Magnesium in PDB 8ej0: Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg

The structure of Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg, PDB code: 8ej0 was solved by T.Bayaraa, T.Lonhienne, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.05 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.908, 178.071, 92.858, 90, 101.72, 90
R / Rfree (%)	19.4 / 23.9

The structure of Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Magnesium atom in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg (pdb code 8ej0). 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 Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg, PDB code: 8ej0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg


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 Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:36.5 occ:1.00 OD2 A:ASP126 2.1 50.8 1.0 OQ1 A:KCX127 2.2 44.3 1.0 OE2 A:GLU449 2.2 50.0 1.0 O2 A:BCT604 2.2 50.9 1.0 OE2 A:GLU89 2.2 49.6 1.0 O1 A:BCT604 2.5 56.9 1.0 C A:BCT604 2.6 54.2 1.0 CD A:GLU89 3.0 47.2 1.0 CD A:GLU449 3.1 52.7 1.0 CX A:KCX127 3.1 42.5 1.0 CG A:ASP126 3.3 47.3 1.0 OQ2 A:KCX127 3.3 42.2 1.0 OE1 A:GLU449 3.3 54.0 1.0 CG A:GLU89 3.6 46.9 1.0 O3 A:BCT604 3.9 49.9 1.0 OE1 A:GLU89 3.9 41.8 1.0 CB A:ASP126 3.9 45.0 1.0 O A:HOH709 4.0 39.7 1.0 OG1 A:THR203 4.0 47.8 1.0 ND2 A:ASN276 4.1 47.3 1.0 O A:HOH728 4.3 44.9 1.0 OD1 A:ASP126 4.3 51.6 1.0 CG A:GLU449 4.4 51.0 1.0 NZ A:KCX127 4.4 40.7 1.0 CB A:THR203 4.5 46.9 1.0 O2 A:BCT603 4.6 63.2 1.0 NH1 A:ARG474 4.6 43.8 1.0 CB A:GLU89 4.7 44.9 1.0 CA A:SER476 4.8 49.3 1.0 OG A:SER476 5.0 54.0 1.0 CE A:KCX127 5.0 40.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg


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 Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:46.3 occ:1.00 OE2 C:GLU89 1.7 50.8 1.0 O2 C:BCT603 1.9 54.4 1.0 OE2 C:GLU449 2.2 53.9 1.0 OQ2 C:KCX127 2.3 49.2 1.0 C C:BCT603 2.6 53.2 1.0 CD C:GLU89 2.8 52.0 1.0 O3 C:BCT603 2.9 55.3 1.0 CD C:GLU449 3.0 56.2 1.0 OE1 C:GLU449 3.2 53.8 1.0 OE1 C:GLU89 3.3 51.0 1.0 CX C:KCX127 3.3 45.4 1.0 OG1 C:THR203 3.4 50.9 1.0 OD1 C:ASP126 3.4 49.6 1.0 CG C:ASP126 3.5 48.7 1.0 OQ1 C:KCX127 3.7 50.8 1.0 O1 C:BCT603 3.8 52.8 1.0 ND2 C:ASN276 3.9 51.7 1.0 OD2 C:ASP126 3.9 53.2 1.0 CB C:THR203 3.9 45.3 1.0 CB C:ASP126 4.1 48.7 1.0 CG C:GLU89 4.1 53.5 1.0 CG C:GLU449 4.4 50.4 1.0 NZ C:KCX127 4.5 49.1 1.0 O A:HOH731 4.5 54.2 1.0 NH1 C:ARG474 4.6 47.2 1.0 CA C:SER476 4.6 53.5 1.0 CG2 C:THR203 4.6 44.3 1.0 N C:GLY477 4.7 47.5 1.0 OG C:SER476 4.8 51.3 1.0 O C:HOH723 4.8 46.8 1.0 CE C:KCX127 5.0 46.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg


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 Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:31.3 occ:1.00 O2 E:BCT604 2.1 51.1 1.0 OE1 E:GLU89 2.2 52.1 1.0 OE2 E:GLU449 2.2 51.3 1.0 OQ2 E:KCX127 2.3 46.4 1.0 C E:BCT604 2.6 54.3 1.0 O3 E:BCT604 2.6 57.3 1.0 OQ1 E:KCX127 2.6 41.4 1.0 OD2 E:ASP126 2.7 45.8 1.0 CX E:KCX127 2.8 41.9 1.0 CD E:GLU89 2.8 50.3 1.0 CG E:ASP126 3.1 46.4 1.0 CD E:GLU449 3.3 53.8 1.0 OE2 E:GLU89 3.4 43.8 1.0 CB E:ASP126 3.5 43.0 1.0 OG1 E:THR203 3.6 44.9 1.0 OE1 E:GLU449 3.7 55.3 1.0 O1 E:BCT604 3.8 52.8 1.0 CG E:GLU89 3.8 45.9 1.0 OD1 E:ASP126 3.9 42.6 1.0 ND2 E:ASN276 4.0 45.1 1.0 CB E:THR203 4.1 41.2 1.0 NZ E:KCX127 4.2 38.5 1.0 O E:HOH742 4.4 41.4 1.0 CG E:GLU449 4.5 50.3 1.0 NH1 E:ARG474 4.6 41.5 1.0 CG2 E:THR203 4.7 39.3 1.0 CB E:GLU89 4.8 43.8 1.0 CG E:ASN276 5.0 43.7 1.0 N E:GLY477 5.0 45.9 1.0 OG E:SER476 5.0 51.3 1.0 CA E:ASP126 5.0 44.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg


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 Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:41.9 occ:1.00 OE2 G:GLU89 2.0 60.8 1.0 O1 G:CO2603 2.0 58.1 1.0 OQ2 G:KCX127 2.1 53.2 1.0 OE1 G:GLU449 2.1 58.0 1.0 OD1 G:ASP126 2.3 54.1 1.0 CD G:GLU89 2.4 56.0 1.0 OE1 G:GLU89 2.8 58.1 1.0 C G:CO2603 3.0 60.2 1.0 CD G:GLU449 3.0 60.5 1.0 CX G:KCX127 3.1 49.4 1.0 OE2 G:GLU449 3.3 65.7 1.0 CG G:GLU89 3.3 52.2 1.0 CG G:ASP126 3.3 53.2 1.0 NZ G:KCX127 3.6 48.9 1.0 OG1 G:THR203 3.8 53.2 1.0 CB G:ASP126 3.9 51.2 1.0 O2 G:CO2603 4.1 57.7 1.0 ND2 G:ASN276 4.2 54.0 1.0 OQ1 G:KCX127 4.2 52.6 1.0 CB G:THR203 4.2 48.5 1.0 CG G:GLU449 4.4 61.0 1.0 OD2 G:ASP126 4.4 54.1 1.0 CB G:GLU89 4.4 51.5 1.0 NH1 G:ARG474 4.5 53.9 1.0 O G:HOH701 4.6 47.0 1.0 CG2 G:THR203 4.8 45.6 1.0 CE G:KCX127 4.9 47.0 1.0

T.Bayaraa, T.Lonhienne, L.W.Guddat. Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg To Be Published.