Magnesium in PDB 3kum: Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr

The structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr, PDB code: 3kum was solved by A.A.Fedorov, E.V.Fedorov, A.Sakai, 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)	24.69 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	163.304, 163.304, 317.625, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 27

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr (pdb code 3kum). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr, PDB code: 3kum:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


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 Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg357 b:36.5 occ:1.00 O A:HOH358 2.1 44.4 1.0 OE2 A:GLU215 2.1 38.1 1.0 OD2 A:ASP189 2.3 39.0 1.0 OD2 A:ASP240 2.4 37.6 1.0 OXT A:TYR356 2.4 45.5 1.0 CD A:GLU215 2.7 38.9 1.0 O A:TYR356 2.9 41.0 1.0 C A:TYR356 3.0 43.9 1.0 CG A:ASP189 3.1 40.4 1.0 CG A:ASP240 3.3 41.9 1.0 OD1 A:ASP189 3.3 40.0 1.0 CG A:GLU215 3.4 34.7 1.0 OE1 A:GLU215 3.6 35.2 1.0 CB A:ASP240 3.6 38.6 1.0 NZ A:LYS159 3.7 43.0 1.0 NZ A:LYS161 4.0 48.0 1.0 ND2 A:ASN191 4.1 39.4 1.0 OE1 A:GLU241 4.2 32.9 1.0 NZ A:LYS264 4.3 38.8 1.0 OD1 A:ASP240 4.4 42.0 1.0 CE A:LYS159 4.4 43.8 1.0 CB A:GLU215 4.4 37.0 1.0 CB A:ASP189 4.5 40.4 1.0 CA A:TYR356 4.5 44.2 1.0 O A:HOH772 4.5 56.5 1.0 ND2 A:ASN262 4.7 43.5 1.0 CG A:ASN191 4.8 40.8 1.0 OD1 A:ASN191 4.8 40.7 1.0 CD A:GLU241 4.9 40.0 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


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 Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg357 b:34.7 occ:1.00 O B:HOH358 2.0 30.6 1.0 OE2 B:GLU215 2.1 31.9 1.0 OD2 B:ASP240 2.1 34.2 1.0 OXT B:TYR356 2.4 37.8 1.0 OD2 B:ASP189 2.4 32.3 1.0 O B:TYR356 2.8 37.3 1.0 CD B:GLU215 2.9 34.0 1.0 C B:TYR356 2.9 38.9 1.0 CG B:ASP240 3.1 31.3 1.0 CG B:ASP189 3.3 31.3 1.0 CB B:ASP240 3.4 29.4 1.0 OD1 B:ASP189 3.5 29.9 1.0 CG B:GLU215 3.6 32.0 1.0 OE1 B:GLU215 3.7 32.8 1.0 NZ B:LYS159 3.8 31.1 1.0 ND2 B:ASN191 4.0 38.9 1.0 OE1 B:GLU241 4.2 32.0 1.0 NZ B:LYS161 4.2 31.8 1.0 NZ B:LYS264 4.2 31.5 1.0 OD1 B:ASP240 4.2 30.0 1.0 ND2 B:ASN262 4.3 30.6 1.0 O B:HOH414 4.3 46.8 1.0 CA B:TYR356 4.4 40.3 1.0 CE B:LYS159 4.5 32.1 1.0 CB B:GLU215 4.6 30.6 1.0 CB B:ASP189 4.7 32.1 1.0 CG B:ASN191 4.8 38.9 1.0 CD B:GLU241 4.9 33.7 1.0 O B:HOH398 4.9 36.5 1.0 CA B:ASP240 5.0 29.9 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


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 Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg357 b:36.8 occ:1.00 OD2 C:ASP240 2.1 39.1 1.0 OE2 C:GLU215 2.1 31.6 1.0 O C:HOH358 2.3 33.6 1.0 OD2 C:ASP189 2.4 35.8 1.0 OXT C:TYR356 2.5 40.9 1.0 O C:TYR356 2.8 39.7 1.0 C C:TYR356 2.9 40.2 1.0 CD C:GLU215 3.0 35.6 1.0 CG C:ASP240 3.1 34.9 1.0 CG C:ASP189 3.3 34.9 1.0 CB C:ASP240 3.5 33.9 1.0 OD1 C:ASP189 3.5 33.5 1.0 CG C:GLU215 3.7 34.3 1.0 NZ C:LYS159 3.7 30.4 1.0 OE1 C:GLU215 3.8 38.2 1.0 ND2 C:ASN191 4.0 34.2 1.0 NZ C:LYS161 4.1 34.1 1.0 NZ C:LYS264 4.2 31.2 1.0 OD1 C:ASP240 4.2 35.8 1.0 OE1 C:GLU241 4.3 36.1 1.0 ND2 C:ASN262 4.4 36.4 1.0 CE C:LYS159 4.4 34.3 1.0 CA C:TYR356 4.4 40.2 1.0 CB C:ASP189 4.6 34.3 1.0 CB C:GLU215 4.6 35.1 1.0 O C:HOH376 4.8 37.6 1.0 CG C:ASN191 4.8 34.7 1.0 CD C:GLU241 5.0 36.8 1.0 CA C:ASP240 5.0 32.9 1.0 OD1 C:ASN191 5.0 32.3 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


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 Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg357 b:37.1 occ:1.00 OE2 D:GLU215 1.9 40.0 1.0 OD2 D:ASP189 2.2 36.9 1.0 OD2 D:ASP240 2.3 37.5 1.0 O D:HOH367 2.5 44.6 1.0 OXT D:TYR356 2.6 48.5 1.0 CD D:GLU215 2.7 43.0 1.0 O D:TYR356 2.8 43.1 1.0 C D:TYR356 3.1 46.4 1.0 CG D:ASP189 3.1 42.1 1.0 CG D:ASP240 3.3 40.2 1.0 OE1 D:GLU215 3.4 41.9 1.0 OD1 D:ASP189 3.5 42.8 1.0 CG D:GLU215 3.5 40.7 1.0 NZ D:LYS159 3.5 44.1 1.0 CB D:ASP240 3.7 38.8 1.0 NZ D:LYS161 4.0 47.2 1.0 CE D:LYS159 4.1 46.4 1.0 NZ D:LYS264 4.3 41.5 1.0 ND2 D:ASN262 4.3 37.7 1.0 CB D:GLU215 4.4 41.3 1.0 CB D:ASP189 4.4 42.4 1.0 OD1 D:ASP240 4.5 35.4 1.0 OE1 D:GLU241 4.5 42.8 1.0 O D:HOH562 4.5 50.2 1.0 ND2 D:ASN191 4.5 42.8 1.0 CA D:TYR356 4.6 47.3 1.0 O D:HOH474 4.9 46.6 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg357 b:35.1 occ:1.00 OD2 E:ASP240 2.0 38.4 1.0 O E:HOH358 2.2 32.2 1.0 OE2 E:GLU215 2.2 35.4 1.0 OXT E:TYR356 2.4 37.6 1.0 OD2 E:ASP189 2.4 33.1 1.0 O E:TYR356 2.8 36.3 1.0 C E:TYR356 2.9 38.1 1.0 CG E:ASP240 3.0 34.5 1.0 CD E:GLU215 3.1 35.5 1.0 CG E:ASP189 3.3 32.9 1.0 CB E:ASP240 3.4 32.2 1.0 OD1 E:ASP189 3.5 31.0 1.0 NZ E:LYS159 3.6 31.0 1.0 CG E:GLU215 3.7 35.0 1.0 ND2 E:ASN191 3.9 35.6 1.0 OE1 E:GLU215 3.9 37.6 1.0 OD1 E:ASP240 4.1 33.1 1.0 NZ E:LYS264 4.2 34.0 1.0 NZ E:LYS161 4.2 35.7 1.0 OE1 E:GLU241 4.2 34.7 1.0 CE E:LYS159 4.4 34.1 1.0 CA E:TYR356 4.4 38.8 1.0 ND2 E:ASN262 4.4 36.8 1.0 CB E:ASP189 4.7 33.2 1.0 CB E:GLU215 4.7 36.5 1.0 CG E:ASN191 4.7 36.2 1.0 CD E:GLU241 4.8 35.2 1.0 CA E:ASP240 4.9 30.7 1.0 O E:HOH386 4.9 33.7 1.0 OD1 E:ASN191 4.9 34.0 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg357 b:41.2 occ:1.00 OE2 F:GLU215 1.9 41.6 1.0 OD2 F:ASP240 2.2 36.8 1.0 OD2 F:ASP189 2.3 39.1 1.0 O F:HOH439 2.4 44.9 1.0 OXT F:TYR356 2.7 48.2 1.0 CD F:GLU215 2.7 42.1 1.0 O F:TYR356 2.8 43.3 1.0 C F:TYR356 3.1 47.2 1.0 CG F:ASP240 3.2 39.5 1.0 CG F:ASP189 3.2 41.4 1.0 OD1 F:ASP189 3.5 42.3 1.0 CB F:ASP240 3.5 36.6 1.0 OE1 F:GLU215 3.5 41.1 1.0 CG F:GLU215 3.6 40.8 1.0 NZ F:LYS159 3.6 41.8 1.0 NZ F:LYS161 4.1 45.9 1.0 NZ F:LYS264 4.2 39.5 1.0 CE F:LYS159 4.3 45.9 1.0 OE1 F:GLU241 4.3 40.1 1.0 OD1 F:ASP240 4.3 34.4 1.0 ND2 F:ASN262 4.3 39.5 1.0 O F:HOH698 4.3 52.3 1.0 ND2 F:ASN191 4.3 42.3 1.0 CB F:GLU215 4.4 39.8 1.0 CB F:ASP189 4.5 41.7 1.0 CA F:TYR356 4.6 49.0 1.0 CG F:ASN191 4.9 44.0 1.0 O F:HOH784 4.9 47.8 1.0 OD1 F:ASN191 5.0 45.0 1.0 CA F:ASP240 5.0 36.3 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg357 b:35.4 occ:1.00 O G:HOH358 2.0 32.5 1.0 OE2 G:GLU215 2.1 41.1 1.0 OD2 G:ASP189 2.2 39.1 1.0 OD2 G:ASP240 2.4 37.2 1.0 OXT G:TYR356 2.5 42.2 1.0 CD G:GLU215 2.8 39.2 1.0 CG G:ASP189 3.0 38.6 1.0 O G:TYR356 3.1 40.2 1.0 C G:TYR356 3.1 43.6 1.0 OD1 G:ASP189 3.3 38.7 1.0 CG G:ASP240 3.3 41.1 1.0 CG G:GLU215 3.4 37.8 1.0 CB G:ASP240 3.6 38.0 1.0 OE1 G:GLU215 3.7 37.3 1.0 NZ G:LYS159 3.9 40.6 1.0 ND2 G:ASN191 3.9 42.1 1.0 NZ G:LYS161 4.0 47.1 1.0 OE1 G:GLU241 4.1 34.0 1.0 NZ G:LYS264 4.3 39.8 1.0 O G:HOH785 4.3 53.1 1.0 OD1 G:ASP240 4.4 40.5 1.0 CB G:ASP189 4.4 40.0 1.0 CB G:GLU215 4.4 38.3 1.0 CE G:LYS159 4.5 42.5 1.0 ND2 G:ASN262 4.5 41.1 1.0 CG G:ASN191 4.6 41.5 1.0 CA G:TYR356 4.6 44.1 1.0 OD1 G:ASN191 4.8 39.9 1.0 CD G:GLU241 4.8 41.0 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Arg-L-Tyr within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg357 b:35.8 occ:1.00 O H:HOH358 2.0 27.0 1.0 OE2 H:GLU215 2.2 31.9 1.0 OD2 H:ASP240 2.2 30.3 1.0 OXT H:TYR356 2.3 39.9 1.0 OD2 H:ASP189 2.5 32.1 1.0 O H:TYR356 2.8 34.8 1.0 C H:TYR356 2.9 38.2 1.0 CD H:GLU215 3.1 32.1 1.0 CG H:ASP240 3.1 31.3 1.0 CG H:ASP189 3.3 30.6 1.0 OD1 H:ASP189 3.4 29.5 1.0 CB H:ASP240 3.5 29.0 1.0 CG H:GLU215 3.8 30.5 1.0 ND2 H:ASN191 3.8 36.1 1.0 NZ H:LYS159 3.8 30.8 1.0 OE1 H:GLU215 3.9 33.5 1.0 OE1 H:GLU241 4.1 30.4 1.0 NZ H:LYS161 4.1 35.0 1.0 NZ H:LYS264 4.2 30.6 1.0 OD1 H:ASP240 4.2 29.6 1.0 CA H:TYR356 4.4 41.2 1.0 ND2 H:ASN262 4.4 33.0 1.0 O H:HOH432 4.4 40.6 1.0 CE H:LYS159 4.5 32.6 1.0 CG H:ASN191 4.7 38.5 1.0 CB H:ASP189 4.7 31.4 1.0 CD H:GLU241 4.7 34.3 1.0 CB H:GLU215 4.7 29.1 1.0 OE2 H:GLU241 4.9 36.0 1.0 OD1 H:ASN191 4.9 37.5 1.0 CA H:ASP240 5.0 28.3 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