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Magnesium in PDB 1ec7: E. Coli Glucarate Dehydratase Native Enzyme

Enzymatic activity of E. Coli Glucarate Dehydratase Native Enzyme

All present enzymatic activity of E. Coli Glucarate Dehydratase Native Enzyme:
4.2.1.40;

Protein crystallography data

The structure of E. Coli Glucarate Dehydratase Native Enzyme, PDB code: 1ec7 was solved by A.M.Gulick, B.K.Hubbard, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.250, 84.550, 98.920, 103.30, 94.00, 113.10
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Glucarate Dehydratase Native Enzyme (pdb code 1ec7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Glucarate Dehydratase Native Enzyme, PDB code: 1ec7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ec7

Go back to Magnesium Binding Sites List in 1ec7
Magnesium binding site 1 out of 4 in the E. Coli Glucarate Dehydratase Native Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Glucarate Dehydratase Native Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg498

b:17.6
occ:1.00
O A:HOH1489 1.9 16.0 1.0
O A:HOH1466 1.9 14.6 1.0
OD1 A:ASN289 1.9 26.3 1.0
OE2 A:GLU260 2.0 22.8 1.0
O A:HOH1488 2.1 30.2 1.0
OD1 A:ASP235 2.1 20.7 1.0
CG A:ASP235 3.0 16.9 1.0
CG A:ASN289 3.0 13.7 1.0
CD A:GLU260 3.1 16.3 1.0
OD2 A:ASP235 3.4 14.1 1.0
O A:HOH1346 3.6 22.6 1.0
CG A:GLU260 3.7 19.5 1.0
ND2 A:ASN289 3.8 19.1 1.0
NZ A:LYS207 3.9 27.2 1.0
OD1 A:ASN237 3.9 72.7 1.0
OE1 A:GLU260 3.9 20.8 1.0
CD2 A:HIS339 3.9 0.0 1.0
OD2 A:ASP261 4.1 13.1 1.0
CB A:ASN289 4.1 8.4 1.0
NE2 A:HIS339 4.3 26.5 1.0
CB A:ASP235 4.3 16.9 1.0
O A:HOH1491 4.5 46.4 1.0
CG A:ASN237 4.6 39.9 1.0
OH A:TYR150 4.7 31.9 1.0
N A:ASN289 4.9 22.4 1.0
ND2 A:ASN237 4.9 22.6 1.0
CA A:ASN289 4.9 22.1 1.0
O A:HOH1082 5.0 33.7 1.0
CB A:GLU260 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in 1ec7

Go back to Magnesium Binding Sites List in 1ec7
Magnesium binding site 2 out of 4 in the E. Coli Glucarate Dehydratase Native Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Glucarate Dehydratase Native Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg498

b:25.7
occ:1.00
O B:HOH1365 2.0 18.6 1.0
O B:HOH1380 2.0 26.9 1.0
OD1 B:ASN289 2.0 15.5 1.0
OE2 B:GLU260 2.1 13.1 1.0
OD1 B:ASP235 2.2 18.7 1.0
O B:HOH1762 2.4 32.6 1.0
CG B:ASN289 3.0 13.6 1.0
CG B:ASP235 3.1 18.4 1.0
CD B:GLU260 3.2 14.1 1.0
ND2 B:ASN289 3.4 13.4 1.0
OD2 B:ASP235 3.6 16.8 1.0
CG B:GLU260 3.8 11.5 1.0
OD1 B:ASN237 3.8 39.2 1.0
NZ B:LYS205 3.9 25.1 1.0
OD2 B:ASP261 3.9 15.6 1.0
OE1 B:GLU260 4.2 23.9 1.0
O B:HOH1535 4.3 41.1 1.0
ND1 B:HIS339 4.3 34.5 1.0
NZ B:LYS207 4.3 38.4 1.0
CB B:ASN289 4.3 14.5 1.0
CB B:ASP235 4.4 21.4 1.0
CG B:ASN237 4.7 31.9 1.0
CE B:LYS205 4.8 33.3 1.0
OH B:TYR150 4.8 33.4 1.0
CD1 B:LEU311 4.8 40.0 1.0
N B:ASN289 4.9 15.7 1.0
CE1 B:HIS339 5.0 21.4 1.0

Magnesium binding site 3 out of 4 in 1ec7

Go back to Magnesium Binding Sites List in 1ec7
Magnesium binding site 3 out of 4 in the E. Coli Glucarate Dehydratase Native Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Glucarate Dehydratase Native Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg498

b:24.8
occ:1.00
OE2 C:GLU260 1.7 19.8 1.0
O C:HOH1572 1.9 18.9 1.0
OD1 C:ASN289 1.9 37.6 1.0
O C:HOH1404 2.0 16.8 1.0
OD1 C:ASP235 2.2 17.5 1.0
O C:HOH1846 2.4 44.4 1.0
CG C:ASN289 2.9 13.8 1.0
CD C:GLU260 2.9 12.6 1.0
CG C:ASP235 3.1 12.8 1.0
ND2 C:ASN289 3.4 20.4 1.0
O C:HOH1403 3.4 35.4 1.0
OD2 C:ASP235 3.5 15.3 1.0
CG C:GLU260 3.7 8.6 1.0
OE1 C:GLU260 3.8 17.5 1.0
NZ C:LYS207 3.9 22.8 1.0
OD2 C:ASP261 4.1 13.1 1.0
CB C:ASN289 4.2 6.6 1.0
ND2 C:ASN237 4.2 53.8 1.0
CB C:ASP235 4.4 9.7 1.0
OH C:TYR150 4.7 32.0 1.0
N C:ASN289 4.8 11.5 1.0
CB C:GLU260 4.9 13.9 1.0
CA C:ASN289 4.9 6.3 1.0
CE C:LYS207 4.9 25.7 1.0

Magnesium binding site 4 out of 4 in 1ec7

Go back to Magnesium Binding Sites List in 1ec7
Magnesium binding site 4 out of 4 in the E. Coli Glucarate Dehydratase Native Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Glucarate Dehydratase Native Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg498

b:23.5
occ:1.00
O D:HOH1448 1.9 18.5 1.0
O D:HOH1447 1.9 15.9 1.0
OD1 D:ASN289 2.0 26.1 1.0
OE2 D:GLU260 2.1 19.2 1.0
O D:HOH1869 2.1 41.2 1.0
OD1 D:ASP235 2.1 15.9 1.0
CG D:ASP235 3.0 14.4 1.0
CG D:ASN289 3.1 18.4 1.0
CD D:GLU260 3.2 13.7 1.0
OD2 D:ASP235 3.4 14.8 1.0
CG D:GLU260 3.7 12.0 1.0
OD1 D:ASN237 3.8 40.5 1.0
ND2 D:ASN289 3.8 16.6 1.0
OD2 D:ASP261 4.1 14.8 1.0
OE1 D:GLU260 4.2 18.2 1.0
CB D:ASN289 4.2 17.1 1.0
NZ D:LYS207 4.3 37.6 1.0
CB D:ASP235 4.3 8.8 1.0
NZ D:LYS205 4.3 63.4 1.0
CG D:ASN237 4.7 27.9 1.0
OH D:TYR150 4.7 27.6 1.0
CE D:LYS205 4.8 0.0 1.0
O D:HOH2081 4.9 51.0 1.0
N D:ASN289 4.9 17.6 1.0
CB D:GLU260 4.9 14.3 1.0
O D:HOH2073 4.9 35.9 1.0

Reference:

A.M.Gulick, B.K.Hubbard, J.A.Gerlt, I.Rayment. Evolution of Enzymatic Activities in the Enolase Superfamily: Crystallographic and Mutagenesis Studies of the Reaction Catalyzed By D-Glucarate Dehydratase From Escherichia Coli. Biochemistry V. 39 4590 2000.
ISSN: ISSN 0006-2960
PubMed: 10769114
DOI: 10.1021/BI992782I
Page generated: Mon Dec 14 05:51:47 2020

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