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Magnesium in PDB 1ec8: E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate

Enzymatic activity of E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate

All present enzymatic activity of E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate:
4.2.1.40;

Protein crystallography data

The structure of E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate, PDB code: 1ec8 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 (°) 71.090, 84.606, 98.858, 103.42, 93.99, 113.06
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate (pdb code 1ec8). 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 Product 2,3-Dihydroxy-5-Oxo- Hexanedioate, PDB code: 1ec8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ec8

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Magnesium binding site 1 out of 4 in the E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate


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 Product 2,3-Dihydroxy-5-Oxo- Hexanedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg498

b:15.3
occ:1.00
O A:HOH1583 1.8 10.1 1.0
OD1 A:ASN289 1.9 22.3 1.0
OD1 A:ASP235 2.1 16.5 1.0
O6B A:GLR499 2.1 18.2 1.0
OE2 A:GLU260 2.1 27.3 1.0
O6A A:GLR499 2.3 25.8 1.0
C6 A:GLR499 2.5 84.7 1.0
CG A:ASN289 3.0 13.0 1.0
CG A:ASP235 3.0 4.0 1.0
CD A:GLU260 3.2 15.9 1.0
OD2 A:ASP235 3.5 8.0 1.0
ND2 A:ASN289 3.6 15.1 1.0
CG A:GLU260 3.7 11.4 1.0
ND2 A:ASN237 3.9 17.4 1.0
NZ A:LYS207 4.0 12.5 1.0
NZ A:LYS205 4.0 22.2 1.0
OD2 A:ASP261 4.0 13.8 1.0
C5 A:GLR499 4.0 33.9 1.0
CB A:ASN289 4.2 9.0 1.0
OE1 A:GLU260 4.2 17.9 1.0
CD2 A:HIS339 4.2 90.5 1.0
CB A:ASP235 4.3 12.8 1.0
CG A:ASN237 4.6 18.1 1.0
CE A:LYS205 4.8 20.8 1.0
O5 A:GLR499 4.8 24.1 1.0
OD1 A:ASN237 4.8 19.8 1.0
N A:ASN289 4.8 21.0 1.0
C4 A:GLR499 4.9 34.9 1.0
CB A:GLU260 4.9 30.1 1.0
NE2 A:HIS339 4.9 29.1 1.0
CA A:ASN289 5.0 21.9 1.0
OH A:TYR150 5.0 23.9 1.0

Magnesium binding site 2 out of 4 in 1ec8

Go back to Magnesium Binding Sites List in 1ec8
Magnesium binding site 2 out of 4 in the E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate


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 Product 2,3-Dihydroxy-5-Oxo- Hexanedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg498

b:18.0
occ:1.00
O6B B:GLR500 1.9 16.5 1.0
O B:HOH1689 2.0 11.8 1.0
OE2 B:GLU260 2.1 16.3 1.0
OD1 B:ASN289 2.1 23.6 1.0
OD1 B:ASP235 2.2 17.0 1.0
O6A B:GLR500 2.2 36.8 1.0
C6 B:GLR500 2.3 42.4 1.0
CG B:ASP235 3.1 11.1 1.0
CG B:ASN289 3.1 17.0 1.0
CD B:GLU260 3.2 20.2 1.0
OD2 B:ASP235 3.6 14.5 1.0
ND2 B:ASN289 3.6 15.5 1.0
CG B:GLU260 3.7 7.4 1.0
C5 B:GLR500 3.8 39.8 1.0
NZ B:LYS205 3.8 18.6 1.0
NZ B:LYS207 3.8 23.3 1.0
ND2 B:ASN237 3.9 24.9 1.0
OE1 B:GLU260 4.2 19.9 1.0
OD2 B:ASP261 4.3 13.1 1.0
CB B:ASP235 4.3 12.0 1.0
CD2 B:HIS339 4.4 30.6 1.0
CB B:ASN289 4.5 14.2 1.0
O5 B:GLR500 4.5 25.9 1.0
CE B:LYS205 4.5 23.4 1.0
CG B:ASN237 4.6 33.8 1.0
C4 B:GLR500 4.7 27.9 1.0
OH B:TYR150 4.7 29.1 1.0
CD1 B:LEU311 4.8 33.9 1.0
OD1 B:ASN237 4.8 24.0 1.0

Magnesium binding site 3 out of 4 in 1ec8

Go back to Magnesium Binding Sites List in 1ec8
Magnesium binding site 3 out of 4 in the E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate


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 Product 2,3-Dihydroxy-5-Oxo- Hexanedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg498

b:13.9
occ:1.00
O6B C:GLR501 1.9 17.5 1.0
OD1 C:ASN289 2.0 19.4 1.0
OE2 C:GLU260 2.0 11.2 1.0
O C:HOH1874 2.1 14.1 1.0
O6A C:GLR501 2.1 18.6 1.0
OD1 C:ASP235 2.2 12.8 1.0
C6 C:GLR501 2.3 34.0 1.0
CG C:ASN289 3.0 15.0 1.0
CG C:ASP235 3.1 10.4 1.0
CD C:GLU260 3.2 9.9 1.0
ND2 C:ASN289 3.4 12.8 1.0
OD2 C:ASP235 3.5 12.2 1.0
CG C:GLU260 3.7 5.8 1.0
C5 C:GLR501 3.8 35.4 1.0
NZ C:LYS205 3.8 18.7 1.0
NZ C:LYS207 3.9 15.0 1.0
ND2 C:ASN237 3.9 13.1 1.0
OE1 C:GLU260 4.1 20.3 1.0
OD2 C:ASP261 4.1 9.9 1.0
CD2 C:HIS339 4.2 32.3 1.0
CB C:ASN289 4.3 9.7 1.0
CB C:ASP235 4.4 6.4 1.0
O5 C:GLR501 4.4 26.5 1.0
CG C:ASN237 4.6 31.3 1.0
C4 C:GLR501 4.7 43.6 1.0
CE C:LYS205 4.8 20.8 1.0
OH C:TYR150 4.8 18.4 1.0
OD1 C:ASN237 4.8 13.3 1.0
CD1 C:LEU311 4.9 19.1 1.0
N C:ASN289 4.9 7.9 1.0

Magnesium binding site 4 out of 4 in 1ec8

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Magnesium binding site 4 out of 4 in the E. Coli Glucarate Dehydratase Bound to Product 2,3-Dihydroxy-5-Oxo- Hexanedioate


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 Product 2,3-Dihydroxy-5-Oxo- Hexanedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg498

b:15.6
occ:1.00
O D:HOH1907 1.9 12.2 1.0
OD1 D:ASN289 1.9 16.9 1.0
OD1 D:ASP235 2.0 10.6 1.0
O6B D:GLR502 2.1 19.5 1.0
OE2 D:GLU260 2.1 17.1 1.0
O6A D:GLR502 2.3 21.0 1.0
C6 D:GLR502 2.5 0.0 1.0
CG D:ASP235 2.9 6.9 1.0
CG D:ASN289 3.0 10.1 1.0
CD D:GLU260 3.2 15.8 1.0
OD2 D:ASP235 3.4 10.8 1.0
ND2 D:ASN289 3.4 14.5 1.0
CG D:GLU260 3.6 14.2 1.0
ND2 D:ASN237 3.8 17.0 1.0
NZ D:LYS205 3.9 23.6 1.0
C5 D:GLR502 4.0 34.4 1.0
NZ D:LYS207 4.0 26.4 1.0
OD2 D:ASP261 4.2 13.2 1.0
OE1 D:GLU260 4.2 22.7 1.0
CB D:ASP235 4.2 12.4 1.0
CB D:ASN289 4.3 15.1 1.0
CD2 D:HIS339 4.5 56.9 1.0
CE D:LYS205 4.5 14.3 1.0
CG D:ASN237 4.6 17.8 1.0
O5 D:GLR502 4.7 25.3 1.0
OD1 D:ASN237 4.9 16.9 1.0
C4 D:GLR502 4.9 33.8 1.0
CD1 D:LEU311 4.9 12.9 1.0
CB D:GLU260 4.9 12.2 1.0
N D:ASN289 4.9 15.9 1.0
OH D:TYR150 5.0 27.3 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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