Magnesium in PDB 3es8: Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.

The structure of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate., PDB code: 3es8 was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.94 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	105.584, 105.695, 105.718, 109.31, 109.47, 109.66
R / Rfree (%)	22.4 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. (pdb code 3es8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate., PDB code: 3es8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:19.0 occ:1.00 OG1 A:THR297 2.0 29.9 1.0 O1B A:LMR392 2.0 35.6 1.0 O2 A:LMR392 2.1 39.6 1.0 OD1 A:ASP42 2.2 32.3 1.0 NE2 A:HIS45 2.3 39.1 1.0 O A:THR297 2.3 33.4 1.0 C1 A:LMR392 2.7 39.0 1.0 C2 A:LMR392 2.9 38.5 1.0 C A:THR297 3.1 34.0 1.0 CB A:THR297 3.1 32.0 1.0 CE1 A:HIS45 3.2 37.6 1.0 CG A:ASP42 3.2 34.4 1.0 CA A:THR297 3.2 33.6 1.0 CD2 A:HIS45 3.3 37.5 1.0 CB A:ASP42 3.7 33.4 1.0 NH2 A:ARG385 3.9 32.3 1.0 O1A A:LMR392 3.9 34.5 1.0 CG2 A:THR297 4.0 32.5 1.0 C3 A:LMR392 4.1 39.2 1.0 O A:HOH397 4.1 30.9 1.0 NH2 A:ARG15 4.1 38.9 1.0 OD2 A:ASP42 4.2 32.3 1.0 NE A:ARG385 4.3 34.8 1.0 ND1 A:HIS45 4.3 38.6 1.0 CG A:HIS45 4.4 38.6 1.0 N A:GLN298 4.4 34.8 1.0 CZ A:ARG385 4.4 34.0 1.0 N A:THR297 4.7 33.2 1.0 O4A A:LMR392 4.8 39.8 1.0 CB A:GLN298 5.0 31.8 1.0 C4 A:LMR392 5.0 41.2 1.0 O A:ASP42 5.0 39.9 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:20.8 occ:1.00 OG1 B:THR297 1.9 35.8 1.0 O1B B:LMR392 2.1 45.4 1.0 OD1 B:ASP42 2.2 37.5 1.0 O B:THR297 2.2 35.2 1.0 NE2 B:HIS45 2.3 42.3 1.0 O2 B:LMR392 2.5 45.3 1.0 C1 B:LMR392 2.9 46.6 1.0 C B:THR297 3.0 36.0 1.0 CB B:THR297 3.0 37.1 1.0 CA B:THR297 3.1 36.4 1.0 C2 B:LMR392 3.2 47.5 1.0 CG B:ASP42 3.2 40.3 1.0 CE1 B:HIS45 3.3 41.0 1.0 CD2 B:HIS45 3.3 41.3 1.0 CB B:ASP42 3.7 39.9 1.0 CG2 B:THR297 3.9 35.7 1.0 O1A B:LMR392 4.0 44.4 1.0 NH2 B:ARG385 4.0 42.2 1.0 NH2 B:ARG15 4.1 37.9 1.0 O B:HOH399 4.2 32.5 1.0 OD2 B:ASP42 4.2 41.2 1.0 N B:GLN298 4.3 37.4 1.0 C3 B:LMR392 4.4 49.2 1.0 NE B:ARG385 4.4 44.7 1.0 ND1 B:HIS45 4.4 41.1 1.0 CG B:HIS45 4.5 41.3 1.0 CZ B:ARG385 4.5 44.2 1.0 N B:THR297 4.6 35.9 1.0 CB B:GLN298 4.9 40.6 1.0 O B:ASP42 5.0 41.9 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg393 b:24.8 occ:1.00 OG1 C:THR297 1.9 37.0 1.0 OD1 C:ASP42 2.1 38.2 1.0 O1B C:LMR392 2.2 51.3 1.0 NE2 C:HIS45 2.2 41.1 1.0 O C:THR297 2.3 38.0 1.0 O2 C:LMR392 2.5 54.9 1.0 C1 C:LMR392 3.0 54.2 1.0 CB C:THR297 3.1 37.2 1.0 C C:THR297 3.1 38.2 1.0 CG C:ASP42 3.1 41.3 1.0 CE1 C:HIS45 3.2 41.2 1.0 CA C:THR297 3.2 37.4 1.0 CD2 C:HIS45 3.2 40.2 1.0 C2 C:LMR392 3.3 54.5 1.0 CB C:ASP42 3.6 40.1 1.0 CG2 C:THR297 3.9 34.5 1.0 NH2 C:ARG385 4.0 40.2 1.0 O1A C:LMR392 4.2 53.3 1.0 OD2 C:ASP42 4.2 41.5 1.0 NH2 C:ARG15 4.2 37.1 1.0 O C:HOH411 4.2 32.7 1.0 ND1 C:HIS45 4.3 41.5 1.0 NE C:ARG385 4.4 42.0 1.0 CG C:HIS45 4.4 42.4 1.0 N C:GLN298 4.4 38.5 1.0 C3 C:LMR392 4.4 55.1 1.0 CZ C:ARG385 4.5 42.0 1.0 N C:THR297 4.7 36.2 1.0 O4A C:LMR392 4.9 57.0 1.0 O C:ASP42 4.9 42.0 1.0 CB C:GLN298 5.0 37.9 1.0 CZ C:PHE271 5.0 35.0 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


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 Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg393 b:18.9 occ:1.00 O1B D:LMR392 2.0 43.0 1.0 OG1 D:THR297 2.0 31.9 1.0 OD1 D:ASP42 2.2 38.3 1.0 O2 D:LMR392 2.2 42.9 1.0 NE2 D:HIS45 2.3 42.3 1.0 O D:THR297 2.3 35.8 1.0 C1 D:LMR392 2.7 44.9 1.0 C2 D:LMR392 2.9 44.1 1.0 C D:THR297 3.1 35.8 1.0 CB D:THR297 3.1 34.4 1.0 CE1 D:HIS45 3.2 41.3 1.0 CA D:THR297 3.2 35.4 1.0 CG D:ASP42 3.2 38.0 1.0 CD2 D:HIS45 3.3 40.5 1.0 CB D:ASP42 3.7 36.5 1.0 O1A D:LMR392 3.9 42.1 1.0 NH2 D:ARG385 4.0 32.0 1.0 CG2 D:THR297 4.0 31.9 1.0 NH2 D:ARG15 4.2 26.6 1.0 C3 D:LMR392 4.2 44.0 1.0 O D:HOH399 4.2 32.7 1.0 OD2 D:ASP42 4.3 40.4 1.0 NE D:ARG385 4.3 34.5 1.0 ND1 D:HIS45 4.3 41.5 1.0 N D:GLN298 4.4 36.1 1.0 CG D:HIS45 4.4 40.3 1.0 CZ D:ARG385 4.4 33.3 1.0 N D:THR297 4.7 35.6 1.0 O4A D:LMR392 4.9 44.4 1.0 CB D:GLN298 4.9 35.4 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg393 b:20.4 occ:1.00 OG1 E:THR297 1.9 31.0 1.0 O1B E:LMR392 2.1 47.8 1.0 OD1 E:ASP42 2.2 33.7 1.0 O E:THR297 2.2 35.0 1.0 O2 E:LMR392 2.2 49.2 1.0 NE2 E:HIS45 2.3 37.0 1.0 C1 E:LMR392 2.8 50.9 1.0 C2 E:LMR392 3.0 50.7 1.0 C E:THR297 3.0 35.5 1.0 CB E:THR297 3.0 33.8 1.0 CA E:THR297 3.1 34.5 1.0 CE1 E:HIS45 3.2 35.5 1.0 CG E:ASP42 3.2 36.4 1.0 CD2 E:HIS45 3.3 36.0 1.0 CB E:ASP42 3.7 36.0 1.0 O1A E:LMR392 3.9 49.4 1.0 CG2 E:THR297 3.9 31.2 1.0 NH2 E:ARG385 4.0 40.1 1.0 C3 E:LMR392 4.2 51.2 1.0 NH2 E:ARG15 4.2 40.4 1.0 OD2 E:ASP42 4.3 37.7 1.0 N E:GLN298 4.3 37.0 1.0 NE E:ARG385 4.4 42.2 1.0 ND1 E:HIS45 4.4 36.4 1.0 CG E:HIS45 4.5 38.3 1.0 CZ E:ARG385 4.5 40.7 1.0 N E:THR297 4.6 34.1 1.0 CB E:GLN298 4.9 36.1 1.0 O4A E:LMR392 4.9 51.9 1.0 CZ E:PHE271 5.0 32.6 1.0 O E:ASP42 5.0 40.5 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg393 b:19.0 occ:1.00 OG1 F:THR297 2.1 33.5 1.0 O1B F:LMR392 2.1 42.6 1.0 OD1 F:ASP42 2.1 36.9 1.0 O2 F:LMR392 2.2 41.9 1.0 O F:THR297 2.3 33.5 1.0 NE2 F:HIS45 2.3 43.5 1.0 C1 F:LMR392 2.8 43.8 1.0 C2 F:LMR392 3.0 42.9 1.0 C F:THR297 3.1 35.5 1.0 CB F:THR297 3.2 34.6 1.0 CE1 F:HIS45 3.2 41.8 1.0 CG F:ASP42 3.2 37.7 1.0 CA F:THR297 3.2 34.8 1.0 CD2 F:HIS45 3.3 42.4 1.0 CB F:ASP42 3.7 37.1 1.0 NH2 F:ARG385 3.9 34.0 1.0 O1A F:LMR392 4.0 41.0 1.0 CG2 F:THR297 4.0 34.8 1.0 NH2 F:ARG15 4.1 35.8 1.0 O F:HOH402 4.1 32.4 1.0 C3 F:LMR392 4.2 43.9 1.0 OD2 F:ASP42 4.2 35.6 1.0 NE F:ARG385 4.3 36.3 1.0 ND1 F:HIS45 4.3 41.6 1.0 N F:GLN298 4.4 36.3 1.0 CZ F:ARG385 4.4 36.0 1.0 CG F:HIS45 4.4 41.9 1.0 N F:THR297 4.7 35.5 1.0 O4A F:LMR392 4.8 46.1 1.0 CB F:GLN298 4.9 37.5 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg393 b:22.6 occ:1.00 O1B G:LMR392 2.1 47.3 1.0 OG1 G:THR297 2.1 36.0 1.0 O2 G:LMR392 2.1 46.7 1.0 OD1 G:ASP42 2.2 34.3 1.0 NE2 G:HIS45 2.3 33.2 1.0 O G:THR297 2.3 37.0 1.0 C1 G:LMR392 2.7 47.6 1.0 C2 G:LMR392 2.9 46.7 1.0 C G:THR297 3.1 37.1 1.0 CE1 G:HIS45 3.1 33.2 1.0 CB G:THR297 3.2 35.8 1.0 CA G:THR297 3.2 36.7 1.0 CG G:ASP42 3.3 36.8 1.0 CD2 G:HIS45 3.3 32.4 1.0 CB G:ASP42 3.8 36.6 1.0 O1A G:LMR392 3.9 46.6 1.0 NH2 G:ARG385 4.0 29.6 1.0 CG2 G:THR297 4.1 34.1 1.0 C3 G:LMR392 4.1 45.8 1.0 NH2 G:ARG15 4.1 39.3 1.0 O G:HOH403 4.2 33.6 1.0 NE G:ARG385 4.2 31.7 1.0 ND1 G:HIS45 4.3 33.0 1.0 OD2 G:ASP42 4.3 34.7 1.0 N G:GLN298 4.4 36.7 1.0 CZ G:ARG385 4.4 29.7 1.0 CG G:HIS45 4.4 32.6 1.0 N G:THR297 4.7 37.5 1.0 O4A G:LMR392 4.7 46.0 1.0 C4 G:LMR392 4.9 45.8 1.0 CB G:GLN298 4.9 36.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Divergent Enolase From Oceanobacillus Iheyensis Complexed with Mg and L-Malate. within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg393 b:25.4 occ:1.00 OG1 H:THR297 2.0 42.4 1.0 O2 H:LMR392 2.2 56.2 1.0 OD1 H:ASP42 2.2 37.2 1.0 NE2 H:HIS45 2.3 31.5 1.0 O H:THR297 2.3 37.1 1.0 O1B H:LMR392 2.4 55.3 1.0 C1 H:LMR392 3.0 56.6 1.0 C2 H:LMR392 3.1 56.8 1.0 C H:THR297 3.1 38.3 1.0 CB H:THR297 3.1 38.9 1.0 CE1 H:HIS45 3.2 33.2 1.0 CG H:ASP42 3.2 40.5 1.0 CA H:THR297 3.2 38.3 1.0 CD2 H:HIS45 3.3 32.4 1.0 CB H:ASP42 3.7 39.7 1.0 NH2 H:ARG385 4.0 35.2 1.0 CG2 H:THR297 4.0 36.6 1.0 O1A H:LMR392 4.1 55.5 1.0 NH2 H:ARG15 4.2 43.8 1.0 OD2 H:ASP42 4.2 38.9 1.0 C3 H:LMR392 4.3 56.5 1.0 NE H:ARG385 4.3 36.0 1.0 ND1 H:HIS45 4.3 33.6 1.0 N H:GLN298 4.4 37.7 1.0 CG H:HIS45 4.4 33.8 1.0 CZ H:ARG385 4.4 34.9 1.0 N H:THR297 4.7 37.7 1.0 O4B H:LMR392 4.7 57.4 1.0 CB H:GLN298 4.9 38.3 1.0 O H:ASP42 5.0 41.8 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