Iron 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:

Magnesium

(Mg)

4 atoms

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mg, PDB code: 8ej0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe601 b:47.3 occ:0.84 FE1 A:FES601 0.0 47.3 0.8 S1 A:FES601 2.2 40.0 0.8 S2 A:FES601 2.2 42.3 0.8 SG A:CYS125 2.4 53.4 1.0 SG A:CYS57 2.6 42.8 1.0 FE2 A:FES601 3.0 62.4 0.8 CB A:CYS125 3.5 42.7 1.0 CB A:CYS57 3.6 42.0 1.0 CA A:CYS125 3.7 41.6 1.0 N A:ASP126 4.2 43.3 1.0 CB A:GLU89 4.3 44.9 1.0 CG A:GLU89 4.3 46.9 1.0 SG A:CYS198 4.3 44.9 1.0 C A:CYS125 4.4 46.5 1.0 OD1 A:ASP126 4.6 51.6 1.0 CD1 C:TRP28 4.6 51.8 1.0 CB A:HIS197 4.7 40.8 1.0 N A:GLU89 4.7 40.4 1.0 NE1 C:TRP28 4.7 51.4 1.0 CG A:ASP126 4.8 47.3 1.0 N A:CYS125 4.9 41.2 1.0 CA A:HIS197 4.9 43.6 1.0 N A:CYS198 4.9 40.6 1.0

Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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 A:Fe601 b:62.4 occ:0.84 FE2 A:FES601 0.0 62.4 0.8 S2 A:FES601 2.2 42.3 0.8 S1 A:FES601 2.2 40.0 0.8 SG A:CYS198 2.5 44.9 1.0 FE1 A:FES601 3.0 47.3 0.8 O A:HOH722 3.2 41.3 1.0 OD1 A:ASP126 3.4 51.6 1.0 OD2 A:ASP126 3.6 50.8 1.0 CG A:ASP126 3.7 47.3 1.0 O1 A:BCT604 3.8 56.9 1.0 CG A:GLU89 4.0 46.9 1.0 CB A:CYS198 4.0 47.8 1.0 O3 A:BCT604 4.0 49.9 1.0 CB A:GLU89 4.2 44.9 1.0 C A:BCT604 4.3 54.2 1.0 NE1 C:TRP28 4.3 51.4 1.0 O1 A:BCT603 4.3 64.4 1.0 O2 A:BCT603 4.7 63.2 1.0 N A:CYS198 4.8 40.6 1.0 CB A:ASP126 4.8 45.0 1.0 C A:BCT603 4.9 63.6 1.0 CE2 C:TRP28 5.0 54.3 1.0 CA A:CYS198 5.0 39.9 1.0 SG A:CYS125 5.0 53.4 1.0

Iron binding site 3 out of 8 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 Iron with other atoms in the Fe 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 C:Fe601 b:47.0 occ:0.87 FE1 C:FES601 0.0 47.0 0.9 S1 C:FES601 2.1 44.0 0.9 S2 C:FES601 2.2 40.1 0.9 SG C:CYS125 2.2 52.5 1.0 SG C:CYS57 2.4 51.6 1.0 CB C:CYS125 3.1 40.3 1.0 FE2 C:FES601 3.1 67.7 0.9 CB C:CYS57 3.2 43.3 1.0 O C:HOH729 3.6 41.3 1.0 CA C:CYS125 3.7 43.7 1.0 N C:CYS198 4.2 46.0 1.0 CB C:HIS197 4.3 40.8 1.0 CA C:HIS197 4.4 47.4 1.0 OD1 C:ASP126 4.4 49.6 1.0 CD1 A:TRP28 4.5 45.8 1.0 N C:ASP126 4.6 45.3 1.0 NE1 A:TRP28 4.6 42.2 1.0 CA C:CYS57 4.7 44.5 1.0 C C:CYS125 4.7 44.7 1.0 SG C:CYS198 4.7 57.1 1.0 N C:CYS125 4.8 44.3 1.0 C C:HIS197 4.8 45.5 1.0 CB C:GLU89 4.9 45.2 1.0 N C:CYS57 5.0 43.2 1.0 CB C:CYS198 5.0 46.0 1.0

Iron binding site 4 out of 8 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 Iron with other atoms in the Fe 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 C:Fe601 b:67.7 occ:0.87 FE2 C:FES601 0.0 67.7 0.9 S2 C:FES601 2.2 40.1 0.9 S1 C:FES601 2.2 44.0 0.9 SG C:CYS198 2.3 57.1 1.0 CB C:CYS198 2.8 46.0 1.0 FE1 C:FES601 3.1 47.0 0.9 O C:HOH731 3.5 45.6 1.0 OD1 C:ASP126 3.8 49.6 1.0 N C:CYS198 3.8 46.0 1.0 NE1 A:TRP28 3.8 42.2 1.0 CA C:CYS198 3.9 49.6 1.0 O3 C:BCT603 3.9 55.3 1.0 OD2 C:ASP126 4.1 53.2 1.0 SG C:CYS125 4.4 52.5 1.0 CG C:ASP126 4.4 48.7 1.0 CE2 A:TRP28 4.5 47.6 1.0 CD1 A:TRP28 4.6 45.8 1.0 C C:BCT603 4.7 53.2 1.0 CZ2 A:TRP28 4.7 47.2 1.0 SG C:CYS57 4.9 51.6 1.0 O1 C:BCT603 4.9 52.8 1.0

Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe601 b:45.5 occ:0.86 FE1 E:FES601 0.0 45.5 0.9 S1 E:FES601 2.2 36.1 0.9 S2 E:FES601 2.2 42.8 0.9 SG E:CYS125 2.4 48.5 1.0 SG E:CYS57 2.6 45.7 1.0 FE2 E:FES601 3.0 54.9 0.9 CB E:CYS125 3.3 43.6 1.0 CB E:CYS57 3.4 41.3 1.0 CA E:CYS125 3.5 39.5 1.0 N E:ASP126 3.9 44.9 1.0 CB E:GLU89 4.1 43.8 1.0 C E:CYS125 4.2 43.6 1.0 OD2 E:ASP126 4.3 45.8 1.0 CG E:ASP126 4.5 46.4 1.0 N E:GLU89 4.6 40.5 1.0 N E:CYS125 4.6 44.7 1.0 SG E:CYS198 4.7 46.2 1.0 CD1 G:TRP28 4.7 52.1 1.0 CB E:HIS197 4.7 39.2 1.0 OD1 E:ASP126 4.8 42.6 1.0 CA E:CYS57 4.8 41.9 1.0 NE1 G:TRP28 4.9 49.7 1.0 CA E:HIS197 5.0 41.9 1.0

Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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:Fe601 b:54.9 occ:0.86 FE2 E:FES601 0.0 54.9 0.9 S1 E:FES601 2.2 36.1 0.9 S2 E:FES601 2.2 42.8 0.9 SG E:CYS198 2.3 46.2 1.0 OD2 E:ASP126 3.0 45.8 1.0 FE1 E:FES601 3.0 45.5 0.9 O E:HOH702 3.1 44.3 1.0 OD1 E:ASP126 3.5 42.6 1.0 CG E:ASP126 3.5 46.4 1.0 CB E:CYS198 3.7 46.2 1.0 NE1 G:TRP28 4.0 49.7 1.0 O1 E:BCT604 4.2 52.8 1.0 O3 E:BCT604 4.3 57.3 1.0 CB E:GLU89 4.3 43.8 1.0 CG E:GLU89 4.4 45.9 1.0 N E:CYS198 4.4 41.1 1.0 C E:BCT604 4.5 54.3 1.0 CA E:CYS198 4.6 41.5 1.0 CE2 G:TRP28 4.7 50.8 1.0 CD1 G:TRP28 4.7 52.1 1.0 SG E:CYS57 4.8 45.7 1.0 CB E:ASP126 4.9 43.0 1.0 SG E:CYS125 4.9 48.5 1.0 CZ2 G:TRP28 4.9 51.9 1.0 N E:ASP126 4.9 44.9 1.0

Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe601 b:46.6 occ:0.82 FE1 G:FES601 0.0 46.6 0.8 S1 G:FES601 2.2 45.7 0.8 S2 G:FES601 2.2 48.9 0.8 SG G:CYS125 2.4 55.2 1.0 SG G:CYS57 2.6 57.8 1.0 FE2 G:FES601 3.0 64.9 0.8 CB G:CYS57 3.4 46.6 1.0 CB G:CYS125 3.4 48.4 1.0 CA G:CYS125 3.7 46.1 1.0 N G:ASP126 4.2 50.0 1.0 SG G:CYS198 4.5 57.3 1.0 OD2 G:ASP126 4.5 54.1 1.0 C G:CYS125 4.5 49.0 1.0 CB G:GLU89 4.5 51.5 1.0 CB G:HIS197 4.6 41.9 1.0 CD1 E:TRP28 4.7 53.8 1.0 N G:CYS198 4.7 49.1 1.0 NE1 E:TRP28 4.7 49.3 1.0 CA G:HIS197 4.7 47.1 1.0 N G:GLU89 4.8 46.2 1.0 CG G:ASP126 4.8 53.2 1.0 N G:CYS125 4.8 40.1 1.0 CA G:CYS57 4.8 46.8 1.0

Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe601 b:64.9 occ:0.82 FE2 G:FES601 0.0 64.9 0.8 S1 G:FES601 2.2 45.7 0.8 S2 G:FES601 2.2 48.9 0.8 SG G:CYS198 2.5 57.3 1.0 FE1 G:FES601 3.0 46.6 0.8 O G:HOH707 3.3 52.2 1.0 OD1 G:ASP126 3.5 54.1 1.0 OD2 G:ASP126 3.6 54.1 1.0 CG G:ASP126 3.8 53.2 1.0 CB G:CYS198 3.8 51.3 1.0 O2 G:CO2603 4.0 57.7 1.0 C G:CO2603 4.3 60.2 1.0 NE1 E:TRP28 4.3 49.3 1.0 CB G:GLU89 4.4 51.5 1.0 OE2 G:GLU89 4.5 60.8 1.0 N G:CYS198 4.6 49.1 1.0 CA G:CYS198 4.8 46.3 1.0 SG G:CYS125 4.8 55.2 1.0 CE2 E:TRP28 4.9 55.8 1.0 O1 G:CO2603 4.9 58.1 1.0 CG G:GLU89 4.9 52.2 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.