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

The structure of Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Lys Dipeptide, PDB code: 3der 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)	24.99 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	190.690, 190.690, 283.106, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 24.4

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Lys Dipeptide (pdb code 3der). 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-Lys Dipeptide, PDB code: 3der:
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-Lys 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-Lys Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.8 occ:1.00 OD2 A:ASP241 2.3 24.1 1.0 OD2 A:ASP188 2.3 22.7 1.0 OE2 A:GLU216 2.3 23.9 1.0 O A:HOH423 2.4 21.9 1.0 O A:LYS412 2.6 26.1 1.0 OXT A:LYS412 2.7 25.9 1.0 C A:LYS412 3.0 26.4 1.0 CG A:ASP188 3.2 21.6 1.0 CG A:ASP241 3.3 23.1 1.0 CD A:GLU216 3.3 24.6 1.0 OD1 A:ASP188 3.5 24.0 1.0 NZ A:LYS159 3.7 24.6 1.0 CB A:ASP241 3.7 22.1 1.0 ND2 A:ASN190 3.9 25.9 1.0 OE1 A:GLU216 3.9 24.3 1.0 ND2 A:ASN263 4.0 24.2 1.0 O A:HOH497 4.1 30.6 1.0 NZ A:LYS265 4.1 29.9 1.0 NZ A:LYS161 4.2 24.5 1.0 CG A:GLU216 4.3 25.1 1.0 CB A:GLU216 4.4 23.7 1.0 OD1 A:ASP241 4.4 22.3 1.0 CA A:LYS412 4.5 26.1 1.0 OE1 A:GLU242 4.5 26.1 1.0 CE A:LYS159 4.5 22.1 1.0 CB A:ASP188 4.5 22.4 1.0 O A:HOH427 4.6 23.4 1.0 CE A:LYS265 4.7 28.0 1.0 CG A:ASN190 4.8 24.1 1.0 OD1 A:ASN190 5.0 23.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Lys 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-Lys Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:27.8 occ:1.00 OD2 B:ASP241 2.2 26.5 1.0 OE2 B:GLU216 2.4 26.7 1.0 OD2 B:ASP188 2.4 25.9 1.0 O B:HOH420 2.4 27.7 1.0 O B:LYS412 2.5 31.4 1.0 OXT B:LYS412 2.5 29.8 1.0 C B:LYS412 2.8 30.0 1.0 CG B:ASP241 3.3 27.5 1.0 CG B:ASP188 3.3 25.2 1.0 CD B:GLU216 3.3 28.7 1.0 OD1 B:ASP188 3.6 26.4 1.0 NZ B:LYS159 3.6 30.6 1.0 CB B:ASP241 3.8 24.2 1.0 ND2 B:ASN190 3.9 25.5 1.0 OE1 B:GLU216 3.9 28.7 1.0 ND2 B:ASN263 3.9 24.9 1.0 NZ B:LYS265 4.1 32.0 1.0 O B:HOH495 4.2 31.9 1.0 NZ B:LYS161 4.2 28.2 1.0 CG B:GLU216 4.3 28.6 1.0 CA B:LYS412 4.3 30.2 1.0 OD1 B:ASP241 4.4 23.8 1.0 O B:HOH439 4.5 27.2 1.0 CB B:GLU216 4.5 27.7 1.0 CE B:LYS159 4.5 31.7 1.0 OE1 B:GLU242 4.6 25.6 1.0 CB B:ASP188 4.6 26.1 1.0 CE B:LYS265 4.6 29.3 1.0 CG B:ASN190 4.7 29.3 1.0 OD1 B:ASN190 4.9 28.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Lys 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-Lys Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:27.2 occ:1.00 OE2 C:GLU216 2.3 23.3 1.0 OD2 C:ASP241 2.3 20.9 1.0 OD2 C:ASP188 2.4 22.3 1.0 O C:HOH565 2.5 21.3 1.0 O C:LYS412 2.6 22.5 1.0 OXT C:LYS412 2.8 23.6 1.0 C C:LYS412 3.0 23.9 1.0 CG C:ASP188 3.3 24.3 1.0 CD C:GLU216 3.3 24.5 1.0 CG C:ASP241 3.4 21.4 1.0 NZ C:LYS159 3.5 21.0 1.0 OD1 C:ASP188 3.6 21.3 1.0 CB C:ASP241 3.7 21.4 1.0 ND2 C:ASN263 3.9 24.7 1.0 OE1 C:GLU216 3.9 23.6 1.0 ND2 C:ASN190 4.0 18.4 1.0 NZ C:LYS265 4.2 25.5 1.0 CB C:GLU216 4.3 22.9 1.0 CG C:GLU216 4.3 25.7 1.0 NZ C:LYS161 4.4 21.9 1.0 O C:HOH634 4.4 30.0 1.0 CE C:LYS159 4.5 18.1 1.0 O C:HOH572 4.5 20.5 1.0 OD1 C:ASP241 4.5 21.0 1.0 CB C:ASP188 4.5 20.7 1.0 CA C:LYS412 4.5 23.8 1.0 CE C:LYS265 4.6 23.3 1.0 OE1 C:GLU242 4.7 21.2 1.0 CG C:ASN190 4.9 23.3 1.0 CG C:ASN263 4.9 26.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Dipeptide Epimerase From Thermotoga Maritima Complexed with L-Ala-L-Lys 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-Lys Dipeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:27.9 occ:1.00 OE2 D:GLU216 2.2 25.7 1.0 OD2 D:ASP241 2.3 27.1 1.0 OD2 D:ASP188 2.3 25.7 1.0 O D:HOH431 2.3 25.4 1.0 O D:LYS412 2.7 26.6 1.0 OXT D:LYS412 2.9 28.4 1.0 C D:LYS412 3.1 27.6 1.0 CD D:GLU216 3.2 27.6 1.0 CG D:ASP188 3.2 26.5 1.0 CG D:ASP241 3.3 27.2 1.0 OD1 D:ASP188 3.5 26.2 1.0 CB D:ASP241 3.6 24.1 1.0 NZ D:LYS159 3.7 26.0 1.0 OE1 D:GLU216 3.8 27.7 1.0 ND2 D:ASN263 3.9 25.6 1.0 ND2 D:ASN190 4.0 21.7 1.0 CG D:GLU216 4.2 28.2 1.0 CB D:GLU216 4.2 25.2 1.0 NZ D:LYS265 4.2 27.5 1.0 NZ D:LYS161 4.4 28.1 1.0 O D:HOH487 4.4 32.9 1.0 OD1 D:ASP241 4.4 26.3 1.0 CB D:ASP188 4.4 26.4 1.0 CE D:LYS159 4.5 26.2 1.0 OE1 D:GLU242 4.5 27.8 1.0 CA D:LYS412 4.6 28.7 1.0 O D:HOH420 4.7 25.2 1.0 CE D:LYS265 4.8 27.5 1.0 CG D:ASN190 4.8 27.1 1.0 CG D:ASN263 5.0 28.0 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