Magnesium in PDB 8ay0: Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide

The structure of Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide, PDB code: 8ay0 was solved by A.M.Hughes, E.J.Dodson, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.74 / 1.51
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.855, 61.31, 124.073, 78.09, 82.67, 61.6
R / Rfree (%)	18.5 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide (pdb code 8ay0). 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 Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide, PDB code: 8ay0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide


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 Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:39.8 occ:1.00 O A:HOH1139 2.0 39.9 1.0 O C:HOH858 2.0 37.5 1.0 O A:HOH729 2.0 31.0 1.0 O C:HOH1011 2.2 37.1 1.0 O A:HOH950 2.3 31.7 1.0 HA A:SER134 3.5 19.3 1.0 O A:HOH1122 3.9 35.3 1.0 O A:SER134 4.0 21.8 1.0 O C:HOH837 4.1 32.9 1.0 OD1 C:ASP410 4.2 24.6 1.0 O A:HOH922 4.3 41.0 1.0 C A:SER134 4.3 21.2 1.0 CA A:SER134 4.3 18.8 1.0 OD2 C:ASP410 4.3 28.2 1.0 O A:ASN133 4.3 19.5 1.0 HE3 C:MET402 4.4 25.4 1.0 CG C:ASP410 4.7 25.1 1.0 HB2 A:SER134 4.8 20.9 1.0 HB3 A:PRO113 4.8 28.4 1.0 HB C:VAL406 5.0 24.5 1.0 HE3 C:LYS415 5.0 45.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide


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 Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:30.4 occ:1.00 O B:HOH754 2.0 34.3 1.0 O B:HOH841 2.1 37.7 1.0 O B:HOH743 2.1 33.0 1.0 O B:HOH1099 2.2 33.5 1.0 HZ3 B:LYS228 3.5 41.1 1.0 OE2 B:GLU21 3.9 56.4 1.0 HE2 B:LYS228 4.0 38.4 1.0 OE1 B:GLU213 4.0 36.2 1.0 OE1 B:GLU21 4.2 48.2 1.0 NZ B:LYS228 4.3 42.3 1.0 OE2 B:GLU213 4.3 34.3 1.0 HE3 B:LYS228 4.4 38.4 1.0 CE B:LYS228 4.5 38.4 1.0 CD B:GLU21 4.5 50.5 1.0 CD B:GLU213 4.6 35.0 1.0 HZ1 B:LYS228 4.6 41.1 1.0 O B:HOH1064 4.7 43.9 1.0 HZ2 B:LYS228 4.9 41.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide


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 Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:42.9 occ:1.00 O B:HOH713 2.0 30.8 1.0 O B:HOH820 2.1 35.1 1.0 O B:HOH1064 2.1 43.9 1.0 O B:HOH1089 2.2 44.8 1.0 O B:HOH712 2.2 38.3 1.0 O B:HOH779 2.3 36.5 1.0 HB3 B:LYS214 3.7 25.0 1.0 HB3 B:ASP227 4.0 29.7 1.0 OD1 B:ASP227 4.0 30.5 1.0 OE1 B:GLU21 4.1 48.2 1.0 HB3 B:GLU213 4.1 28.1 1.0 OE1 B:GLU213 4.1 36.2 1.0 HA B:ASP227 4.3 27.8 1.0 O B:ASP227 4.3 27.7 1.0 O B:HOH754 4.4 34.3 1.0 O B:LYS214 4.5 26.2 1.0 H B:LYS214 4.6 25.2 1.0 CB B:LYS214 4.7 25.8 1.0 CB B:ASP227 4.7 30.0 1.0 CG B:ASP227 4.8 30.3 1.0 CA B:ASP227 4.9 28.4 1.0 HG2 B:LYS214 4.9 24.9 1.0 N B:LYS214 5.0 25.4 1.0 OD1 B:ASP216 5.0 51.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide


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 Peptide Binding Protein Dppe From Bacillus Subtilis in Complex with Murein Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:21.1 occ:1.00 O B:HOH783 2.1 23.5 1.0 O B:HOH988 2.1 24.6 1.0 OE2 B:GLU177 4.1 21.4 1.0 OE1 B:GLU177 4.2 20.2 1.0 O B:HOH1100 4.2 24.3 1.0 O B:HOH1130 4.3 33.9 1.0 CD B:GLU177 4.4 19.3 1.0 O B:HOH714 4.8 33.4 1.0

A.M.Hughes, J.F.Darby, E.J.Dodson, S.J.Wilson, J.P.Turkenburg, G.H.Thomas, A.J.Wilkinson. Peptide Transport in Bacillus Subtilis - Structure and Specificity in the Extracellular Solute Binding Proteins Oppa and Dppe. Microbiology (Reading, V. 168 2022ENGL.).
ISSN: ESSN 1465-2080
PubMed: 36748525
DOI: 10.1099/MIC.0.001274