Magnesium in PDB 1jdf: Glucarate Dehydratase From E.Coli N341D Mutant

All present enzymatic activity of Glucarate Dehydratase From E.Coli N341D Mutant:
4.2.1.40;

The structure of Glucarate Dehydratase From E.Coli N341D Mutant, PDB code: 1jdf 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)	20.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.925, 83.926, 98.222, 104.11, 93.75, 113.12
R / Rfree (%)	19.8 / 23.3

The binding sites of Magnesium atom in the Glucarate Dehydratase From E.Coli N341D Mutant (pdb code 1jdf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Glucarate Dehydratase From E.Coli N341D Mutant, PDB code: 1jdf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Glucarate Dehydratase From E.Coli N341D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glucarate Dehydratase From E.Coli N341D Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4500 b:33.0 occ:1.00 OD1 A:ASN289 2.0 33.7 1.0 O A:HOH4655 2.1 28.7 1.0 OD1 A:ASP235 2.1 23.6 1.0 O6A A:GLR2510 2.2 45.8 1.0 OE2 A:GLU260 2.2 34.5 1.0 O6B A:GLR2510 2.3 43.3 1.0 C6 A:GLR2510 2.6 47.2 1.0 CG A:ASP235 2.9 26.6 1.0 CG A:ASN289 3.1 30.6 1.0 CD A:GLU260 3.2 29.9 1.0 OD2 A:ASP235 3.2 25.4 1.0 CG A:GLU260 3.5 28.1 1.0 ND2 A:ASN289 3.7 27.4 1.0 ND2 A:ASN237 3.8 31.5 1.0 OD2 A:ASP261 3.8 26.5 1.0 C5 A:GLR2510 4.0 46.0 1.0 NZ A:LYS207 4.1 27.8 1.0 CB A:ASP235 4.2 27.5 1.0 OE1 A:GLU260 4.2 29.0 1.0 NZ A:LYS205 4.3 36.9 1.0 CB A:ASN289 4.4 29.2 1.0 CG A:ASN237 4.4 32.6 1.0 OD1 A:ASN237 4.6 34.4 1.0 CB A:GLU260 4.7 28.7 1.0 N A:ASN289 4.7 27.3 1.0 CG A:ASP261 4.8 29.1 1.0 O5 A:GLR2510 4.8 47.5 1.0 C4 A:GLR2510 4.9 43.1 1.0 CD2 A:HIS339 4.9 32.4 1.0 CE A:LYS205 4.9 37.2 1.0 CB A:ASP261 5.0 26.3 1.0

Magnesium binding site 2 out of 4 in the Glucarate Dehydratase From E.Coli N341D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glucarate Dehydratase From E.Coli N341D Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4501 b:33.8 occ:1.00 OE2 B:GLU260 2.0 26.9 1.0 OD1 B:ASN289 2.0 27.6 1.0 O B:HOH4638 2.1 26.6 1.0 O6A B:GLR2511 2.1 41.4 1.0 O6B B:GLR2511 2.1 39.5 1.0 OD1 B:ASP235 2.1 27.1 1.0 C6 B:GLR2511 2.4 43.2 1.0 CD B:GLU260 3.0 28.5 1.0 CG B:ASP235 3.1 31.9 1.0 CG B:ASN289 3.1 26.4 1.0 CG B:GLU260 3.5 27.3 1.0 OD2 B:ASP235 3.5 31.4 1.0 ND2 B:ASN289 3.7 24.7 1.0 NZ B:LYS205 3.8 33.2 1.0 C5 B:GLR2511 3.9 42.8 1.0 NZ B:LYS207 4.1 25.1 1.0 OD2 B:ASP261 4.1 28.4 1.0 OE1 B:GLU260 4.1 28.6 1.0 ND2 B:ASN237 4.1 28.3 1.0 CB B:ASP235 4.3 29.9 1.0 CB B:ASN289 4.4 24.2 1.0 CD2 B:HIS339 4.6 27.5 1.0 CD1 B:LEU311 4.6 24.3 1.0 CE B:LYS205 4.6 34.4 1.0 O5 B:GLR2511 4.7 43.1 1.0 CB B:GLU260 4.7 27.0 1.0 C4 B:GLR2511 4.8 39.0 1.0 CG B:ASN237 4.8 29.0 1.0 N B:ASN289 4.9 22.8 1.0

Magnesium binding site 3 out of 4 in the Glucarate Dehydratase From E.Coli N341D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glucarate Dehydratase From E.Coli N341D Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg4502 b:30.2 occ:1.00 OE2 C:GLU260 1.9 22.2 1.0 OD1 C:ASN289 2.0 27.3 1.0 OD1 C:ASP235 2.1 21.0 1.0 O6A C:GLR2512 2.1 39.4 1.0 O C:HOH4698 2.1 22.3 1.0 O6B C:GLR2512 2.1 39.6 1.0 C6 C:GLR2512 2.4 42.6 1.0 CD C:GLU260 3.0 23.6 1.0 CG C:ASP235 3.0 25.1 1.0 CG C:ASN289 3.1 23.8 1.0 OD2 C:ASP235 3.4 22.2 1.0 CG C:GLU260 3.5 20.6 1.0 ND2 C:ASN289 3.6 22.4 1.0 NZ C:LYS205 3.8 31.9 1.0 C5 C:GLR2512 3.9 42.1 1.0 ND2 C:ASN237 3.9 25.2 1.0 NZ C:LYS207 4.0 28.2 1.0 OE1 C:GLU260 4.0 23.3 1.0 OD2 C:ASP261 4.1 24.5 1.0 CB C:ASP235 4.2 22.6 1.0 CB C:ASN289 4.4 21.2 1.0 CE C:LYS205 4.6 30.9 1.0 CG C:ASN237 4.6 27.3 1.0 CD2 C:HIS339 4.6 27.3 1.0 O5 C:GLR2512 4.6 42.5 1.0 OD1 C:ASN237 4.7 27.6 1.0 CB C:GLU260 4.7 21.8 1.0 C4 C:GLR2512 4.8 39.4 1.0 CD1 C:LEU311 4.8 23.7 1.0 N C:ASN289 4.8 19.1 1.0

Magnesium binding site 4 out of 4 in the Glucarate Dehydratase From E.Coli N341D Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glucarate Dehydratase From E.Coli N341D Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4503 b:26.6 occ:1.00 OE2 D:GLU260 2.0 24.4 1.0 OD1 D:ASN289 2.0 28.6 1.0 OD1 D:ASP235 2.1 24.2 1.0 O6A D:GLR2513 2.1 41.7 1.0 O6B D:GLR2513 2.1 42.8 1.0 O D:HOH4679 2.2 23.4 1.0 C6 D:GLR2513 2.4 45.0 1.0 CG D:ASP235 3.0 27.0 1.0 CG D:ASN289 3.1 25.1 1.0 CD D:GLU260 3.1 27.0 1.0 OD2 D:ASP235 3.4 23.8 1.0 ND2 D:ASN289 3.6 25.0 1.0 CG D:GLU260 3.8 23.1 1.0 NZ D:LYS205 3.8 34.8 1.0 C5 D:GLR2513 3.9 43.6 1.0 NZ D:LYS207 4.0 24.1 1.0 ND2 D:ASN237 4.0 26.5 1.0 OD2 D:ASP261 4.1 24.7 1.0 OE1 D:GLU260 4.1 25.7 1.0 CB D:ASP235 4.3 22.9 1.0 CB D:ASN289 4.4 24.1 1.0 CD2 D:HIS339 4.6 29.3 1.0 CE D:LYS205 4.6 35.1 1.0 O5 D:GLR2513 4.7 43.9 1.0 CG D:ASN237 4.7 25.7 1.0 C4 D:GLR2513 4.7 41.0 1.0 OD1 D:ASN237 4.9 28.6 1.0 CD1 D:LEU311 4.9 18.5 1.0 CB D:GLU260 4.9 23.6 1.0 N D:ASN289 4.9 24.4 1.0 OH D:TYR150 5.0 37.5 1.0

A.M.Gulick, B.K.Hubbard, J.A.Gerlt, I.Rayment. Evolution of Enzymatic Activities in the Enolase Superfamily: Identification of the General Acid Catalyst in the Active Site of D-Glucarate Dehydratase From Escherichia Coli. Biochemistry V. 40 10054 2001.
ISSN: ISSN 0006-2960
PubMed: 11513584
DOI: 10.1021/BI010733B