Magnesium in PDB 3hpf: Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate

The structure of Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate, PDB code: 3hpf was solved by A.A.Fedorov, E.V.Fedorov, J.F.Rakus, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 1.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	119.966, 119.966, 122.165, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate (pdb code 3hpf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate, PDB code: 3hpf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.5 occ:1.00 OE1 A:GLU221 2.0 22.3 1.0 NE2 A:HIS246 2.1 24.1 1.0 O A:HOH397 2.1 23.8 1.0 O6A A:GAE411 2.2 27.7 1.0 OD2 A:ASP193 2.3 25.4 1.0 O6B A:GAE411 2.4 27.6 1.0 C6 A:GAE411 2.6 29.1 1.0 CD2 A:HIS246 3.0 22.4 1.0 CE1 A:HIS246 3.1 22.6 1.0 CD A:GLU221 3.1 24.5 1.0 CG A:ASP193 3.2 24.9 1.0 OD1 A:ASP193 3.5 25.1 1.0 CG A:GLU221 3.6 20.6 1.0 OH A:TYR89 4.1 26.6 1.0 O A:HOH418 4.1 21.5 1.0 C5 A:GAE411 4.1 29.2 1.0 ND1 A:HIS246 4.2 22.6 1.0 CG A:HIS246 4.2 21.7 1.0 OE2 A:GLU221 4.2 22.4 1.0 OG A:SER222 4.2 21.1 1.0 NH2 A:ARG162 4.3 27.4 1.0 O A:HOH597 4.4 34.3 1.0 O A:HOH398 4.4 23.4 1.0 CB A:GLU221 4.5 19.9 1.0 OD1 A:ASN266 4.6 26.0 1.0 CB A:ASP193 4.6 23.6 1.0 O5 A:GAE411 4.8 27.9 1.0 C4 A:GAE411 5.0 29.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.3 occ:1.00 OD1 A:ASP42 2.1 24.4 1.0 OG1 A:THR297 2.1 21.1 1.0 O2 A:GAE411 2.1 25.1 1.0 O A:THR297 2.2 24.7 1.0 O1A A:GAE411 2.2 26.1 1.0 NE2 A:HIS45 2.3 22.9 1.0 C1 A:GAE411 3.0 28.4 1.0 C A:THR297 3.0 24.8 1.0 C2 A:GAE411 3.1 29.6 1.0 CG A:ASP42 3.1 24.3 1.0 CB A:THR297 3.1 23.0 1.0 CA A:THR297 3.2 22.0 1.0 CE1 A:HIS45 3.2 26.3 1.0 CD2 A:HIS45 3.3 23.3 1.0 CB A:ASP42 3.6 22.9 1.0 NH2 A:ARG385 3.9 26.0 1.0 CG2 A:THR297 3.9 23.1 1.0 NH2 A:ARG15 4.1 24.9 1.0 OD2 A:ASP42 4.2 23.2 1.0 O1B A:GAE411 4.2 27.8 1.0 O A:HOH412 4.2 25.2 1.0 N A:GLN298 4.3 24.4 1.0 O3 A:GAE411 4.3 32.8 1.0 C3 A:GAE411 4.3 29.9 1.0 ND1 A:HIS45 4.3 24.1 1.0 NE A:ARG385 4.4 26.4 1.0 CG A:HIS45 4.4 23.9 1.0 CZ A:ARG385 4.4 28.7 1.0 N A:THR297 4.6 22.5 1.0 O4 A:GAE411 4.7 27.5 1.0 O A:ASP42 4.8 23.6 1.0 CB A:GLN298 4.8 26.8 1.0 O A:GLN298 5.0 27.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:30.6 occ:1.00 OE1 B:GLU221 2.1 23.6 1.0 O B:HOH404 2.1 24.2 1.0 OD2 B:ASP193 2.1 24.9 1.0 O6A B:GAE411 2.2 28.9 1.0 NE2 B:HIS246 2.2 24.0 1.0 O6B B:GAE411 2.2 28.0 1.0 C6 B:GAE411 2.5 30.3 1.0 CG B:ASP193 3.1 24.8 1.0 CD2 B:HIS246 3.2 21.8 1.0 CE1 B:HIS246 3.2 22.6 1.0 CD B:GLU221 3.2 26.6 1.0 OD1 B:ASP193 3.5 23.8 1.0 CG B:GLU221 3.6 23.7 1.0 C5 B:GAE411 4.0 29.1 1.0 OH B:TYR89 4.1 28.5 1.0 O B:HOH430 4.1 26.4 1.0 NH2 B:ARG162 4.1 29.4 1.0 OG B:SER222 4.3 23.9 1.0 OE2 B:GLU221 4.3 22.5 1.0 ND1 B:HIS246 4.3 23.4 1.0 CG B:HIS246 4.3 21.9 1.0 O B:HOH451 4.4 23.8 1.0 O B:HOH595 4.4 31.8 1.0 CB B:ASP193 4.5 23.6 1.0 CB B:GLU221 4.5 23.1 1.0 OD1 B:ASN266 4.7 24.8 1.0 O5 B:GAE411 4.7 28.4 1.0 C4 B:GAE411 4.9 27.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Mutant Y90F of Divergent Galactarate Dehydratase From Oceanobacillus Iheyensis Complexed with Mg and Galactarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:28.0 occ:1.00 OD1 B:ASP42 2.1 24.2 1.0 OG1 B:THR297 2.1 24.1 1.0 O2 B:GAE411 2.2 25.8 1.0 O B:THR297 2.2 25.6 1.0 O1A B:GAE411 2.2 27.7 1.0 NE2 B:HIS45 2.3 22.5 1.0 C1 B:GAE411 3.0 27.9 1.0 C B:THR297 3.1 25.0 1.0 C2 B:GAE411 3.1 28.2 1.0 CG B:ASP42 3.1 22.4 1.0 CE1 B:HIS45 3.2 23.8 1.0 CB B:THR297 3.2 23.6 1.0 CA B:THR297 3.2 23.3 1.0 CD2 B:HIS45 3.3 22.0 1.0 CB B:ASP42 3.6 22.7 1.0 NH2 B:ARG385 3.8 26.7 1.0 CG2 B:THR297 4.0 25.6 1.0 NH2 B:ARG15 4.1 25.6 1.0 O1B B:GAE411 4.2 29.9 1.0 O B:HOH408 4.2 25.5 1.0 OD2 B:ASP42 4.2 23.3 1.0 O3 B:GAE411 4.3 30.9 1.0 ND1 B:HIS45 4.3 22.5 1.0 C3 B:GAE411 4.3 29.4 1.0 N B:GLN298 4.3 25.1 1.0 NE B:ARG385 4.4 28.6 1.0 CZ B:ARG385 4.4 31.1 1.0 CG B:HIS45 4.4 22.0 1.0 N B:THR297 4.7 22.8 1.0 O4 B:GAE411 4.7 28.4 1.0 CB B:GLN298 4.8 28.6 1.0 O B:ASP42 4.9 24.1 1.0 O B:GLN298 4.9 26.3 1.0

J.F.Rakus, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, F.P.Mills-Groninger, R.Toro, J.Bonanno, K.Bain, J.M.Sauder, S.K.Burley, S.C.Almo, M.P.Jacobson, J.A.Gerlt. Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis . Biochemistry V. 48 11546 2009.
ISSN: ISSN 0006-2960
PubMed: 19883118
DOI: 10.1021/BI901731C