Atomistry » Magnesium » PDB 3py8-3q86 » 3q45
Atomistry »
  Magnesium »
    PDB 3py8-3q86 »
      3q45 »

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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Go back to Magnesium Binding Sites List in 3q45
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy