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

Protein crystallography data

The structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-L-Tyr, PDB code: 3jzu was solved by A.A.Fedorov, E.V.Fedorov, H.J.Imker, 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) 24.77 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 163.855, 163.855, 318.684, 90.00, 90.00, 120.00
R / Rfree (%) 24.7 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-L-Tyr (pdb code 3jzu). 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-Leu-L-Tyr, PDB code: 3jzu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3jzu

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Magnesium binding site 1 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg357

b:31.6
occ:1.00
 OE2 A:GLU215 2.1 27.4 1.0
O A:HOH358 2.2 31.4 1.0
OD2 A:ASP189 2.3 25.0 1.0
OD2 A:ASP240 2.3 32.8 1.0
OXT A:TYR356 2.5 27.7 1.0
O A:TYR356 2.6 28.3 1.0
CD A:GLU215 2.8 29.1 1.0
C A:TYR356 2.9 30.0 1.0
CG A:ASP240 3.2 28.8 1.0
CG A:ASP189 3.2 26.6 1.0
OE1 A:GLU215 3.5 31.5 1.0
OD1 A:ASP189 3.5 26.7 1.0
NZ A:LYS159 3.5 24.4 1.0
CG A:GLU215 3.5 26.9 1.0
CB A:ASP240 3.6 26.2 1.0
ND2 A:ASN191 4.0 30.0 1.0
NZ A:LYS161 4.1 22.6 1.0
ND2 A:ASN262 4.2 24.3 1.0
CE A:LYS159 4.3 30.3 1.0
OD1 A:ASP240 4.3 30.7 1.0
NZ A:LYS264 4.4 23.0 1.0
CA A:TYR356 4.4 29.3 1.0
OE1 A:GLU241 4.4 26.9 1.0
CB A:GLU215 4.5 27.6 1.0
CB A:ASP189 4.6 26.7 1.0
O A:HOH436 4.6 41.1 1.0
CG A:ASN191 4.8 30.1 1.0
O A:LEU355 4.8 29.3 1.0
OD1 A:ASN191 4.9 30.4 1.0
O A:HOH378 5.0 29.0 1.0
CG A:ASN262 5.0 25.2 1.0

Magnesium binding site 2 out of 8 in 3jzu

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Magnesium binding site 2 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg357

b:28.4
occ:1.00
 O B:HOH358 2.0 37.0 1.0
OE2 B:GLU215 2.1 36.1 1.0
OD2 B:ASP240 2.3 33.3 1.0
OD2 B:ASP189 2.3 34.3 1.0
OXT B:TYR356 2.3 35.8 1.0
O B:TYR356 2.8 35.7 1.0
C B:TYR356 2.9 36.0 1.0
CD B:GLU215 2.9 36.8 1.0
CG B:ASP189 3.2 35.9 1.0
CG B:ASP240 3.2 35.0 1.0
OD1 B:ASP189 3.4 34.2 1.0
CG B:GLU215 3.6 35.2 1.0
CB B:ASP240 3.6 33.2 1.0
NZ B:LYS159 3.7 38.8 1.0
OE1 B:GLU215 3.7 37.5 1.0
ND2 B:ASN191 4.0 37.9 1.0
NZ B:LYS161 4.0 31.6 1.0
NZ B:LYS264 4.2 29.9 1.0
OE1 B:GLU241 4.3 31.2 1.0
O B:HOH387 4.3 46.0 1.0
OD1 B:ASP240 4.3 31.4 1.0
CA B:TYR356 4.4 37.1 1.0
CE B:LYS159 4.4 39.7 1.0
CB B:ASP189 4.5 33.8 1.0
CB B:GLU215 4.5 33.2 1.0
ND2 B:ASN262 4.5 38.1 1.0
CG B:ASN191 4.7 37.5 1.0
OD1 B:ASN191 4.8 37.7 1.0
O B:HOH388 4.8 37.8 1.0
O B:LEU355 4.9 38.7 1.0
CD B:GLU241 4.9 35.8 1.0
CB B:TYR356 4.9 37.5 1.0

Magnesium binding site 3 out of 8 in 3jzu

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Magnesium binding site 3 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg357

b:38.3
occ:1.00
 OE2 C:GLU215 2.0 43.3 1.0
OD2 C:ASP240 2.2 38.2 1.0
OD2 C:ASP189 2.3 52.5 1.0
OXT C:TYR356 2.5 55.6 1.0
O C:HOH358 2.7 44.4 1.0
O C:TYR356 2.9 54.0 1.0
CD C:GLU215 2.9 46.6 1.0
C C:TYR356 3.0 54.2 1.0
CG C:ASP240 3.3 40.8 1.0
CG C:ASP189 3.3 52.8 1.0
OD1 C:ASP189 3.6 52.0 1.0
OE1 C:GLU215 3.6 46.3 1.0
CB C:ASP240 3.7 38.8 1.0
CG C:GLU215 3.7 46.1 1.0
ND2 C:ASN262 4.1 40.8 1.0
ND2 C:ASN191 4.1 50.2 1.0
NZ C:LYS264 4.1 49.0 1.0
O C:HOH363 4.1 40.3 1.0
NZ C:LYS161 4.2 57.7 1.0
NZ C:LYS159 4.2 65.2 1.0
CB C:GLU215 4.4 45.5 1.0
OD1 C:ASP240 4.4 37.9 1.0
CE C:LYS159 4.4 62.7 1.0
OE1 C:GLU241 4.4 44.3 1.0
CA C:TYR356 4.5 54.8 1.0
CB C:ASP189 4.6 51.6 1.0
O C:HOH399 4.7 42.5 1.0
CG C:ASN262 4.8 41.8 1.0
O C:LEU355 4.9 51.3 1.0

Magnesium binding site 4 out of 8 in 3jzu

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Magnesium binding site 4 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg357

b:32.2
occ:1.00
 OE2 D:GLU215 2.2 28.3 1.0
OD2 D:ASP240 2.2 33.2 1.0
O D:HOH358 2.3 33.9 1.0
OXT D:TYR356 2.3 35.9 1.0
OD2 D:ASP189 2.3 33.6 1.0
O D:TYR356 2.8 34.6 1.0
C D:TYR356 2.9 33.1 1.0
CD D:GLU215 3.0 31.7 1.0
CG D:ASP240 3.2 29.8 1.0
CG D:ASP189 3.2 32.4 1.0
OD1 D:ASP189 3.5 31.8 1.0
CB D:ASP240 3.5 28.3 1.0
NZ D:LYS159 3.7 30.4 1.0
OE1 D:GLU215 3.8 31.7 1.0
CG D:GLU215 3.8 32.2 1.0
ND2 D:ASN191 4.0 33.3 1.0
NZ D:LYS161 4.1 31.4 1.0
NZ D:LYS264 4.2 31.9 1.0
OD1 D:ASP240 4.3 30.9 1.0
O D:HOH407 4.3 45.8 1.0
OE1 D:GLU241 4.3 27.6 1.0
ND2 D:ASN262 4.4 37.7 1.0
CA D:TYR356 4.4 33.5 1.0
CE D:LYS159 4.4 34.7 1.0
CB D:GLU215 4.6 32.0 1.0
CB D:ASP189 4.6 34.5 1.0
CG D:ASN191 4.8 33.5 1.0
O D:LEU355 4.8 33.1 1.0
O D:HOH380 4.9 32.6 1.0
CB D:TYR356 5.0 34.6 1.0
CD D:GLU241 5.0 29.8 1.0

Magnesium binding site 5 out of 8 in 3jzu

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Magnesium binding site 5 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg357

b:31.6
occ:1.00
 OE2 E:GLU215 1.9 31.1 1.0
O E:HOH358 2.3 28.8 1.0
OD2 E:ASP240 2.3 28.1 1.0
OD2 E:ASP189 2.4 27.4 1.0
OXT E:TYR356 2.5 28.7 1.0
O E:TYR356 2.7 28.0 1.0
CD E:GLU215 2.8 26.6 1.0
C E:TYR356 2.9 29.6 1.0
CG E:ASP240 3.2 27.3 1.0
CG E:ASP189 3.3 23.8 1.0
CB E:ASP240 3.5 25.4 1.0
OD1 E:ASP189 3.5 26.1 1.0
CG E:GLU215 3.5 27.4 1.0
OE1 E:GLU215 3.6 31.0 1.0
NZ E:LYS159 3.7 26.0 1.0
ND2 E:ASN191 4.0 30.6 1.0
NZ E:LYS161 4.2 25.6 1.0
ND2 E:ASN262 4.2 26.0 1.0
OD1 E:ASP240 4.3 27.5 1.0
OE1 E:GLU241 4.3 25.0 1.0
NZ E:LYS264 4.4 28.2 1.0
CE E:LYS159 4.4 31.3 1.0
CA E:TYR356 4.4 30.4 1.0
CB E:GLU215 4.5 26.3 1.0
CB E:ASP189 4.6 26.3 1.0
CG E:ASN191 4.7 31.1 1.0
O E:HOH412 4.8 39.7 1.0
OD1 E:ASN191 4.9 31.1 1.0
O E:LEU355 5.0 28.7 1.0
CD E:GLU241 5.0 27.7 1.0

Magnesium binding site 6 out of 8 in 3jzu

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Magnesium binding site 6 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg357

b:31.7
occ:1.00
 OE2 F:GLU215 2.1 40.9 1.0
O F:HOH358 2.1 30.4 1.0
OXT F:TYR356 2.2 33.8 1.0
OD2 F:ASP189 2.3 30.8 1.0
OD2 F:ASP240 2.3 31.1 1.0
C F:TYR356 2.9 34.5 1.0
O F:TYR356 2.9 32.5 1.0
CD F:GLU215 3.0 38.5 1.0
CG F:ASP189 3.1 34.2 1.0
CG F:ASP240 3.2 32.5 1.0
OD1 F:ASP189 3.3 31.2 1.0
CB F:ASP240 3.6 31.9 1.0
CG F:GLU215 3.7 38.0 1.0
ND2 F:ASN191 3.8 37.3 1.0
OE1 F:GLU215 4.0 39.5 1.0
NZ F:LYS161 4.1 35.7 1.0
O F:HOH421 4.1 42.6 1.0
OE1 F:GLU241 4.2 32.5 1.0
OD1 F:ASP240 4.3 29.7 1.0
CA F:TYR356 4.4 35.6 1.0
NZ F:LYS159 4.4 50.2 1.0
NZ F:LYS264 4.4 33.1 1.0
ND2 F:ASN262 4.5 36.9 1.0
CB F:GLU215 4.5 34.6 1.0
CB F:ASP189 4.5 32.3 1.0
CG F:ASN191 4.6 36.9 1.0
OD1 F:ASN191 4.7 36.5 1.0
CE F:LYS159 4.7 50.9 1.0
O F:HOH422 4.9 33.4 1.0
CD F:GLU241 4.9 37.0 1.0
CB F:TYR356 4.9 36.4 1.0
O F:LEU355 5.0 37.9 1.0

Magnesium binding site 7 out of 8 in 3jzu

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Magnesium binding site 7 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg357

b:41.5
occ:1.00
 OE2 G:GLU215 2.0 44.5 1.0
OD2 G:ASP240 2.1 40.2 1.0
OXT G:TYR356 2.4 53.3 1.0
O G:HOH358 2.5 43.2 1.0
OD2 G:ASP189 2.5 51.5 1.0
O G:TYR356 2.9 51.3 1.0
CD G:GLU215 3.0 45.3 1.0
C G:TYR356 3.0 52.9 1.0
CG G:ASP240 3.2 41.4 1.0
CG G:ASP189 3.5 52.1 1.0
CB G:ASP240 3.6 39.4 1.0
NZ G:LYS159 3.7 58.4 1.0
CG G:GLU215 3.7 46.5 1.0
ND2 G:ASN191 3.7 54.1 1.0
OD1 G:ASP189 3.8 52.6 1.0
OE1 G:GLU215 3.8 45.9 1.0
NZ G:LYS264 4.1 46.9 1.0
O G:HOH368 4.1 44.9 1.0
ND2 G:ASN262 4.2 42.8 1.0
NZ G:LYS161 4.2 56.7 1.0
OD1 G:ASP240 4.3 38.7 1.0
OE1 G:GLU241 4.3 42.1 1.0
CE G:LYS159 4.4 58.0 1.0
CB G:GLU215 4.5 46.2 1.0
CA G:TYR356 4.5 53.9 1.0
CB G:ASP189 4.8 51.7 1.0
CG G:ASN262 4.9 43.0 1.0
O G:LEU355 5.0 51.8 1.0

Magnesium binding site 8 out of 8 in 3jzu

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Magnesium binding site 8 out of 8 in the Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Leu-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-Leu-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg357

b:31.0
occ:1.00
 OD2 H:ASP240 2.0 34.6 1.0
OE2 H:GLU215 2.1 34.4 1.0
O H:HOH359 2.2 30.9 1.0
OXT H:TYR356 2.2 32.1 1.0
OD2 H:ASP189 2.4 29.6 1.0
O H:TYR356 2.8 31.9 1.0
C H:TYR356 2.9 31.1 1.0
CD H:GLU215 3.0 32.8 1.0
CG H:ASP240 3.0 32.5 1.0
CG H:ASP189 3.3 29.6 1.0
CB H:ASP240 3.4 30.3 1.0
OD1 H:ASP189 3.5 27.3 1.0
NZ H:LYS159 3.7 31.9 1.0
CG H:GLU215 3.8 32.8 1.0
ND2 H:ASN191 3.8 30.8 1.0
OE1 H:GLU215 3.8 33.3 1.0
NZ H:LYS264 4.1 35.4 1.0
NZ H:LYS161 4.1 30.9 1.0
OD1 H:ASP240 4.1 32.6 1.0
O H:HOH390 4.2 41.9 1.0
OE1 H:GLU241 4.3 28.0 1.0
CA H:TYR356 4.3 32.9 1.0
ND2 H:ASN262 4.4 35.4 1.0
CE H:LYS159 4.4 34.8 1.0
CB H:GLU215 4.6 33.2 1.0
CB H:ASP189 4.6 31.4 1.0
CG H:ASN191 4.7 31.6 1.0
O H:LEU355 4.9 31.8 1.0
CD H:GLU241 4.9 29.6 1.0
CB H:TYR356 4.9 32.2 1.0
CA H:ASP240 5.0 26.4 1.0
OD1 H:ASN191 5.0 31.2 1.0
O H:HOH364 5.0 32.0 1.0

Reference:

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
Page generated: Wed Aug 14 17:43:06 2024

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