Magnesium in PDB 3deq: Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide

The structure of Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide, PDB code: 3deq was solved by A.A.Fedorov, E.V.Fedorov, H.J.Imker, 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 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	191.581, 191.581, 283.234, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 25.9

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide (pdb code 3deq). 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 Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide, PDB code: 3deq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide


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 Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.6 occ:1.00 O A:HOH443 2.3 34.1 1.0 OD2 A:ASP188 2.3 33.9 1.0 OD2 A:ASP241 2.3 32.7 1.0 OE2 A:GLU216 2.4 33.0 1.0 O A:LEU412 2.5 37.8 1.0 OXT A:LEU412 2.6 43.8 1.0 C A:LEU412 2.9 42.3 1.0 CG A:ASP188 3.3 33.1 1.0 CD A:GLU216 3.3 32.5 1.0 CG A:ASP241 3.4 32.5 1.0 OD1 A:ASP188 3.7 32.7 1.0 NZ A:LYS159 3.7 34.3 1.0 OE1 A:GLU216 3.8 33.8 1.0 CB A:ASP241 3.8 29.2 1.0 ND2 A:ASN263 3.9 33.9 1.0 ND2 A:ASN190 3.9 35.0 1.0 NZ A:LYS265 4.2 35.3 1.0 O A:HOH479 4.2 44.3 1.0 NZ A:LYS161 4.2 36.6 1.0 CG A:GLU216 4.4 31.9 1.0 CA A:LEU412 4.4 43.5 1.0 OD1 A:ASP241 4.5 31.2 1.0 O A:HOH460 4.5 33.5 1.0 CB A:ASP188 4.5 29.7 1.0 CE A:LYS159 4.6 30.7 1.0 CE A:LYS265 4.6 32.5 1.0 CB A:GLU216 4.6 31.0 1.0 OE1 A:GLU242 4.7 33.4 1.0 CG A:ASN190 4.8 33.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide


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 Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:38.9 occ:1.00 OE2 B:GLU216 2.2 38.4 1.0 OD2 B:ASP241 2.2 37.9 1.0 OD2 B:ASP188 2.4 36.3 1.0 O B:HOH431 2.4 34.5 1.0 O B:LEU412 2.5 45.1 1.0 OXT B:LEU412 2.7 47.8 1.0 C B:LEU412 3.0 47.4 1.0 CD B:GLU216 3.1 39.9 1.0 CG B:ASP188 3.3 36.4 1.0 CG B:ASP241 3.4 38.1 1.0 NZ B:LYS159 3.6 44.8 1.0 OD1 B:ASP188 3.6 38.7 1.0 OE1 B:GLU216 3.7 40.2 1.0 ND2 B:ASN263 3.8 32.1 1.0 CB B:ASP241 3.9 33.9 1.0 NZ B:LYS265 4.1 38.7 1.0 ND2 B:ASN190 4.1 38.7 1.0 NZ B:LYS161 4.2 38.8 1.0 CG B:GLU216 4.2 38.8 1.0 O B:HOH443 4.4 40.4 1.0 O B:HOH452 4.4 40.9 1.0 CB B:GLU216 4.4 37.2 1.0 OD1 B:ASP241 4.4 37.4 1.0 CE B:LYS159 4.4 44.5 1.0 CA B:LEU412 4.5 48.2 1.0 CE B:LYS265 4.5 35.6 1.0 CB B:ASP188 4.5 35.5 1.0 OE1 B:GLU242 4.9 36.1 1.0 CG B:ASN263 4.9 34.0 1.0 CG B:ASN190 4.9 39.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide


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 Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:33.6 occ:1.00 O C:HOH483 2.2 28.8 1.0 OD2 C:ASP241 2.2 30.6 1.0 OE2 C:GLU216 2.3 32.1 1.0 OD2 C:ASP188 2.4 29.2 1.0 O C:LEU412 2.7 33.8 1.0 OXT C:LEU412 2.8 38.6 1.0 C C:LEU412 3.1 38.5 1.0 CG C:ASP188 3.2 32.7 1.0 CG C:ASP241 3.3 30.1 1.0 CD C:GLU216 3.4 32.3 1.0 OD1 C:ASP188 3.5 29.9 1.0 CB C:ASP241 3.7 28.7 1.0 NZ C:LYS159 3.7 32.2 1.0 ND2 C:ASN263 3.9 32.5 1.0 ND2 C:ASN190 4.0 25.5 1.0 OE1 C:GLU216 4.0 30.7 1.0 NZ C:LYS265 4.2 34.2 1.0 CB C:GLU216 4.3 29.2 1.0 NZ C:LYS161 4.3 27.6 1.0 O C:HOH505 4.3 29.7 1.0 OD1 C:ASP241 4.4 30.2 1.0 CG C:GLU216 4.4 32.1 1.0 OE1 C:GLU242 4.5 31.4 1.0 CB C:ASP188 4.5 27.2 1.0 CE C:LYS265 4.6 33.0 1.0 CA C:LEU412 4.6 40.2 1.0 O C:HOH491 4.6 32.2 1.0 CE C:LYS159 4.6 30.5 1.0 CG C:ASN190 4.8 31.2 1.0 OE2 C:GLU242 4.9 34.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide


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 Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Leu Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:33.8 occ:1.00 OD2 D:ASP241 2.1 34.8 1.0 O D:HOH434 2.2 35.6 1.0 OE2 D:GLU216 2.3 36.1 1.0 OD2 D:ASP188 2.5 36.2 1.0 OXT D:LEU412 2.8 47.3 1.0 O D:LEU412 2.8 41.5 1.0 CG D:ASP241 3.1 35.1 1.0 C D:LEU412 3.2 45.4 1.0 CG D:ASP188 3.4 36.9 1.0 CD D:GLU216 3.4 38.1 1.0 CB D:ASP241 3.5 31.4 1.0 OD1 D:ASP188 3.6 36.0 1.0 ND2 D:ASN263 3.9 35.4 1.0 NZ D:LYS159 3.9 38.6 1.0 O D:HOH475 3.9 39.2 1.0 NZ D:LYS265 4.0 37.0 1.0 ND2 D:ASN190 4.0 34.3 1.0 OE1 D:GLU216 4.1 37.9 1.0 OD1 D:ASP241 4.2 34.9 1.0 CB D:GLU216 4.3 33.7 1.0 OE1 D:GLU242 4.4 36.6 1.0 CG D:GLU216 4.4 35.8 1.0 NZ D:LYS161 4.5 38.0 1.0 CE D:LYS265 4.6 35.2 1.0 CB D:ASP188 4.6 35.8 1.0 CA D:LEU412 4.7 46.4 1.0 CE D:LYS159 4.8 38.6 1.0 O D:HOH418 4.9 41.3 1.0 OE2 D:GLU242 4.9 37.8 1.0 CG D:ASN190 4.9 37.3 1.0 CD D:GLU242 4.9 36.6 1.0 CG D:ASN263 5.0 37.4 1.0

C.Kalyanaraman, H.J.Imker, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Discovery of A Dipeptide Epimerase Enzymatic Function Guided By Homology Modeling and Virtual Screening. Structure V. 16 1668 2008.
ISSN: ISSN 0969-2126
PubMed: 19000819
DOI: 10.1016/J.STR.2008.08.015