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Magnesium in PDB 3q4d: Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala

Enzymatic activity of Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala

All present enzymatic activity of Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala:
5.5.1.7;

Protein crystallography data

The structure of Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala, PDB code: 3q4d was solved by T.Lukk, J.A.Gerlt, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.560, 158.090, 182.180, 90.00, 100.04, 90.00
R / Rfree (%) 23 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala (pdb code 3q4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala, PDB code: 3q4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3q4d

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Magnesium binding site 1 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:58.0
occ:1.00
 OD2 A:ASP241 2.0 70.1 1.0
OE1 A:GLU216 2.2 59.8 1.0
OD2 A:ASP190 2.3 67.0 1.0
OXT A:ALA2473 2.5 57.0 1.0
O A:ALA2473 2.9 55.9 1.0
C A:ALA2473 3.0 55.1 1.0
CG A:ASP241 3.1 61.6 1.0
CG A:ASP190 3.3 61.6 1.0
CD A:GLU216 3.4 70.3 1.0
OD1 A:ASP190 3.6 62.0 1.0
CB A:ASP241 3.7 60.3 1.0
NZ A:LYS160 3.9 63.5 1.0
ND2 A:ASN263 3.9 59.4 1.0
OD1 A:ASN192 4.0 71.2 1.0
NZ A:LYS265 4.1 78.2 1.0
OD1 A:ASP241 4.1 54.3 1.0
NZ A:LYS162 4.1 64.2 1.0
CB A:GLU216 4.2 56.6 1.0
OE2 A:GLU216 4.2 64.5 1.0
OE1 A:GLU242 4.2 57.0 1.0
CG A:GLU216 4.3 69.1 1.0
CE A:LYS265 4.4 50.1 1.0
CA A:ALA2473 4.5 54.0 1.0
CE A:LYS160 4.6 60.7 1.0
CB A:ASP190 4.7 58.0 1.0
CG A:ASN263 4.9 58.2 1.0
CG A:ASN192 4.9 61.8 1.0

Magnesium binding site 2 out of 9 in 3q4d

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Magnesium binding site 2 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:53.0
occ:1.00
 OD2 B:ASP241 2.2 64.7 1.0
OD2 B:ASP190 2.5 63.2 1.0
OE1 B:GLU216 2.6 68.7 1.0
OXT B:ALA2471 2.8 65.9 1.0
CG B:ASP241 3.0 66.7 1.0
OD1 B:ASP190 3.1 67.2 1.0
O B:ALA2471 3.1 65.2 1.0
CB B:ASP241 3.2 61.7 1.0
CG B:ASP190 3.2 60.0 1.0
C B:ALA2471 3.4 65.6 1.0
OE1 B:GLU242 3.5 58.5 1.0
OD1 B:ASN192 3.6 68.4 1.0
CD B:GLU216 3.7 66.4 1.0
CB B:GLU216 3.7 56.8 1.0
OD1 B:ASP241 4.1 57.5 1.0
CG B:GLU216 4.2 66.4 1.0
CD B:GLU242 4.5 57.2 1.0
ND2 B:ASN263 4.5 55.7 1.0
CG B:ASN192 4.5 67.2 1.0
CB B:ASP190 4.6 59.0 1.0
NZ B:LYS162 4.6 62.9 1.0
CB B:GLU217 4.7 55.0 1.0
OE2 B:GLU216 4.7 71.3 1.0
CA B:ASP241 4.7 56.6 1.0
OE2 B:GLU242 4.7 49.6 1.0
NZ B:LYS160 4.7 59.7 1.0
NZ B:LYS265 4.9 84.2 1.0
CA B:GLU216 4.9 46.3 1.0
CA B:ALA2471 5.0 65.3 1.0
C B:GLU216 5.0 55.9 1.0

Magnesium binding site 3 out of 9 in 3q4d

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Magnesium binding site 3 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:59.8
occ:1.00
 OD2 C:ASP241 2.3 70.8 1.0
OD2 C:ASP190 2.3 69.6 1.0
OE1 C:GLU216 2.6 72.5 1.0
O C:ALA2475 2.7 64.7 1.0
OXT C:ALA2475 2.9 65.9 1.0
OD1 C:ASP190 2.9 78.3 1.0
CG C:ASP190 3.0 69.3 1.0
CG C:ASP241 3.1 67.5 1.0
C C:ALA2475 3.2 65.0 1.0
CB C:ASP241 3.4 64.0 1.0
OD1 C:ASN192 3.4 71.6 1.0
OE1 C:GLU242 3.6 58.3 1.0
CD C:GLU216 3.7 72.8 1.0
CB C:GLU216 3.7 59.0 1.0
CG C:GLU216 4.2 75.5 1.0
OD1 C:ASP241 4.3 61.9 1.0
NZ C:LYS162 4.3 60.4 1.0
CG C:ASN192 4.3 64.0 1.0
CB C:ASP190 4.4 58.6 1.0
CD C:GLU242 4.5 62.8 1.0
ND2 C:ASN263 4.6 55.0 1.0
NZ C:LYS160 4.6 73.5 1.0
OE2 C:GLU216 4.6 74.1 1.0
CA C:ALA2475 4.7 64.6 1.0
OE2 C:GLU242 4.7 46.6 1.0
CB C:GLU217 4.8 58.2 1.0
ND2 C:ASN192 4.9 54.2 1.0
CA C:ASP241 4.9 61.4 1.0
NZ C:LYS265 4.9 84.1 1.0
CA C:GLU216 5.0 54.3 1.0

Magnesium binding site 4 out of 9 in 3q4d

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Magnesium binding site 4 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:87.5
occ:1.00
 OD2 D:ASP241 2.4 72.8 1.0
OXT D:ALA2477 2.6 81.1 1.0
OD2 D:ASP190 2.9 76.0 1.0
OD1 D:ASN192 2.9 74.0 1.0
CG D:ASP241 3.1 71.3 1.0
OE1 D:GLU242 3.1 66.9 1.0
OD1 D:ASP190 3.3 79.2 1.0
OE1 D:GLU216 3.4 76.4 1.0
CB D:ASP241 3.4 66.0 1.0
CG D:ASP190 3.5 72.4 1.0
C D:ALA2477 3.5 81.0 1.0
O D:ALA2477 3.6 81.6 1.0
CD D:GLU242 3.9 70.2 1.0
CG D:ASN192 3.9 75.5 1.0
OD1 D:ASP241 4.0 62.5 1.0
OE2 D:GLU242 4.1 61.7 1.0
NZ D:LYS162 4.3 62.9 1.0
CD D:GLU216 4.5 79.1 1.0
CB D:GLU216 4.5 66.2 1.0
ND2 D:ASN192 4.6 68.4 1.0
CA D:ALA2477 4.8 80.7 1.0
NZ D:LYS265 4.9 83.0 1.0
CE D:LYS265 4.9 66.2 1.0
CB D:GLU217 4.9 58.4 1.0
CA D:ASN192 4.9 65.3 1.0
CA D:ASP241 5.0 59.0 1.0
CB D:ASP190 5.0 68.0 1.0
CB D:ASN192 5.0 68.4 1.0

Magnesium binding site 5 out of 9 in 3q4d

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Magnesium binding site 5 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1605

b:76.5
occ:1.00
 OD2 E:ASP241 2.4 76.2 1.0
OD2 E:ASP190 2.5 74.7 1.0
OXT E:ALA2479 2.6 68.2 1.0
OE1 E:GLU216 2.9 70.5 1.0
OD1 E:ASP190 3.0 74.5 1.0
CG E:ASP190 3.1 68.3 1.0
O E:ALA2479 3.1 67.4 1.0
CG E:ASP241 3.2 66.7 1.0
OD1 E:ASN192 3.2 80.7 1.0
C E:ALA2479 3.3 67.8 1.0
OE1 E:GLU242 3.3 65.7 1.0
CB E:ASP241 3.4 64.5 1.0
CB E:GLU216 4.0 59.8 1.0
CD E:GLU216 4.0 72.5 1.0
CG E:ASN192 4.1 71.6 1.0
CD E:GLU242 4.2 73.7 1.0
OD1 E:ASP241 4.2 61.4 1.0
NZ E:LYS162 4.3 63.1 1.0
OE2 E:GLU242 4.4 62.0 1.0
CG E:GLU216 4.5 72.6 1.0
CB E:ASP190 4.6 65.2 1.0
CB E:GLU217 4.6 60.5 1.0
ND2 E:ASN192 4.7 64.4 1.0
CA E:ALA2479 4.7 67.9 1.0
ND2 E:ASN263 4.9 70.3 1.0
CA E:ASP241 4.9 62.0 1.0
NZ E:LYS160 4.9 71.4 1.0
CA E:ASN192 4.9 66.8 1.0
OE2 E:GLU216 5.0 75.5 1.0

Magnesium binding site 6 out of 9 in 3q4d

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Magnesium binding site 6 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1606

b:96.2
occ:1.00
 OD2 F:ASP241 2.3 68.0 1.0
OD2 F:ASP190 2.4 69.9 1.0
OE1 F:GLU216 2.7 74.9 1.0
OD1 F:ASP190 3.0 72.9 1.0
CG F:ASP241 3.0 73.4 1.0
CG F:ASP190 3.1 65.0 1.0
O F:ALA2481 3.2 72.3 1.0
CB F:ASP241 3.3 61.9 1.0
OXT F:ALA2481 3.3 71.9 1.0
OD1 F:ASN192 3.4 73.7 1.0
OE1 F:GLU242 3.4 59.7 1.0
C F:ALA2481 3.6 71.8 1.0
CD F:GLU216 3.8 74.4 1.0
CB F:GLU216 3.8 60.3 1.0
OD1 F:ASP241 4.2 66.8 1.0
CG F:ASN192 4.3 72.0 1.0
CG F:GLU216 4.3 75.3 1.0
CD F:GLU242 4.4 69.7 1.0
NZ F:LYS162 4.4 64.1 1.0
OE2 F:GLU242 4.5 62.6 1.0
CB F:ASP190 4.5 63.7 1.0
CB F:GLU217 4.7 56.2 1.0
ND2 F:ASN263 4.7 66.2 1.0
NZ F:LYS160 4.7 66.1 1.0
OE2 F:GLU216 4.8 73.7 1.0
CA F:ASP241 4.8 56.1 1.0
ND2 F:ASN192 4.9 61.8 1.0
NZ F:LYS265 5.0 80.2 1.0

Magnesium binding site 7 out of 9 in 3q4d

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Magnesium binding site 7 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1607

b:58.5
occ:1.00
 OD2 G:ASP241 2.3 76.1 1.0
OD2 G:ASP190 2.4 71.4 1.0
OE1 G:GLU216 2.7 66.0 1.0
OXT G:ALA2483 2.8 67.7 1.0
O G:ALA2483 2.9 66.6 1.0
OD1 G:ASP190 3.1 72.1 1.0
CG G:ASP241 3.1 72.3 1.0
CG G:ASP190 3.1 65.5 1.0
C G:ALA2483 3.3 66.7 1.0
CB G:ASP241 3.4 65.7 1.0
OD1 G:ASN192 3.4 69.1 1.0
OE1 G:GLU242 3.5 54.6 1.0
CD G:GLU216 3.8 70.9 1.0
CB G:GLU216 3.9 60.0 1.0
OD1 G:ASP241 4.2 58.4 1.0
NZ G:LYS162 4.3 59.8 1.0
CG G:ASN192 4.3 70.3 1.0
CG G:GLU216 4.4 69.0 1.0
CD G:GLU242 4.5 66.5 1.0
CB G:ASP190 4.5 57.9 1.0
ND2 G:ASN263 4.6 59.8 1.0
NZ G:LYS160 4.6 62.2 1.0
OE2 G:GLU242 4.7 61.5 1.0
OE2 G:GLU216 4.7 70.8 1.0
CA G:ALA2483 4.8 65.9 1.0
ND2 G:ASN192 4.8 65.5 1.0
NZ G:LYS265 4.9 79.2 1.0
CB G:GLU217 4.9 58.2 1.0
CA G:ASP241 4.9 58.2 1.0
CE G:LYS265 5.0 66.4 1.0

Magnesium binding site 8 out of 9 in 3q4d

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Magnesium binding site 8 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


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 Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1608

b:88.7
occ:1.00
 OD2 H:ASP241 2.5 78.1 1.0
OD2 H:ASP190 2.8 78.1 1.0
OE1 H:GLU242 3.0 64.4 1.0
CG H:ASP241 3.0 73.5 1.0
OD1 H:ASP190 3.0 73.7 1.0
CB H:ASP241 3.0 67.5 1.0
OE1 H:GLU216 3.1 75.0 1.0
OXT H:ALA2485 3.1 88.5 1.0
CG H:ASP190 3.2 71.0 1.0
OD1 H:ASN192 3.3 77.6 1.0
O H:ALA2485 3.7 88.3 1.0
CB H:GLU216 3.8 65.0 1.0
C H:ALA2485 3.9 88.3 1.0
CD H:GLU242 4.0 70.4 1.0
OD1 H:ASP241 4.1 68.7 1.0
CD H:GLU216 4.1 79.5 1.0
CG H:ASN192 4.2 79.2 1.0
CB H:GLU217 4.2 59.4 1.0
OE2 H:GLU242 4.2 59.7 1.0
CG H:GLU216 4.5 74.4 1.0
CA H:ASP241 4.6 61.2 1.0
CB H:ASP190 4.7 64.0 1.0
CA H:ASN192 4.8 61.2 1.0
NZ H:LYS162 4.8 68.2 1.0
C H:GLU216 4.8 65.8 1.0
ND2 H:ASN192 4.9 70.6 1.0
N H:ASN192 4.9 58.2 1.0
N H:GLU242 4.9 51.1 1.0
CA H:GLU216 4.9 57.4 1.0
ND2 H:ASN263 4.9 67.9 1.0
N H:GLU217 5.0 62.0 1.0

Magnesium binding site 9 out of 9 in 3q4d

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Magnesium binding site 9 out of 9 in the Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1609

b:78.9
occ:1.00
 OD2 I:ASP241 2.1 84.1 1.0
OD2 I:ASP190 2.1 85.0 1.0
OE1 I:GLU216 2.2 70.8 1.0
O I:ALA2487 2.4 0.7 1.0
OXT I:ALA2487 2.6 0.6 1.0
C I:ALA2487 2.9 0.5 1.0
CG I:ASP190 3.1 76.3 1.0
CG I:ASP241 3.1 76.3 1.0
OD1 I:ASP190 3.3 78.3 1.0
CD I:GLU216 3.4 78.5 1.0
CB I:ASP241 3.6 65.9 1.0
OD1 I:ASN192 3.8 74.6 1.0
CB I:GLU216 3.9 68.4 1.0
NZ I:LYS160 4.0 69.4 1.0
ND2 I:ASN263 4.1 71.0 1.0
OE1 I:GLU242 4.1 68.8 1.0
NZ I:LYS162 4.1 64.9 1.0
OD1 I:ASP241 4.2 71.8 1.0
CG I:GLU216 4.2 81.1 1.0
OE2 I:GLU216 4.3 67.5 1.0
NZ I:LYS265 4.4 85.7 1.0
CA I:ALA2487 4.4 0.1 1.0
CB I:ASP190 4.4 65.4 1.0
CE I:LYS265 4.7 65.7 1.0
CE I:LYS160 4.7 64.7 1.0
CG I:ASN192 4.7 73.7 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: Thu Aug 15 09:54:25 2024

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