189 4.0 36.7 1.0 CG D:HIS247 4.0 49.1 1.0 ND1 D:HIS247 4.0 50.3 1.0 N D:GLY189 4.1 34.6 1.0 CG D:GLU251 4.1 43.7 1.0 CA D:GLU188 4.4 33.4 1.0 O D:ALA186 4.4 33.4 1.0 CB D:GLU188 4.5 34.1 1.0 C D:GLY189 4.6 37.6 1.0 N D:GLU188 4.6 34.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Nitrocefin Acyl-Dd-Peptidase 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 Nitrocefin Acyl-Dd-Peptidase From Actinomadura R39. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg511 b:12.5 occ:1.00 ND1 D:HIS462 2.0 29.2 1.0 CE1 D:HIS462 2.9 33.1 1.0 CG D:HIS462 3.0 32.5 1.0 CB D:HIS462 3.4 32.2 1.0 CG2 D:VAL406 3.7 31.9 1.0 NE2 D:HIS462 4.0 34.0 1.0 CD2 D:HIS462 4.1 32.3 1.0 CA D:HIS462 4.1 33.0 1.0 O D:ALA402 4.3 31.7 1.0 O D:HOH2182 4.6 31.0 1.0 N D:GLN463 4.7 37.1 1.0 O D:GLN463 4.8 42.7 1.0 C D:HIS462 5.0 34.7 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