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Magnesium in PDB 1ecq: E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate

Enzymatic activity of E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate

All present enzymatic activity of E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate:
4.2.1.40;

Protein crystallography data

The structure of E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate, PDB code: 1ecq 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 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.108, 84.602, 98.779, 103.46, 93.97, 113.03
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate (pdb code 1ecq). 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 Bound to 4-Deoxyglucarate, PDB code: 1ecq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ecq

Go back to Magnesium Binding Sites List in 1ecq
Magnesium binding site 1 out of 4 in the E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate


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 Bound to 4-Deoxyglucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg498

b:28.9
occ:1.00
O A:HOH1323 1.9 20.2 1.0
O6B A:DXG499 1.9 26.0 1.0
OD1 A:ASN289 2.0 38.3 1.0
OE2 A:GLU260 2.2 38.6 1.0
OD1 A:ASP235 2.2 25.8 1.0
O6A A:DXG499 2.2 38.1 1.0
C6 A:DXG499 2.4 81.1 1.0
CG A:ASN289 3.1 28.5 1.0
CD A:GLU260 3.1 33.9 1.0
CG A:ASP235 3.2 18.6 1.0
OD2 A:ASP235 3.7 18.4 1.0
CG A:GLU260 3.7 25.5 1.0
NZ A:LYS207 3.7 33.0 1.0
ND2 A:ASN289 3.8 34.3 1.0
C5 A:DXG499 3.8 62.7 1.0
NZ A:LYS205 3.9 17.6 0.5
CD2 A:HIS339 4.0 0.0 1.0
OE1 A:GLU260 4.0 31.2 1.0
CB A:ASN289 4.1 11.8 1.0
ND2 A:ASN237 4.1 49.5 1.0
OD2 A:ASP261 4.2 21.4 1.0
CB A:ASP235 4.4 24.2 1.0
OH A:TYR150 4.5 89.1 1.0
NE2 A:HIS339 4.6 25.8 1.0
CE A:LYS205 4.6 34.5 0.5
O5 A:DXG499 4.6 36.6 1.0
C4 A:DXG499 4.8 57.1 1.0
N A:ASN289 4.9 43.2 1.0
CG A:ASN237 4.9 49.5 1.0
CA A:ASN289 4.9 15.5 1.0
CD1 A:LEU311 5.0 15.9 1.0

Magnesium binding site 2 out of 4 in 1ecq

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Magnesium binding site 2 out of 4 in the E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate


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 Bound to 4-Deoxyglucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg498

b:38.2
occ:1.00
OD1 B:ASN289 1.9 32.4 1.0
O6B B:DXG500 1.9 36.8 1.0
O B:HOH1456 2.1 32.3 1.0
OE2 B:GLU260 2.1 20.4 1.0
O6A B:DXG500 2.2 48.1 1.0
OD1 B:ASP235 2.2 26.6 1.0
C6 B:DXG500 2.3 54.4 1.0
CG B:ASN289 2.9 22.1 1.0
CG B:ASP235 3.2 43.3 1.0
CD B:GLU260 3.3 26.9 1.0
ND2 B:ASN289 3.4 22.9 1.0
OD2 B:ASP235 3.7 21.4 1.0
NZ B:LYS205 3.7 43.9 1.0
CG B:GLU260 3.8 11.1 1.0
C5 B:DXG500 3.8 67.5 1.0
NZ B:LYS207 3.9 40.3 1.0
ND2 B:ASN237 4.1 34.6 1.0
CB B:ASN289 4.2 24.9 1.0
OE1 B:GLU260 4.2 35.4 1.0
CD2 B:HIS339 4.3 27.0 1.0
OD2 B:ASP261 4.4 19.1 1.0
CB B:ASP235 4.5 32.5 1.0
O5 B:DXG500 4.5 46.6 1.0
CE B:LYS205 4.6 50.6 1.0
C4 B:DXG500 4.7 68.3 1.0
OH B:TYR150 4.9 45.0 1.0
N B:ASN289 4.9 16.5 1.0
CG B:ASN237 4.9 41.4 1.0

Magnesium binding site 3 out of 4 in 1ecq

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Magnesium binding site 3 out of 4 in the E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate


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 Bound to 4-Deoxyglucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg498

b:30.0
occ:1.00
O6B C:DXG501 1.9 25.2 1.0
OE2 C:GLU260 1.9 26.8 1.0
OD1 C:ASN289 2.0 36.8 1.0
O C:HOH1324 2.1 26.0 1.0
O6A C:DXG501 2.2 31.8 1.0
OD1 C:ASP235 2.2 20.3 1.0
C6 C:DXG501 2.3 63.7 1.0
CG C:ASN289 3.0 31.8 1.0
CD C:GLU260 3.1 23.1 1.0
CG C:ASP235 3.1 23.3 1.0
ND2 C:ASN289 3.5 21.8 1.0
OD2 C:ASP235 3.6 21.8 1.0
NZ C:LYS205 3.6 37.8 1.0
ND2 C:ASN237 3.7 42.1 1.0
CG C:GLU260 3.8 20.7 1.0
C5 C:DXG501 3.8 52.9 1.0
NZ C:LYS207 3.9 43.6 1.0
OE1 C:GLU260 3.9 36.7 1.0
OD2 C:ASP261 4.1 20.1 1.0
CB C:ASN289 4.3 16.2 1.0
CB C:ASP235 4.3 13.7 1.0
CD2 C:HIS339 4.4 0.0 1.0
O5 C:DXG501 4.6 46.3 1.0
CG C:ASN237 4.6 33.6 1.0
CE C:LYS205 4.7 51.2 1.0
OH C:TYR150 4.7 39.3 1.0
C4 C:DXG501 4.7 0.0 1.0
OD1 C:ASN237 4.8 22.4 1.0
N C:ASN289 4.9 14.1 1.0

Magnesium binding site 4 out of 4 in 1ecq

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Magnesium binding site 4 out of 4 in the E. Coli Glucarate Dehydratase Bound to 4-Deoxyglucarate


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 Bound to 4-Deoxyglucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg498

b:34.8
occ:1.00
O6A D:DXG502 1.8 0.0 1.0
O D:HOH1325 2.0 25.8 1.0
OD1 D:ASN289 2.0 32.7 1.0
OE2 D:GLU260 2.2 38.6 1.0
OD1 D:ASP235 2.3 20.8 1.0
C6 D:DXG502 2.4 97.6 1.0
O6B D:DXG502 2.5 64.1 1.0
CG D:ASN289 3.0 34.0 1.0
CD D:GLU260 3.3 28.0 1.0
CG D:ASP235 3.3 27.9 1.0
ND2 D:ASN289 3.7 26.9 1.0
OD1 D:ASN237 3.8 51.8 1.0
OD2 D:ASP235 3.8 21.6 1.0
CG D:GLU260 3.9 23.6 1.0
C5 D:DXG502 3.9 57.9 1.0
NZ D:LYS205 4.0 63.2 1.0
NZ D:LYS207 4.1 43.6 1.0
CB D:ASN289 4.1 30.6 1.0
OE1 D:GLU260 4.2 40.7 1.0
CD2 D:HIS339 4.3 0.0 1.0
OD2 D:ASP261 4.4 20.0 1.0
C4 D:DXG502 4.4 45.5 1.0
CB D:ASP235 4.6 19.7 1.0
CE D:LYS205 4.6 0.0 1.0
OH D:TYR150 4.6 70.0 1.0
CG D:ASN237 4.7 26.5 1.0
O5 D:DXG502 4.8 42.1 1.0
O D:HOH1404 4.9 33.7 1.0
CD1 D:LEU311 5.0 19.7 1.0
N D:ASN289 5.0 19.2 1.0
NE2 D:HIS339 5.0 43.0 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 05:51:51 2020

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