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

The structure of Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Phe Dipeptide, PDB code: 3des 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)	24.92 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	191.672, 191.672, 283.085, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Phe Dipeptide (pdb code 3des). 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-Phe Dipeptide, PDB code: 3des:
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-Phe 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-Phe Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:34.6 occ:1.00 O A:HOH449 2.1 24.7 1.0 OD2 A:ASP188 2.3 25.3 1.0 OD2 A:ASP241 2.4 30.9 1.0 OXT A:PHE412 2.5 29.4 1.0 OE2 A:GLU216 2.6 27.9 1.0 O A:PHE412 2.8 27.2 1.0 C A:PHE412 2.9 29.0 1.0 CG A:ASP188 3.1 25.9 1.0 OD1 A:ASP188 3.3 28.6 1.0 CG A:ASP241 3.4 30.4 1.0 CD A:GLU216 3.5 26.6 1.0 ND2 A:ASN190 3.6 27.8 1.0 CB A:ASP241 3.8 26.5 1.0 NZ A:LYS159 4.0 23.1 1.0 O A:HOH457 4.1 30.8 1.0 NZ A:LYS161 4.1 25.7 1.0 OE1 A:GLU216 4.2 28.2 1.0 NZ A:LYS265 4.3 31.1 1.0 ND2 A:ASN263 4.3 28.8 1.0 CB A:GLU216 4.4 25.7 1.0 OE1 A:GLU242 4.4 28.0 1.0 CG A:GLU216 4.4 26.9 1.0 CA A:PHE412 4.4 28.9 1.0 CB A:ASP188 4.4 22.4 1.0 CG A:ASN190 4.5 26.9 1.0 OD1 A:ASP241 4.5 28.1 1.0 OE2 A:GLU242 4.6 29.4 1.0 OD1 A:ASN190 4.8 25.2 1.0 CE A:LYS159 4.8 22.9 1.0 CD A:GLU242 4.9 30.0 1.0 CE A:LYS265 4.9 27.6 1.0 O A:HOH434 5.0 31.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Phe 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-Phe Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:33.6 occ:1.00 OD2 B:ASP241 2.2 32.3 1.0 OD2 B:ASP188 2.3 29.8 1.0 O B:HOH433 2.4 27.6 1.0 OE2 B:GLU216 2.4 30.7 1.0 OXT B:PHE412 2.5 30.4 1.0 O B:PHE412 2.5 30.2 1.0 C B:PHE412 2.8 31.8 1.0 CG B:ASP188 3.2 28.8 1.0 CG B:ASP241 3.3 32.2 1.0 CD B:GLU216 3.4 31.9 1.0 OD1 B:ASP188 3.5 30.1 1.0 ND2 B:ASN190 3.7 28.3 1.0 NZ B:LYS159 3.8 33.3 1.0 CB B:ASP241 3.8 28.2 1.0 NZ B:LYS265 3.9 31.1 1.0 OE1 B:GLU216 4.0 29.7 1.0 ND2 B:ASN263 4.0 26.6 1.0 NZ B:LYS161 4.2 35.2 1.0 O B:HOH438 4.3 31.8 1.0 CA B:PHE412 4.3 32.1 1.0 CG B:GLU216 4.4 30.3 1.0 OD1 B:ASP241 4.4 31.7 1.0 CB B:GLU216 4.4 30.0 1.0 CB B:ASP188 4.5 28.6 1.0 O B:HOH434 4.5 31.0 1.0 CE B:LYS159 4.6 34.3 1.0 CG B:ASN190 4.6 30.1 1.0 OE1 B:GLU242 4.6 28.9 1.0 CE B:LYS265 4.7 29.1 1.0 OE2 B:GLU242 4.9 31.4 1.0 OD1 B:ASN190 4.9 28.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Phe 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-Phe Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:38.0 occ:1.00 O C:HOH526 2.0 25.2 1.0 OD2 C:ASP241 2.3 30.3 1.0 OXT C:PHE412 2.4 26.0 1.0 OD2 C:ASP188 2.4 26.6 1.0 OE2 C:GLU216 2.6 27.6 1.0 O C:PHE412 2.7 25.5 1.0 C C:PHE412 2.9 25.1 1.0 CG C:ASP188 3.2 24.0 1.0 CG C:ASP241 3.3 28.3 1.0 OD1 C:ASP188 3.5 24.3 1.0 CD C:GLU216 3.6 24.9 1.0 ND2 C:ASN190 3.6 24.6 1.0 CB C:ASP241 3.7 25.7 1.0 NZ C:LYS159 4.0 19.0 1.0 O C:HOH548 4.0 26.7 1.0 NZ C:LYS265 4.1 29.7 1.0 OE1 C:GLU242 4.2 26.8 1.0 NZ C:LYS161 4.2 23.9 1.0 OE1 C:GLU216 4.3 23.9 1.0 OD1 C:ASP241 4.3 27.7 1.0 ND2 C:ASN263 4.3 23.6 1.0 CA C:PHE412 4.3 24.9 1.0 CB C:GLU216 4.5 23.5 1.0 CG C:ASN190 4.5 25.8 1.0 CB C:ASP188 4.6 21.8 1.0 CG C:GLU216 4.6 25.4 1.0 OE2 C:GLU242 4.7 29.9 1.0 CE C:LYS265 4.7 26.1 1.0 OD1 C:ASN190 4.7 23.8 1.0 O C:HOH529 4.8 29.7 1.0 CE C:LYS159 4.8 21.9 1.0 CD C:GLU242 4.8 27.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Phe 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-Phe Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:32.9 occ:1.00 O D:HOH542 2.2 34.7 1.0 OD2 D:ASP188 2.3 30.7 1.0 OD2 D:ASP241 2.3 32.6 1.0 OE2 D:GLU216 2.4 31.0 1.0 OXT D:PHE412 2.6 30.2 1.0 O D:PHE412 2.9 29.1 1.0 CG D:ASP188 3.1 28.8 1.0 C D:PHE412 3.1 30.3 1.0 CG D:ASP241 3.3 31.5 1.0 OD1 D:ASP188 3.3 30.3 1.0 CD D:GLU216 3.4 32.3 1.0 ND2 D:ASN190 3.7 29.0 1.0 CB D:ASP241 3.7 27.3 1.0 NZ D:LYS159 3.9 27.2 1.0 OE1 D:GLU216 4.1 31.6 1.0 O D:HOH555 4.1 33.9 1.0 NZ D:LYS265 4.2 31.8 1.0 CB D:GLU216 4.2 28.2 1.0 ND2 D:ASN263 4.3 30.6 1.0 NZ D:LYS161 4.4 29.2 1.0 CG D:GLU216 4.4 29.8 1.0 CB D:ASP188 4.4 27.4 1.0 OE1 D:GLU242 4.4 30.4 1.0 OD1 D:ASP241 4.4 28.9 1.0 CG D:ASN190 4.5 32.3 1.0 CA D:PHE412 4.6 30.6 1.0 OE2 D:GLU242 4.6 33.1 1.0 CE D:LYS159 4.7 28.5 1.0 CD D:GLU242 4.8 31.5 1.0 OD1 D:ASN190 4.9 31.6 1.0 CE D:LYS265 4.9 29.7 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