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Magnesium in PDB 3q45: Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Val

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

All present enzymatic activity of Crystal Structure of Dipeptide Epimerase From Cytophaga Hutchinsonii Complexed with Mg and Dipeptide D-Ala-L-Val:
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-Val, PDB code: 3q45 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 (°) 94.000, 158.200, 182.740, 90.00, 100.28, 90.00
R / Rfree (%) 22.7 / 25.1

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-Val (pdb code 3q45). 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-Val, PDB code: 3q45:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:61.7
occ:1.00
 OD2 A:ASP241 2.2 68.7 1.0
OE1 A:GLU216 2.6 73.0 1.0
OD2 A:ASP190 2.6 76.4 1.0
OXT A:VAL2471 2.8 67.1 1.0
CG A:ASP241 3.0 71.1 1.0
O A:VAL2471 3.1 67.1 1.0
OD1 A:ASP190 3.2 76.4 1.0
CG A:ASP190 3.3 68.2 1.0
CB A:ASP241 3.3 63.4 1.0
C A:VAL2471 3.3 67.0 1.0
OE1 A:GLU242 3.6 64.0 1.0
OD1 A:ASN192 3.6 71.6 1.0
CD A:GLU216 3.7 67.9 1.0
CB A:GLU216 3.9 64.5 1.0
OD1 A:ASP241 4.1 67.7 1.0
ND2 A:ASN263 4.2 61.0 1.0
CG A:GLU216 4.3 68.7 1.0
NZ A:LYS265 4.4 77.0 1.0
NZ A:LYS160 4.5 55.7 1.0
NZ A:LYS162 4.6 66.8 1.0
CD A:GLU242 4.6 62.0 1.0
OE2 A:GLU216 4.6 75.2 1.0
CG A:ASN192 4.7 73.9 1.0
CB A:ASP190 4.7 67.5 1.0
CA A:VAL2471 4.8 66.0 1.0
CE A:LYS265 4.8 63.2 1.0
OE2 A:GLU242 4.8 61.5 1.0
CA A:ASP241 4.8 58.7 1.0

Magnesium binding site 2 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:56.4
occ:1.00
 OD2 B:ASP241 2.3 69.3 1.0
OE1 B:GLU216 2.3 69.1 1.0
OD2 B:ASP190 2.4 71.8 1.0
O B:VAL2473 2.7 47.8 1.0
OXT B:VAL2473 2.8 48.5 1.0
C B:VAL2473 3.1 48.0 1.0
CG B:ASP241 3.3 67.2 1.0
CG B:ASP190 3.3 61.9 1.0
CD B:GLU216 3.5 69.7 1.0
OD1 B:ASP190 3.5 60.3 1.0
CB B:ASP241 3.8 63.0 1.0
ND2 B:ASN263 3.8 59.4 1.0
NZ B:LYS160 3.9 60.3 1.0
OD1 B:ASN192 3.9 74.7 1.0
NZ B:LYS265 3.9 76.2 1.0
CB B:GLU216 4.1 61.8 1.0
NZ B:LYS162 4.2 67.6 1.0
OE1 B:GLU242 4.2 65.1 1.0
OD1 B:ASP241 4.3 71.4 1.0
OE2 B:GLU216 4.3 65.2 1.0
CG B:GLU216 4.3 68.9 1.0
CE B:LYS265 4.5 59.5 1.0
CB B:ASP190 4.6 63.0 1.0
CA B:VAL2473 4.6 47.5 1.0
CE B:LYS160 4.7 65.3 1.0
CG B:ASN192 4.9 69.2 1.0
CG B:ASN263 4.9 61.9 1.0

Magnesium binding site 3 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:60.3
occ:1.00
 OD2 C:ASP241 2.4 67.9 1.0
OD2 C:ASP190 2.8 79.3 1.0
OE1 C:GLU216 2.8 76.2 1.0
O C:VAL2475 2.9 71.1 1.0
OXT C:VAL2475 2.9 71.6 1.0
CG C:ASP241 3.0 66.5 1.0
OD1 C:ASP190 3.1 79.1 1.0
CB C:ASP241 3.1 69.0 1.0
CG C:ASP190 3.3 75.7 1.0
OE1 C:GLU242 3.3 60.0 1.0
C C:VAL2475 3.3 71.2 1.0
OD1 C:ASN192 3.5 70.0 1.0
CB C:GLU216 3.7 63.1 1.0
CD C:GLU216 3.8 70.5 1.0
OD1 C:ASP241 4.1 65.6 1.0
CD C:GLU242 4.2 63.2 1.0
CG C:GLU216 4.3 76.7 1.0
ND2 C:ASN263 4.5 62.2 1.0
OE2 C:GLU242 4.5 55.8 1.0
CB C:GLU217 4.5 66.1 1.0
CG C:ASN192 4.5 68.2 1.0
CA C:ASP241 4.6 67.1 1.0
CB C:ASP190 4.7 69.1 1.0
NZ C:LYS162 4.7 64.9 1.0
NZ C:LYS265 4.8 72.7 1.0
CA C:VAL2475 4.8 70.9 1.0
OE2 C:GLU216 4.9 68.0 1.0
NZ C:LYS160 4.9 67.2 1.0
C C:GLU216 4.9 60.1 1.0
CA C:GLU216 4.9 57.4 1.0

Magnesium binding site 4 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:96.2
occ:1.00
 OD2 D:ASP241 2.0 74.9 1.0
OXT D:VAL2477 2.4 91.5 1.0
OE1 D:GLU216 2.7 83.0 1.0
OD2 D:ASP190 2.7 83.4 1.0
CG D:ASP241 2.9 75.8 1.0
CB D:ASP241 3.2 67.3 1.0
C D:VAL2477 3.3 91.7 1.0
O D:VAL2477 3.3 92.0 1.0
OD1 D:ASP190 3.4 81.2 1.0
CG D:ASP190 3.4 78.5 1.0
OE1 D:GLU242 3.5 71.9 1.0
OD1 D:ASN192 3.6 77.1 1.0
CD D:GLU216 3.8 80.6 1.0
OD1 D:ASP241 3.9 71.7 1.0
CB D:GLU216 4.0 71.7 1.0
ND2 D:ASN263 4.2 70.3 1.0
NZ D:LYS265 4.3 81.1 1.0
CD D:GLU242 4.4 71.4 1.0
CG D:GLU216 4.4 78.2 1.0
NZ D:LYS162 4.6 71.1 1.0
NZ D:LYS160 4.6 72.7 1.0
CE D:LYS265 4.6 73.3 1.0
CG D:ASN192 4.7 79.3 1.0
OE2 D:GLU242 4.7 70.4 1.0
CA D:VAL2477 4.7 91.7 1.0
CA D:ASP241 4.7 62.2 1.0
OE2 D:GLU216 4.8 75.1 1.0
CB D:ASP190 4.9 77.7 1.0

Magnesium binding site 5 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1605

b:89.2
occ:1.00
 OD2 E:ASP241 2.3 79.6 1.0
OXT E:VAL2479 2.4 73.9 1.0
OD2 E:ASP190 2.6 80.8 1.0
OE1 E:GLU216 2.9 72.4 1.0
O E:VAL2479 3.1 74.0 1.0
C E:VAL2479 3.1 73.7 1.0
CG E:ASP241 3.1 73.0 1.0
OD1 E:ASP190 3.3 73.9 1.0
CG E:ASP190 3.3 74.6 1.0
OD1 E:ASN192 3.3 81.5 1.0
CB E:ASP241 3.4 68.3 1.0
OE1 E:GLU242 3.5 70.0 1.0
CD E:GLU216 4.0 71.4 1.0
OD1 E:ASP241 4.1 76.2 1.0
CB E:GLU216 4.2 68.9 1.0
NZ E:LYS265 4.3 83.2 1.0
CD E:GLU242 4.3 69.1 1.0
NZ E:LYS162 4.3 66.4 1.0
CG E:ASN192 4.4 78.3 1.0
ND2 E:ASN263 4.5 67.6 1.0
CA E:VAL2479 4.5 73.5 1.0
OE2 E:GLU242 4.5 61.4 1.0
CG E:GLU216 4.6 71.2 1.0
NZ E:LYS160 4.7 71.9 1.0
CG1 E:VAL2479 4.7 72.7 1.0
CB E:ASP190 4.7 74.6 1.0
CE E:LYS265 4.8 66.4 1.0
OE2 E:GLU216 4.9 72.0 1.0
CA E:ASP241 5.0 65.1 1.0

Magnesium binding site 6 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1606

b:67.3
occ:1.00
 OE1 F:GLU216 2.2 82.7 1.0
OD2 F:ASP241 2.3 69.4 1.0
OD2 F:ASP190 2.4 76.8 1.0
OXT F:VAL2481 3.0 84.8 1.0
CG F:ASP190 3.1 73.3 1.0
CG F:ASP241 3.1 70.5 1.0
OD1 F:ASP190 3.1 74.0 1.0
O F:VAL2481 3.2 85.2 1.0
CD F:GLU216 3.2 78.0 1.0
CB F:ASP241 3.3 64.6 1.0
C F:VAL2481 3.5 84.6 1.0
CB F:GLU216 3.5 62.8 1.0
CG F:GLU216 3.9 75.0 1.0
OD1 F:ASN192 3.9 71.7 1.0
ND2 F:ASN263 3.9 65.9 1.0
OE1 F:GLU242 3.9 70.2 1.0
NZ F:LYS160 4.2 66.2 1.0
OE2 F:GLU216 4.2 77.8 1.0
OD1 F:ASP241 4.3 71.7 1.0
CB F:ASP190 4.5 71.7 1.0
NZ F:LYS162 4.5 69.1 1.0
NZ F:LYS265 4.6 67.9 1.0
CA F:ASP241 4.9 65.2 1.0
CA F:GLU216 4.9 65.2 1.0
CG F:ASN192 4.9 73.9 1.0
CD F:GLU242 4.9 67.9 1.0
CE F:LYS160 4.9 65.0 1.0
CE F:LYS265 5.0 72.5 1.0
CG F:ASN263 5.0 66.2 1.0

Magnesium binding site 7 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1607

b:46.4
occ:1.00
 OE1 G:GLU216 2.2 79.5 1.0
OD2 G:ASP241 2.3 71.0 1.0
OD2 G:ASP190 2.4 76.9 1.0
O G:HOH379 2.7 53.9 1.0
O G:VAL2483 2.8 61.6 1.0
OXT G:VAL2483 3.0 62.5 1.0
CG G:ASP190 3.2 70.5 1.0
CG G:ASP241 3.2 71.6 1.0
CD G:GLU216 3.3 69.9 1.0
OD1 G:ASP190 3.3 70.6 1.0
C G:VAL2483 3.4 62.2 1.0
CB G:ASP241 3.5 69.6 1.0
CB G:GLU216 3.7 63.5 1.0
ND2 G:ASN263 3.8 61.5 1.0
OD1 G:ASN192 4.0 70.3 1.0
CG G:GLU216 4.0 74.4 1.0
OE1 G:GLU242 4.1 67.2 1.0
NZ G:LYS160 4.1 62.8 1.0
OE2 G:GLU216 4.2 64.6 1.0
OD1 G:ASP241 4.3 71.9 1.0
NZ G:LYS265 4.3 74.8 1.0
NZ G:LYS162 4.4 72.7 1.0
CB G:ASP190 4.5 69.8 1.0
CE G:LYS265 4.8 71.4 1.0
CE G:LYS160 4.8 66.1 1.0
CG G:ASN263 4.9 69.6 1.0
CG G:ASN192 4.9 73.8 1.0
CA G:VAL2483 4.9 61.6 1.0
CA G:ASP241 5.0 60.4 1.0

Magnesium binding site 8 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1608

b:83.2
occ:1.00
 OD2 H:ASP190 2.4 85.2 1.0
OD2 H:ASP241 2.5 78.8 1.0
O H:VAL2485 2.6 83.2 1.0
OE1 H:GLU216 2.8 76.4 1.0
OXT H:VAL2485 2.9 83.9 1.0
CG H:ASP190 3.1 79.2 1.0
OD1 H:ASP190 3.2 80.5 1.0
C H:VAL2485 3.2 83.6 1.0
OD1 H:ASN192 3.2 77.1 1.0
CG H:ASP241 3.3 71.8 1.0
OE1 H:GLU242 3.6 68.8 1.0
CB H:ASP241 3.6 71.8 1.0
CD H:GLU216 3.9 78.4 1.0
CB H:GLU216 4.1 72.1 1.0
NZ H:LYS162 4.2 75.4 1.0
CG H:ASN192 4.3 80.9 1.0
OD1 H:ASP241 4.3 75.4 1.0
NZ H:LYS265 4.4 74.4 1.0
ND2 H:ASN263 4.4 68.1 1.0
NZ H:LYS160 4.5 74.6 1.0
CD H:GLU242 4.5 70.4 1.0
CB H:ASP190 4.6 71.0 1.0
CG H:GLU216 4.6 76.7 1.0
CA H:VAL2485 4.6 83.7 1.0
OE2 H:GLU242 4.7 65.1 1.0
ND2 H:ASN192 4.8 70.8 1.0
OE2 H:GLU216 4.9 69.6 1.0
CE H:LYS265 4.9 67.2 1.0

Magnesium binding site 9 out of 9 in 3q45

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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-Val


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-Val within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1609

b:90.1
occ:1.00
 OD2 I:ASP190 2.4 89.0 1.0
OD2 I:ASP241 2.4 83.4 1.0
OE1 I:GLU216 2.4 80.0 1.0
OXT I:VAL2487 2.7 0.7 1.0
O I:VAL2487 2.9 0.5 1.0
CG I:ASP190 3.1 79.0 1.0
OD1 I:ASP190 3.1 80.4 1.0
CG I:ASP241 3.2 78.7 1.0
C I:VAL2487 3.2 0.8 1.0
CB I:ASP241 3.5 69.3 1.0
CD I:GLU216 3.5 79.8 1.0
OD1 I:ASN192 3.6 74.6 1.0
CB I:GLU216 3.8 69.9 1.0
OE1 I:GLU242 3.8 71.4 1.0
ND2 I:ASN263 4.1 69.5 1.0
CG I:GLU216 4.2 81.3 1.0
OD1 I:ASP241 4.3 84.3 1.0
NZ I:LYS162 4.4 70.6 1.0
NZ I:LYS160 4.4 69.9 1.0
NZ I:LYS265 4.4 85.5 1.0
CB I:ASP190 4.5 75.3 1.0
OE2 I:GLU216 4.5 68.5 1.0
CG I:ASN192 4.6 79.7 1.0
CA I:VAL2487 4.7 0.7 1.0
CD I:GLU242 4.8 76.0 1.0
CE I:LYS265 4.9 70.5 1.0
OE2 I:GLU242 5.0 74.6 1.0
CA I:ASP241 5.0 67.2 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 09:54:03 2024

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