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Magnesium in PDB 3jw7: Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Ile-L-Tyr

Protein crystallography data

The structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Ile-L-Tyr, PDB code: 3jw7 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) 25.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 194.918, 187.442, 91.894, 90.00, 89.99, 90.00
R / Rfree (%) 22.1 / 25.4

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-Ile-L-Tyr (pdb code 3jw7). 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-Ile-L-Tyr, PDB code: 3jw7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg358

b:18.9
occ:1.00
OD2 A:ASP189 2.3 15.3 1.0
OE2 A:GLU215 2.3 19.3 1.0
OXT A:TYR356 2.3 16.0 1.0
OD2 A:ASP240 2.3 17.5 1.0
O A:HOH360 2.4 14.2 1.0
O A:TYR356 2.8 16.3 1.0
C A:TYR356 2.9 18.0 1.0
CD A:GLU215 3.2 21.8 1.0
CG A:ASP189 3.2 16.3 1.0
CG A:ASP240 3.3 18.2 1.0
OD1 A:ASP189 3.5 15.5 1.0
NZ A:LYS159 3.6 16.5 1.0
CB A:ASP240 3.7 16.1 1.0
OE1 A:GLU215 3.8 19.5 1.0
ND2 A:ASN191 4.0 16.0 1.0
NZ A:LYS161 4.1 13.1 1.0
ND2 A:ASN262 4.1 19.0 1.0
CG A:GLU215 4.1 22.2 1.0
O A:HOH648 4.2 28.8 1.0
NZ A:LYS264 4.2 18.8 1.0
CB A:GLU215 4.3 20.7 1.0
CE A:LYS159 4.3 17.8 1.0
CA A:TYR356 4.4 18.3 1.0
OD1 A:ASP240 4.4 16.6 1.0
OE1 A:GLU241 4.4 17.4 1.0
CB A:ASP189 4.6 14.2 1.0
CG A:ASN191 4.8 18.1 1.0
O A:HOH369 4.8 15.5 1.0
OD1 A:ASN191 5.0 17.1 1.0

Magnesium binding site 2 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg358

b:18.7
occ:1.00
OE2 B:GLU215 2.3 21.6 1.0
OD2 B:ASP189 2.3 13.5 1.0
OXT B:TYR356 2.3 15.7 1.0
OD2 B:ASP240 2.3 17.1 1.0
O B:HOH359 2.4 14.9 1.0
O B:TYR356 2.7 15.1 1.0
C B:TYR356 2.8 15.7 1.0
CD B:GLU215 3.2 23.2 1.0
CG B:ASP189 3.2 17.0 1.0
CG B:ASP240 3.3 17.9 1.0
OD1 B:ASP189 3.5 14.4 1.0
NZ B:LYS159 3.6 17.0 1.0
CB B:ASP240 3.7 14.7 1.0
OE1 B:GLU215 3.9 21.1 1.0
ND2 B:ASN191 4.0 15.7 1.0
CG B:GLU215 4.0 23.4 1.0
NZ B:LYS161 4.0 13.2 1.0
O B:HOH1322 4.2 28.6 1.0
ND2 B:ASN262 4.2 19.5 1.0
NZ B:LYS264 4.3 18.9 1.0
CE B:LYS159 4.3 16.9 1.0
CA B:TYR356 4.3 16.5 1.0
OE1 B:GLU241 4.3 16.8 1.0
CB B:GLU215 4.4 21.1 1.0
OD1 B:ASP240 4.4 16.4 1.0
CB B:ASP189 4.6 13.7 1.0
O B:HOH369 4.8 15.6 1.0
CG B:ASN191 4.8 16.8 1.0
O B:ILE355 4.9 18.6 1.0
OD1 B:ASN191 4.9 18.0 1.0
CB B:TYR356 5.0 17.1 1.0
CD B:GLU241 5.0 19.1 1.0

Magnesium binding site 3 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg358

b:30.0
occ:1.00
OE2 C:GLU215 2.2 29.0 1.0
OD2 C:ASP240 2.3 28.4 1.0
OD2 C:ASP189 2.3 24.7 1.0
O C:HOH363 2.4 30.8 1.0
OXT C:TYR356 2.5 29.2 1.0
O C:TYR356 2.8 28.7 1.0
C C:TYR356 3.0 30.2 1.0
CD C:GLU215 3.0 28.9 1.0
CG C:ASP189 3.2 25.4 1.0
CG C:ASP240 3.3 26.2 1.0
OD1 C:ASP189 3.5 25.0 1.0
NZ C:LYS159 3.5 28.9 1.0
CB C:ASP240 3.6 24.5 1.0
OE1 C:GLU215 3.7 31.7 1.0
CG C:GLU215 3.8 29.7 1.0
NZ C:LYS161 4.1 24.5 1.0
ND2 C:ASN191 4.1 24.7 1.0
ND2 C:ASN262 4.1 26.7 1.0
NZ C:LYS264 4.2 26.7 1.0
CB C:GLU215 4.2 28.3 1.0
OE1 C:GLU241 4.3 23.6 1.0
CE C:LYS159 4.3 29.7 1.0
O C:HOH1430 4.3 30.3 1.0
OD1 C:ASP240 4.4 24.5 1.0
CA C:TYR356 4.5 30.3 1.0
CB C:ASP189 4.5 25.6 1.0
O C:HOH364 4.9 26.1 1.0
CG C:ASN191 4.9 26.3 1.0

Magnesium binding site 4 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg358

b:29.4
occ:1.00
OE2 D:GLU215 2.1 30.1 1.0
OD2 D:ASP240 2.3 27.0 1.0
OD2 D:ASP189 2.4 25.5 1.0
O D:HOH925 2.4 30.9 1.0
OXT D:TYR356 2.5 29.9 1.0
O D:TYR356 2.8 30.8 1.0
CD D:GLU215 2.9 29.7 1.0
C D:TYR356 3.0 32.1 1.0
CG D:ASP189 3.3 26.2 1.0
CG D:ASP240 3.3 25.3 1.0
NZ D:LYS159 3.5 27.7 1.0
OD1 D:ASP189 3.6 25.4 1.0
OE1 D:GLU215 3.6 31.5 1.0
CB D:ASP240 3.6 23.7 1.0
CG D:GLU215 3.8 29.4 1.0
ND2 D:ASN262 4.1 28.6 1.0
NZ D:LYS161 4.1 22.9 1.0
ND2 D:ASN191 4.1 25.6 1.0
CB D:GLU215 4.2 27.8 1.0
CE D:LYS159 4.2 27.4 1.0
NZ D:LYS264 4.3 29.0 1.0
O D:HOH1007 4.4 29.9 1.0
OD1 D:ASP240 4.4 25.3 1.0
OE1 D:GLU241 4.4 22.7 1.0
CA D:TYR356 4.5 31.8 1.0
CB D:ASP189 4.6 26.3 1.0
CG D:ASN191 4.9 25.3 1.0
O D:HOH397 4.9 28.2 1.0
OD1 D:ASN191 5.0 27.1 1.0
CG D:ASN262 5.0 28.6 1.0

Magnesium binding site 5 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg358

b:19.2
occ:1.00
OE2 E:GLU215 2.2 21.5 1.0
OD2 E:ASP240 2.3 19.2 1.0
O E:HOH368 2.3 15.6 1.0
OXT E:TYR356 2.3 17.1 1.0
OD2 E:ASP189 2.4 17.0 1.0
O E:TYR356 2.7 15.9 1.0
C E:TYR356 2.8 14.6 1.0
CD E:GLU215 3.1 21.1 1.0
CG E:ASP240 3.2 19.3 1.0
CG E:ASP189 3.4 17.9 1.0
NZ E:LYS159 3.6 15.4 1.0
CB E:ASP240 3.6 16.3 1.0
OD1 E:ASP189 3.6 17.5 1.0
OE1 E:GLU215 3.9 21.6 1.0
CG E:GLU215 3.9 20.9 1.0
ND2 E:ASN191 3.9 15.1 1.0
O E:HOH1402 4.1 36.8 1.0
NZ E:LYS264 4.1 15.3 1.0
NZ E:LYS161 4.1 13.6 1.0
CA E:TYR356 4.3 16.3 1.0
OD1 E:ASP240 4.3 18.6 1.0
ND2 E:ASN262 4.3 20.3 1.0
CE E:LYS159 4.4 16.0 1.0
OE1 E:GLU241 4.4 17.1 1.0
CB E:GLU215 4.4 16.9 1.0
CB E:ASP189 4.7 14.5 1.0
CG E:ASN191 4.8 14.8 1.0
O E:HOH387 4.8 15.5 1.0
CB E:TYR356 4.9 16.6 1.0
O E:ILE355 4.9 16.6 1.0
CD E:GLU241 5.0 18.7 1.0
OD1 E:ASN191 5.0 14.8 1.0

Magnesium binding site 6 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg358

b:23.6
occ:1.00
OD2 F:ASP240 2.2 25.7 1.0
OE2 F:GLU215 2.2 24.2 1.0
O F:HOH393 2.2 18.4 1.0
OD2 F:ASP189 2.4 25.1 1.0
OXT F:TYR356 2.4 24.5 1.0
O F:TYR356 2.8 23.3 1.0
C F:TYR356 2.9 22.6 1.0
CD F:GLU215 3.1 23.2 1.0
CG F:ASP240 3.1 23.8 1.0
CG F:ASP189 3.3 23.4 1.0
CB F:ASP240 3.5 21.0 1.0
OD1 F:ASP189 3.6 24.2 1.0
NZ F:LYS159 3.8 21.9 1.0
OE1 F:GLU215 3.8 23.9 1.0
CG F:GLU215 3.9 24.4 1.0
ND2 F:ASN191 4.1 19.9 1.0
NZ F:LYS264 4.1 22.8 1.0
O F:HOH660 4.2 31.6 1.0
OD1 F:ASP240 4.2 23.7 1.0
ND2 F:ASN262 4.2 23.7 1.0
NZ F:LYS161 4.3 19.3 1.0
OE1 F:GLU241 4.3 22.3 1.0
CB F:GLU215 4.3 22.8 1.0
CE F:LYS159 4.4 24.4 1.0
CA F:TYR356 4.4 23.4 1.0
CB F:ASP189 4.7 21.0 1.0
CG F:ASN191 4.9 22.9 1.0
O F:HOH390 4.9 21.1 1.0
CD F:GLU241 4.9 23.6 1.0

Magnesium binding site 7 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg358

b:23.4
occ:1.00
OD2 G:ASP240 2.2 22.8 1.0
OE2 G:GLU215 2.2 24.5 1.0
O G:HOH384 2.3 17.7 1.0
OXT G:TYR356 2.4 24.0 1.0
OD2 G:ASP189 2.4 24.5 1.0
O G:TYR356 2.8 24.2 1.0
C G:TYR356 2.9 23.5 1.0
CD G:GLU215 3.1 23.1 1.0
CG G:ASP240 3.2 19.7 1.0
CG G:ASP189 3.4 22.6 1.0
CB G:ASP240 3.6 18.6 1.0
OD1 G:ASP189 3.7 25.3 1.0
NZ G:LYS159 3.8 20.6 1.0
OE1 G:GLU215 3.8 24.2 1.0
CG G:GLU215 3.9 24.0 1.0
ND2 G:ASN191 4.0 19.0 1.0
NZ G:LYS264 4.1 21.8 1.0
O G:HOH2521 4.2 26.0 1.0
NZ G:LYS161 4.2 18.6 1.0
ND2 G:ASN262 4.2 22.8 1.0
OD1 G:ASP240 4.2 21.2 1.0
OE1 G:GLU241 4.3 23.1 1.0
CB G:GLU215 4.4 20.7 1.0
CE G:LYS159 4.4 23.4 1.0
CA G:TYR356 4.4 23.6 1.0
CB G:ASP189 4.7 21.2 1.0
CG G:ASN191 4.8 22.7 1.0
CD G:GLU241 4.9 22.4 1.0
O G:HOH406 4.9 21.9 1.0

Magnesium binding site 8 out of 8 in 3jw7

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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-Ile-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-Ile-L-Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg358

b:19.5
occ:1.00
OE2 H:GLU215 2.2 21.1 1.0
OD2 H:ASP240 2.3 16.0 1.0
O H:HOH359 2.3 14.7 1.0
OXT H:TYR356 2.3 17.0 1.0
OD2 H:ASP189 2.4 18.2 1.0
O H:TYR356 2.7 15.2 1.0
C H:TYR356 2.8 16.0 1.0
CD H:GLU215 3.1 21.3 1.0
CG H:ASP240 3.2 16.7 1.0
CG H:ASP189 3.3 18.1 1.0
OD1 H:ASP189 3.5 17.9 1.0
NZ H:LYS159 3.6 15.8 1.0
CB H:ASP240 3.6 13.9 1.0
ND2 H:ASN191 3.8 13.4 1.0
OE1 H:GLU215 3.9 22.3 1.0
CG H:GLU215 4.0 21.7 1.0
O H:HOH1070 4.1 31.1 1.0
NZ H:LYS161 4.1 11.2 1.0
NZ H:LYS264 4.2 16.1 1.0
CA H:TYR356 4.3 16.1 1.0
OD1 H:ASP240 4.3 17.7 1.0
ND2 H:ASN262 4.3 19.5 1.0
OE1 H:GLU241 4.4 17.5 1.0
CE H:LYS159 4.4 14.9 1.0
CB H:GLU215 4.4 17.6 1.0
CB H:ASP189 4.7 15.6 1.0
CG H:ASN191 4.7 13.5 1.0
O H:HOH417 4.9 16.5 1.0
CB H:TYR356 5.0 17.5 1.0
CD H:GLU241 5.0 18.9 1.0
O H:ILE355 5.0 15.2 1.0
OD1 H:ASN191 5.0 14.6 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 17:15:12 2024

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