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Magnesium in PDB 3k1g: Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Ser-L-Tyr

Protein crystallography data

The structure of Crystal Structure of Dipeptide Epimerase From Enterococcus Faecalis V583 Complexed with Mg and Dipeptide L-Ser-L-Tyr, PDB code: 3k1g 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) 24.73 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 163.663, 163.663, 318.051, 90.00, 90.00, 120.00
R / Rfree (%) 24.5 / 28.2

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-Ser-L-Tyr (pdb code 3k1g). 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-Ser-L-Tyr, PDB code: 3k1g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3k1g

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

b:34.9
occ:1.00
O A:HOH359 2.0 40.1 1.0
OD2 A:ASP189 2.2 39.3 1.0
OE2 A:GLU215 2.3 40.5 1.0
OD2 A:ASP240 2.4 41.4 1.0
OXT A:TYR356 2.6 43.0 1.0
CD A:GLU215 2.8 39.7 1.0
O A:TYR356 2.9 40.7 1.0
CG A:ASP189 3.0 39.8 1.0
C A:TYR356 3.1 42.4 1.0
OD1 A:ASP189 3.2 40.7 1.0
CG A:GLU215 3.3 37.7 1.0
CG A:ASP240 3.3 40.9 1.0
OE1 A:GLU215 3.6 39.3 1.0
CB A:ASP240 3.7 38.7 1.0
NZ A:LYS159 3.7 45.9 1.0
NZ A:LYS161 4.0 41.9 1.0
ND2 A:ASN191 4.1 38.6 1.0
NZ A:LYS264 4.2 35.9 1.0
CB A:GLU215 4.3 37.1 1.0
OE1 A:GLU241 4.3 37.2 1.0
CE A:LYS159 4.3 45.6 1.0
CB A:ASP189 4.4 38.6 1.0
ND2 A:ASN262 4.4 39.5 1.0
OD1 A:ASP240 4.4 41.5 1.0
O A:HOH422 4.4 44.0 1.0
CA A:TYR356 4.6 41.8 1.0
CG A:ASN191 4.8 37.1 1.0
CD A:GLU241 4.9 41.4 1.0
OD1 A:ASN191 4.9 34.6 1.0
O A:HOH370 4.9 39.1 1.0

Magnesium binding site 2 out of 8 in 3k1g

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

b:37.9
occ:1.00
O B:HOH359 2.0 32.6 1.0
OE2 B:GLU215 2.0 32.9 1.0
OD2 B:ASP240 2.1 30.5 1.0
OXT B:TYR356 2.4 37.5 1.0
OD2 B:ASP189 2.5 29.0 1.0
O B:TYR356 2.7 35.8 1.0
CD B:GLU215 2.9 33.5 1.0
C B:TYR356 2.9 38.0 1.0
CG B:ASP240 3.1 29.6 1.0
CG B:ASP189 3.3 30.1 1.0
OD1 B:ASP189 3.4 27.1 1.0
CB B:ASP240 3.5 27.1 1.0
CG B:GLU215 3.6 31.1 1.0
OE1 B:GLU215 3.7 33.8 1.0
NZ B:LYS159 3.8 33.6 1.0
ND2 B:ASN191 3.8 33.0 1.0
OE1 B:GLU241 4.1 29.5 1.0
NZ B:LYS264 4.2 29.5 1.0
NZ B:LYS161 4.2 33.9 1.0
OD1 B:ASP240 4.3 29.0 1.0
ND2 B:ASN262 4.4 31.1 1.0
CA B:TYR356 4.4 38.5 1.0
CE B:LYS159 4.5 34.6 1.0
O B:HOH381 4.5 46.2 1.0
CB B:GLU215 4.6 28.0 1.0
CB B:ASP189 4.7 31.3 1.0
CG B:ASN191 4.7 35.7 1.0
O B:HOH404 4.9 32.0 1.0
CD B:GLU241 4.9 29.2 1.0

Magnesium binding site 3 out of 8 in 3k1g

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

b:33.6
occ:1.00
OD2 C:ASP240 2.0 37.8 1.0
OE2 C:GLU215 2.1 35.1 1.0
O C:HOH359 2.2 36.9 1.0
OXT C:TYR356 2.3 40.3 1.0
OD2 C:ASP189 2.4 35.5 1.0
O C:TYR356 2.7 37.1 1.0
C C:TYR356 2.8 38.5 1.0
CD C:GLU215 2.9 36.3 1.0
CG C:ASP240 3.1 34.6 1.0
CG C:ASP189 3.3 35.0 1.0
CB C:ASP240 3.5 33.9 1.0
OD1 C:ASP189 3.6 35.3 1.0
NZ C:LYS159 3.6 32.5 1.0
CG C:GLU215 3.7 34.7 1.0
OE1 C:GLU215 3.8 36.9 1.0
NZ C:LYS161 4.1 39.8 1.0
NZ C:LYS264 4.1 30.7 1.0
ND2 C:ASN191 4.2 32.0 1.0
OD1 C:ASP240 4.2 33.3 1.0
OE1 C:GLU241 4.3 32.5 1.0
CA C:TYR356 4.3 38.4 1.0
CE C:LYS159 4.4 37.7 1.0
CB C:GLU215 4.5 34.7 1.0
CB C:ASP189 4.6 36.8 1.0
ND2 C:ASN262 4.7 37.7 1.0
O C:HOH377 4.8 40.5 1.0
CG C:ASN191 4.8 34.4 1.0
OD1 C:ASN191 4.9 31.4 1.0
CD C:GLU241 5.0 34.7 1.0

Magnesium binding site 4 out of 8 in 3k1g

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

b:42.5
occ:1.00
OE2 D:GLU215 1.8 46.2 1.0
OD2 D:ASP189 2.2 49.2 1.0
OD2 D:ASP240 2.2 40.2 1.0
OXT D:TYR356 2.6 50.3 1.0
CD D:GLU215 2.7 48.2 1.0
O D:TYR356 2.8 46.6 1.0
C D:TYR356 3.0 49.2 1.0
CG D:ASP189 3.2 50.8 1.0
CG D:ASP240 3.2 40.4 1.0
OE1 D:GLU215 3.5 48.1 1.0
CG D:GLU215 3.5 46.4 1.0
CB D:ASP240 3.5 40.5 1.0
OD1 D:ASP189 3.6 52.9 1.0
O D:HOH371 4.1 57.1 1.0
NZ D:LYS159 4.1 63.7 1.0
NZ D:LYS161 4.2 57.5 1.0
CB D:GLU215 4.2 45.7 1.0
NZ D:LYS264 4.2 45.3 1.0
OD1 D:ASP240 4.3 38.1 1.0
CE D:LYS159 4.3 61.7 1.0
OE1 D:GLU241 4.4 42.8 1.0
ND2 D:ASN262 4.4 40.5 1.0
CB D:ASP189 4.5 51.0 1.0
CA D:TYR356 4.5 50.5 1.0
ND2 D:ASN191 4.9 48.7 1.0
CA D:ASP240 5.0 39.5 1.0

Magnesium binding site 5 out of 8 in 3k1g

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

b:32.1
occ:1.00
OD2 E:ASP240 2.0 37.0 1.0
OE2 E:GLU215 2.2 38.5 1.0
O E:HOH359 2.3 29.5 1.0
OXT E:TYR356 2.3 36.0 1.0
OD2 E:ASP189 2.4 28.8 1.0
O E:TYR356 2.8 33.4 1.0
C E:TYR356 2.9 37.1 1.0
CG E:ASP240 3.0 32.9 1.0
CD E:GLU215 3.0 37.0 1.0
CG E:ASP189 3.3 29.5 1.0
CB E:ASP240 3.4 32.5 1.0
OD1 E:ASP189 3.5 27.6 1.0
NZ E:LYS159 3.8 31.8 1.0
CG E:GLU215 3.8 34.6 1.0
OE1 E:GLU215 3.9 38.0 1.0
ND2 E:ASN191 4.0 36.1 1.0
NZ E:LYS264 4.1 30.7 1.0
OD1 E:ASP240 4.1 33.2 1.0
NZ E:LYS161 4.1 37.9 1.0
OE1 E:GLU241 4.2 32.0 1.0
CA E:TYR356 4.4 37.5 1.0
CE E:LYS159 4.5 37.4 1.0
CB E:GLU215 4.6 34.0 1.0
CB E:ASP189 4.6 31.0 1.0
ND2 E:ASN262 4.7 37.2 1.0
CG E:ASN191 4.8 36.1 1.0
CD E:GLU241 4.8 35.0 1.0
O E:HOH386 4.9 36.0 1.0
OD1 E:ASN191 4.9 35.0 1.0
CA E:ASP240 4.9 31.2 1.0
OE2 E:GLU241 4.9 32.1 1.0

Magnesium binding site 6 out of 8 in 3k1g

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

b:41.2
occ:1.00
OE2 F:GLU215 1.8 43.0 1.0
OD2 F:ASP240 2.1 35.4 1.0
OD2 F:ASP189 2.3 48.8 1.0
O F:HOH365 2.6 45.1 1.0
OXT F:TYR356 2.7 53.9 1.0
O F:TYR356 2.7 50.2 1.0
CD F:GLU215 2.8 45.9 1.0
C F:TYR356 3.1 53.1 1.0
CG F:ASP240 3.1 37.8 1.0
CG F:ASP189 3.3 50.9 1.0
CB F:ASP240 3.5 36.6 1.0
CG F:GLU215 3.6 44.2 1.0
OE1 F:GLU215 3.6 47.1 1.0
OD1 F:ASP189 3.7 51.7 1.0
NZ F:LYS161 3.8 59.5 1.0
NZ F:LYS264 4.1 43.4 1.0
NZ F:LYS159 4.1 61.6 1.0
O F:HOH463 4.1 53.0 1.0
OD1 F:ASP240 4.2 34.9 1.0
ND2 F:ASN262 4.2 39.5 1.0
CB F:GLU215 4.3 44.2 1.0
CE F:LYS159 4.4 60.1 1.0
OE1 F:GLU241 4.4 44.4 1.0
CB F:ASP189 4.6 51.3 1.0
CA F:TYR356 4.6 54.5 1.0
OD1 F:ASN191 4.8 53.2 1.0
CG F:ASN262 5.0 39.8 1.0
CA F:ASP240 5.0 36.1 1.0
ND2 F:ASN191 5.0 52.0 1.0

Magnesium binding site 7 out of 8 in 3k1g

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

b:33.9
occ:1.00
O G:HOH359 1.9 34.7 1.0
OE2 G:GLU215 2.1 44.2 1.0
OD2 G:ASP189 2.2 37.3 1.0
OXT G:TYR356 2.5 41.1 1.0
OD2 G:ASP240 2.5 42.1 1.0
O G:TYR356 2.8 38.4 1.0
CD G:GLU215 2.8 41.4 1.0
C G:TYR356 3.0 41.8 1.0
CG G:ASP189 3.1 36.7 1.0
OD1 G:ASP189 3.2 36.8 1.0
CG G:ASP240 3.3 41.8 1.0
CG G:GLU215 3.4 39.8 1.0
OE1 G:GLU215 3.6 39.7 1.0
CB G:ASP240 3.7 39.1 1.0
NZ G:LYS159 3.8 45.1 1.0
NZ G:LYS161 4.0 43.1 1.0
ND2 G:ASN191 4.2 38.1 1.0
OE1 G:GLU241 4.2 34.7 1.0
NZ G:LYS264 4.2 36.4 1.0
OD1 G:ASP240 4.4 41.5 1.0
CE G:LYS159 4.4 45.5 1.0
CB G:GLU215 4.4 38.3 1.0
O G:HOH417 4.4 50.5 1.0
CB G:ASP189 4.5 36.5 1.0
CA G:TYR356 4.5 41.8 1.0
ND2 G:ASN262 4.7 42.8 1.0
CG G:ASN191 4.8 37.5 1.0
OD1 G:ASN191 4.8 37.4 1.0
CD G:GLU241 4.9 39.1 1.0

Magnesium binding site 8 out of 8 in 3k1g

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

b:32.0
occ:1.00
OE2 H:GLU215 2.0 31.6 1.0
O H:HOH359 2.1 27.0 1.0
OD2 H:ASP240 2.1 26.0 1.0
OXT H:TYR356 2.4 38.7 1.0
OD2 H:ASP189 2.5 31.1 1.0
O H:TYR356 2.7 34.8 1.0
C H:TYR356 2.9 38.2 1.0
CD H:GLU215 2.9 30.6 1.0
CG H:ASP240 3.1 27.1 1.0
CG H:ASP189 3.4 29.5 1.0
CB H:ASP240 3.5 24.0 1.0
OD1 H:ASP189 3.5 25.3 1.0
ND2 H:ASN191 3.6 34.9 1.0
CG H:GLU215 3.7 27.2 1.0
OE1 H:GLU215 3.8 31.6 1.0
NZ H:LYS159 3.8 30.9 1.0
OE1 H:GLU241 4.1 29.6 1.0
NZ H:LYS264 4.2 29.4 1.0
OD1 H:ASP240 4.2 23.6 1.0
NZ H:LYS161 4.2 32.1 1.0
CA H:TYR356 4.4 40.5 1.0
ND2 H:ASN262 4.4 30.4 1.0
CE H:LYS159 4.5 33.4 1.0
O H:HOH420 4.6 35.0 1.0
CG H:ASN191 4.7 36.5 1.0
CB H:GLU215 4.7 24.7 1.0
CB H:ASP189 4.8 28.7 1.0
CD H:GLU241 4.8 29.0 1.0
O H:HOH405 4.9 33.2 1.0
CA H:ASP240 5.0 23.6 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 17:52:39 2024

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