Magnesium in PDB 1jpm: L-Ala-D/L-Glu Epimerase

The structure of L-Ala-D/L-Glu Epimerase, PDB code: 1jpm was solved by A.M.Gulick, D.M.Z.Schmidt, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.25
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	157.630, 157.630, 168.320, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.4

The binding sites of Magnesium atom in the L-Ala-D/L-Glu Epimerase (pdb code 1jpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the L-Ala-D/L-Glu Epimerase, PDB code: 1jpm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the L-Ala-D/L-Glu Epimerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L-Ala-D/L-Glu Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:22.9 occ:1.00 OE2 A:GLU219 2.0 22.8 1.0 OD2 A:ASP244 2.1 20.4 1.0 OD2 A:ASP191 2.1 25.8 1.0 O A:HOH2039 2.2 20.7 1.0 O A:HOH2041 2.2 22.4 1.0 O A:HOH2040 2.3 20.0 1.0 CD A:GLU219 3.0 23.6 1.0 CG A:ASP191 3.1 27.0 1.0 CG A:ASP244 3.3 20.4 1.0 OD1 A:ASP191 3.4 25.9 1.0 CB A:ASP244 3.8 18.4 1.0 OE1 A:GLU219 3.8 24.1 1.0 O A:HOH2107 3.8 33.4 1.0 CG A:GLU219 3.9 26.1 1.0 OE2 A:GLU245 3.9 22.4 1.0 NZ A:LYS268 4.0 19.3 1.0 OD1 A:ASN193 4.1 32.6 1.0 OE1 A:GLU245 4.2 18.3 1.0 O A:HOH2131 4.3 40.8 1.0 OD1 A:ASP244 4.3 19.4 1.0 OD1 A:ASN266 4.4 23.6 1.0 CD A:GLU245 4.5 22.3 1.0 CB A:ASP191 4.5 25.7 1.0 CB A:GLU219 4.6 21.2 1.0 CE A:LYS268 4.6 22.9 1.0 O A:HOH2058 4.8 28.8 1.0 CG A:ASN193 4.9 32.2 1.0

Magnesium binding site 2 out of 4 in the L-Ala-D/L-Glu Epimerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L-Ala-D/L-Glu Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:20.9 occ:1.00 O B:HOH1127 2.0 18.4 1.0 OD2 B:ASP244 2.1 24.2 1.0 O B:HOH1126 2.1 20.2 1.0 OD2 B:ASP191 2.2 20.1 1.0 O B:HOH1125 2.2 21.3 1.0 OE2 B:GLU219 2.2 27.6 1.0 CG B:ASP191 3.1 22.2 1.0 CG B:ASP244 3.2 22.0 1.0 CD B:GLU219 3.2 26.8 1.0 OD1 B:ASP191 3.4 21.9 1.0 CB B:ASP244 3.6 20.3 1.0 OE1 B:GLU219 3.8 29.0 1.0 O B:HOH1077 3.9 30.5 1.0 OD1 B:ASN266 4.0 23.6 1.0 CB B:GLU219 4.1 22.4 1.0 OE2 B:GLU245 4.1 20.8 1.0 NZ B:LYS268 4.1 16.8 1.0 OE1 B:GLU245 4.2 19.5 1.0 CG B:GLU219 4.2 26.9 1.0 OD1 B:ASP244 4.3 23.1 1.0 OD1 B:ASN193 4.4 29.9 1.0 CB B:ASP191 4.4 22.6 1.0 CD B:GLU245 4.6 22.4 1.0 CE B:LYS268 4.7 22.2 1.0 O B:HOH1060 4.8 23.2 1.0

Magnesium binding site 3 out of 4 in the L-Ala-D/L-Glu Epimerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L-Ala-D/L-Glu Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1004 b:27.0 occ:1.00 OE2 C:GLU219 2.0 28.8 1.0 OD2 C:ASP244 2.1 23.2 1.0 O C:HOH1094 2.1 23.4 1.0 O C:HOH1059 2.2 24.1 1.0 O C:HOH1058 2.2 22.8 1.0 OD2 C:ASP191 2.2 26.3 1.0 CD C:GLU219 3.0 28.8 1.0 CG C:ASP244 3.2 23.8 1.0 CG C:ASP191 3.2 25.5 1.0 OD1 C:ASP191 3.4 23.8 1.0 CB C:ASP244 3.7 22.5 1.0 OE1 C:GLU219 3.8 28.1 1.0 OE2 C:GLU245 3.8 20.2 1.0 CG C:GLU219 3.9 29.6 1.0 NZ C:LYS268 3.9 22.8 1.0 OE1 C:GLU245 4.1 20.1 1.0 OD1 C:ASN193 4.1 30.5 1.0 O C:HOH1025 4.1 37.9 1.0 OD1 C:ASP244 4.2 24.0 1.0 OD1 C:ASN266 4.3 24.6 1.0 CD C:GLU245 4.3 21.5 1.0 CB C:ASP191 4.6 24.4 1.0 CB C:GLU219 4.6 23.4 1.0 O C:HOH1062 4.6 28.3 1.0 CE C:LYS268 4.6 26.2 1.0 CG C:ASN193 5.0 30.1 1.0

Magnesium binding site 4 out of 4 in the L-Ala-D/L-Glu Epimerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L-Ala-D/L-Glu Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:26.9 occ:1.00 OD2 D:ASP244 2.1 25.9 1.0 O D:HOH1032 2.2 25.7 1.0 OD2 D:ASP191 2.2 25.6 1.0 O D:HOH1091 2.2 22.2 1.0 O D:HOH1056 2.2 23.5 1.0 OE2 D:GLU219 2.3 25.0 1.0 CG D:ASP244 3.2 23.6 1.0 CG D:ASP191 3.2 26.6 1.0 CD D:GLU219 3.4 27.2 1.0 OD1 D:ASP191 3.5 26.7 1.0 CB D:ASP244 3.7 19.7 1.0 O D:HOH1092 3.8 33.2 1.0 NZ D:LYS268 3.9 16.4 1.0 OE1 D:GLU219 4.0 32.2 1.0 OE2 D:GLU245 4.1 25.0 1.0 OD1 D:ASN266 4.1 25.3 1.0 CB D:GLU219 4.2 24.6 1.0 OD1 D:ASP244 4.3 24.2 1.0 O D:HOH1116 4.3 45.3 1.0 OD1 D:ASN193 4.3 31.2 1.0 OE1 D:GLU245 4.3 25.5 1.0 CG D:GLU219 4.4 24.4 1.0 CB D:ASP191 4.5 24.9 1.0 CE D:LYS268 4.6 21.1 1.0 CD D:GLU245 4.6 25.7 1.0 O D:HOH1058 4.9 24.8 1.0

A.M.Gulick, D.M.Schmidt, J.A.Gerlt, I.Rayment. Evolution of Enzymatic Activities in the Enolase Superfamily: Crystal Structures of the L-Ala-D/L-Glu Epimerases From Escherichia Coli and Bacillus Subtilis. Biochemistry V. 40 15716 2001.
ISSN: ISSN 0006-2960
PubMed: 11747448
DOI: 10.1021/BI011641P