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Magnesium in PDB 1ec9: E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate

Enzymatic activity of E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate

All present enzymatic activity of E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate:
4.2.1.40;

Protein crystallography data

The structure of E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate, PDB code: 1ec9 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 (°) 71.294, 84.836, 98.987, 103.14, 94.31, 113.20
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate (pdb code 1ec9). 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 Xylarohydroxamate, PDB code: 1ec9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ec9

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Magnesium binding site 1 out of 4 in the E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate


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 Xylarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg498

b:21.2
occ:1.00
OD1 A:ASN289 1.9 17.8 1.0
OE2 A:GLU260 2.0 18.0 1.0
O A:HOH1760 2.1 14.6 1.0
OD1 A:ASP235 2.1 17.3 1.0
OH6 A:XYH499 2.2 33.2 1.0
OH5 A:XYH499 2.2 34.3 1.0
N6 A:XYH499 2.9 50.2 1.0
C5 A:XYH499 3.0 27.6 1.0
CG A:ASN289 3.0 14.1 1.0
CG A:ASP235 3.1 15.4 1.0
CD A:GLU260 3.2 21.6 1.0
OD2 A:ASP235 3.6 11.4 1.0
ND2 A:ASN289 3.6 27.8 1.0
CG A:GLU260 3.7 18.5 1.0
NZ A:LYS207 3.7 18.8 1.0
NZ A:LYS205 3.8 27.5 1.0
ND2 A:ASN237 4.1 15.1 1.0
OE1 A:GLU260 4.1 20.1 1.0
OD2 A:ASP261 4.3 22.4 1.0
OH4 A:XYH499 4.3 49.1 1.0
CB A:ASN289 4.3 9.0 1.0
CB A:ASP235 4.3 12.9 1.0
CD2 A:HIS339 4.4 22.3 1.0
C4 A:XYH499 4.5 57.3 1.0
CE A:LYS205 4.6 19.0 1.0
CG A:ASN237 4.8 27.9 1.0
OH A:TYR150 4.8 24.8 1.0
OD1 A:ASN237 4.9 24.2 1.0
CE A:LYS207 5.0 23.3 1.0
O A:HOH1212 5.0 35.0 1.0

Magnesium binding site 2 out of 4 in 1ec9

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


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 Xylarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg498

b:25.0
occ:1.00
OH6 B:XYH500 2.0 40.6 1.0
OE2 B:GLU260 2.0 19.8 1.0
OD1 B:ASN289 2.1 18.0 1.0
OH5 B:XYH500 2.1 21.6 1.0
OD1 B:ASP235 2.1 19.8 1.0
O B:HOH1755 2.3 22.7 1.0
N6 B:XYH500 2.8 42.6 1.0
C5 B:XYH500 2.9 25.1 1.0
CG B:ASN289 3.1 18.2 1.0
CD B:GLU260 3.2 21.9 1.0
CG B:ASP235 3.2 17.9 1.0
ND2 B:ASN289 3.5 13.7 1.0
NZ B:LYS207 3.6 28.1 1.0
NZ B:LYS205 3.7 28.8 1.0
OD2 B:ASP235 3.8 15.4 1.0
CG B:GLU260 3.8 9.7 1.0
ND2 B:ASN237 4.0 21.6 1.0
OE1 B:GLU260 4.1 18.7 1.0
CD2 B:HIS339 4.4 18.6 1.0
C4 B:XYH500 4.4 55.7 1.0
CB B:ASP235 4.4 17.3 1.0
OH4 B:XYH500 4.4 32.1 1.0
CB B:ASN289 4.5 16.6 1.0
CE B:LYS205 4.5 20.0 1.0
OD2 B:ASP261 4.6 16.7 1.0
CG B:ASN237 4.7 32.3 1.0
OH B:TYR150 4.8 28.2 1.0
OD1 B:ASN237 4.8 24.1 1.0
CE B:LYS207 4.9 17.1 1.0
O B:HOH1758 5.0 41.9 1.0

Magnesium binding site 3 out of 4 in 1ec9

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


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 Xylarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg498

b:23.1
occ:1.00
OD1 C:ASN289 1.9 19.3 1.0
OE2 C:GLU260 2.0 13.0 1.0
O C:HOH1856 2.0 16.3 1.0
OD1 C:ASP235 2.2 19.1 1.0
OH5 C:XYH501 2.2 29.8 1.0
OH6 C:XYH501 2.3 26.1 1.0
CG C:ASN289 3.0 24.5 1.0
C5 C:XYH501 3.0 34.6 1.0
N6 C:XYH501 3.1 31.3 1.0
CG C:ASP235 3.1 19.9 1.0
CD C:GLU260 3.2 16.8 1.0
ND2 C:ASN289 3.4 15.3 1.0
OD2 C:ASP235 3.6 14.3 1.0
NZ C:LYS205 3.7 29.4 1.0
CG C:GLU260 3.8 14.5 1.0
NZ C:LYS207 3.9 16.5 1.0
ND2 C:ASN237 4.0 14.4 1.0
OE1 C:GLU260 4.1 21.0 1.0
OD2 C:ASP261 4.2 18.0 1.0
OH4 C:XYH501 4.2 78.2 1.0
CB C:ASN289 4.3 10.4 1.0
CB C:ASP235 4.4 11.1 1.0
CD2 C:HIS339 4.4 48.8 1.0
C4 C:XYH501 4.5 75.9 1.0
CE C:LYS205 4.7 30.4 1.0
CG C:ASN237 4.8 26.0 1.0
CD1 C:LEU311 4.9 15.2 1.0
O C:HOH1564 4.9 24.5 1.0
OD1 C:ASN237 4.9 18.7 1.0
N C:ASN289 4.9 13.2 1.0
OH C:TYR150 5.0 31.2 1.0

Magnesium binding site 4 out of 4 in 1ec9

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


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 Xylarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg498

b:23.6
occ:1.00
OD1 D:ASN289 1.9 17.8 1.0
OH6 D:XYH502 2.0 39.0 1.0
O D:HOH1757 2.1 18.1 1.0
OD1 D:ASP235 2.1 15.3 1.0
OE2 D:GLU260 2.1 18.6 1.0
OH5 D:XYH502 2.2 23.6 1.0
N6 D:XYH502 2.8 28.9 1.0
C5 D:XYH502 2.9 24.9 1.0
CG D:ASN289 3.0 19.1 1.0
CG D:ASP235 3.1 24.3 1.0
CD D:GLU260 3.2 17.9 1.0
ND2 D:ASN289 3.4 18.4 1.0
OD2 D:ASP235 3.7 24.8 1.0
NZ D:LYS205 3.7 23.6 1.0
NZ D:LYS207 3.8 23.4 1.0
CG D:GLU260 3.8 14.9 1.0
ND2 D:ASN237 4.0 20.5 1.0
OE1 D:GLU260 4.1 23.0 1.0
CD2 D:HIS339 4.3 21.9 1.0
CB D:ASN289 4.4 19.2 1.0
CB D:ASP235 4.4 21.0 1.0
C4 D:XYH502 4.4 47.8 1.0
CE D:LYS205 4.5 14.1 1.0
OD2 D:ASP261 4.5 17.0 1.0
OH4 D:XYH502 4.5 41.7 1.0
O D:HOH1066 4.7 27.1 1.0
CG D:ASN237 4.8 21.4 1.0
OH D:TYR150 4.9 23.6 1.0
OD1 D:ASN237 4.9 22.6 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 05:51:50 2020

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