Magnesium in PDB 3ijq: Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Productive Substrate Binding.

The structure of Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Productive Substrate Binding., PDB code: 3ijq 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)	24.93 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.710, 99.865, 60.851, 90.00, 90.32, 90.00
R / Rfree (%)	24.7 / 28.7

The binding sites of Magnesium atom in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Productive Substrate Binding. (pdb code 3ijq). 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-Ala-D-Glu; Productive Substrate Binding., PDB code: 3ijq:
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-Ala-D-Glu; Productive 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-Ala-D-Glu; Productive Substrate Binding. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg386 b:53.4 occ:1.00 O A:HOH387 2.0 49.5 1.0 OE1 A:GLU251 2.0 43.4 1.0 OD2 A:ASP276 2.1 54.1 1.0 OD2 A:ASP224 2.3 61.3 1.0 CD A:GLU251 3.1 47.3 1.0 CG A:ASP276 3.2 54.3 1.0 CG A:ASP224 3.3 59.5 1.0 O A:DGL385 3.3 52.2 1.0 OXT A:DGL385 3.6 55.7 1.0 OD1 A:ASP224 3.6 59.3 1.0 O A:HOH446 3.6 45.1 1.0 NZ A:LYS298 3.8 47.5 1.0 C A:DGL385 3.8 51.9 1.0 OE2 A:GLU251 3.9 45.7 1.0 CB A:ASP276 3.9 55.0 1.0 CG A:GLU251 4.1 50.0 1.0 OE2 A:GLU277 4.1 58.7 1.0 OD1 A:ASP276 4.2 53.5 1.0 OD1 A:ASN226 4.3 65.8 1.0 NZ A:LYS198 4.5 43.9 1.0 CB A:ASP224 4.6 58.8 1.0 ND2 A:ASN296 4.7 55.1 1.0 OE1 A:GLU277 4.9 58.5 1.0 CD A:GLU277 4.9 60.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Dipeptide Epimerase From Bacteroides Thetaiotaomicron Complexed with L-Ala-D-Glu; Productive 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-Ala-D-Glu; Productive Substrate Binding. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg386 b:37.9 occ:1.00 O B:HOH388 1.7 28.9 1.0 OD2 B:ASP276 2.1 38.0 1.0 OE1 B:GLU251 2.1 39.8 1.0 OXT B:DGL385 2.4 40.0 1.0 OD2 B:ASP224 2.5 46.9 1.0 O B:DGL385 2.7 35.5 1.0 C B:DGL385 2.9 38.8 1.0 CD B:GLU251 3.1 41.3 1.0 CG B:ASP276 3.3 34.7 1.0 CG B:ASP224 3.3 50.1 1.0 NZ B:LYS298 3.5 36.5 1.0 OD1 B:ASP224 3.5 50.4 1.0 OE2 B:GLU251 3.8 40.2 1.0 CB B:ASP276 4.0 35.4 1.0 CG B:GLU251 4.1 42.2 1.0 OD1 B:ASP276 4.2 34.7 1.0 NZ B:LYS198 4.3 37.9 1.0 CA B:DGL385 4.4 35.9 1.0 ND2 B:ASN296 4.4 39.3 1.0 OE1 B:GLU277 4.4 45.6 1.0 CE B:LYS298 4.4 30.9 1.0 OE2 B:GLU277 4.5 48.9 1.0 CB B:ASP224 4.5 50.1 1.0 ND2 B:ASN226 4.7 68.2 1.0 O B:HOH405 4.8 31.2 1.0 CD B:GLU277 4.9 48.7 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