Magnesium in PDB 3ijl: Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding.

The structure of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding., PDB code: 3ijl was solved by A.A.Fedorov, E.V.Fedorov, T.Lukk, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.91 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.897, 100.074, 60.075, 90.00, 90.34, 90.00
R / Rfree (%)	19.2 / 20.5

The binding sites of Magnesium atom in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding. (pdb code 3ijl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding., PDB code: 3ijl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg386 b:15.5 occ:1.00 OE1 A:GLU251 2.0 15.4 1.0 O A:HOH451 2.0 15.4 1.0 OD2 A:ASP276 2.0 17.1 1.0 OD2 A:ASP224 2.1 15.2 1.0 O A:HOH536 2.1 17.2 1.0 O A:HOH471 2.2 17.5 1.0 CD A:GLU251 2.9 15.5 1.0 CG A:ASP276 3.1 16.9 1.0 CG A:ASP224 3.1 16.6 1.0 OD1 A:ASP224 3.5 16.0 1.0 CB A:ASP276 3.5 16.7 1.0 OE2 A:GLU251 3.6 16.9 1.0 CG A:GLU251 3.7 17.7 1.0 O A:HOH459 3.9 26.3 1.0 NZ A:LYS298 4.0 16.1 1.0 OE2 A:GLU277 4.0 27.3 1.0 OD1 A:ASN226 4.1 29.6 1.0 OD1 A:ASP276 4.2 16.6 1.0 OE1 A:GLU277 4.2 20.2 1.0 ND2 A:ASN296 4.2 15.2 1.0 O A:DGL385 4.3 17.7 1.0 O A:HOH452 4.4 16.9 1.0 CB A:ASP224 4.4 16.2 1.0 CD A:GLU277 4.6 23.1 1.0 OXT A:DGL385 4.6 17.8 1.0 CE A:LYS298 4.7 15.3 1.0 C A:DGL385 4.7 16.9 1.0 O A:HOH506 4.7 18.5 1.0 CB A:GLU251 4.9 18.9 1.0 CG A:ASN226 5.0 26.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Pro-D-Glu; Nonproductive Substrate Binding. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg386 b:12.4 occ:1.00 OE1 B:GLU251 2.0 15.2 1.0 OD2 B:ASP276 2.0 14.6 1.0 O B:HOH394 2.1 12.9 1.0 O B:HOH473 2.1 12.8 1.0 O B:HOH466 2.1 14.4 1.0 OD2 B:ASP224 2.1 12.9 1.0 CD B:GLU251 2.9 14.9 1.0 CG B:ASP276 3.1 14.1 1.0 CG B:ASP224 3.1 11.9 1.0 OD1 B:ASP224 3.5 13.7 1.0 CB B:ASP276 3.5 14.9 1.0 OE2 B:GLU251 3.6 14.4 1.0 CG B:GLU251 3.7 18.6 1.0 OD1 B:ASN226 3.8 30.8 1.0 O B:HOH616 3.9 19.6 1.0 NZ B:LYS298 4.0 13.1 1.0 OE2 B:GLU277 4.1 23.3 1.0 OD1 B:ASP276 4.2 16.1 1.0 ND2 B:ASN296 4.2 12.0 1.0 O B:DGL385 4.2 14.4 1.0 OE1 B:GLU277 4.2 17.9 1.0 O B:HOH424 4.4 14.0 1.0 CB B:ASP224 4.4 13.4 1.0 OXT B:DGL385 4.5 14.3 1.0 CD B:GLU277 4.6 21.4 1.0 C B:DGL385 4.6 13.8 1.0 CE B:LYS298 4.7 12.9 1.0 CB B:GLU251 4.8 18.7 1.0 CG B:ASN226 4.8 27.9 1.0 O B:HOH502 4.9 15.9 1.0

T.Lukk, A.Sakai, C.Kalyanaraman, S.D.Brown, H.J.Imker, L.Song, A.A.Fedorov, E.V.Fedorov, R.Toro, B.Hillerich, R.Seidel, Y.Patskovsky, M.W.Vetting, S.K.Nair, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Homology Models Guide Discovery of Diverse Enzyme Specificities Among Dipeptide Epimerases in the Enolase Superfamily. Proc.Natl.Acad.Sci.Usa V. 109 4122 2012.
ISSN: ISSN 0027-8424
PubMed: 22392983
DOI: 10.1073/PNAS.1112081109