Atomistry » Magnesium » PDB 3py8-3q86 » 3q4d
Atomistry »
  Magnesium »
    PDB 3py8-3q86 »
      3q4d »

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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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

Go back to Magnesium Binding Sites List in 3q4d
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: Mon Aug 11 02:18:15 2025

Last articles

Mg in 4DV5
Mg in 4DV4
Mg in 4DV3
Mg in 4DV2
Mg in 4DV0
Mg in 4DV1
Mg in 4DUZ
Mg in 4DUY
Mg in 4DR7
Mg in 4DR6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy