Atomistry » Magnesium » PDB 1e9b-1enn » 1ec8
Atomistry »
  Magnesium »
    PDB 1e9b-1enn »
      1ec8 »

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

Go back to Magnesium Binding Sites List in 1ec8
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

Go back to Magnesium Binding Sites List in 1ec8
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy