Iron in PDB 8epz: Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mn

The structure of Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mn, PDB code: 8epz 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)	48.11 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	96.639, 113.135, 182.891, 90, 90, 90
R / Rfree (%)	21 / 25.1

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

Manganese

(Mn)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mn (pdb code 8epz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Fe-S Cluster-Dependent Dehydratase From Paralcaligenes Ureilyticus in Complex with Mn, PDB code: 8epz:
Jump to Iron binding site number: 1; 2; 3; 4;

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


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:77.1 occ:1.00 FE1 A:FES601 0.0 77.1 1.0 S1 A:FES601 2.2 63.9 1.0 S2 A:FES601 2.2 76.1 1.0 SG A:CYS198 2.8 56.8 1.0 FE2 A:FES601 3.0 67.9 1.0 OD1 A:ASP126 3.3 69.2 1.0 CB A:CYS198 3.9 52.6 1.0 NE1 B:TRP28 4.1 49.6 1.0 CG A:ASP126 4.1 67.2 1.0 O2 A:CO2603 4.1 56.9 1.0 O2 B:BCT701 4.3 71.6 1.0 OD2 A:ASP126 4.5 78.4 1.0 OE2 A:GLU89 4.5 82.6 1.0 N A:CYS198 4.6 52.4 1.0 CE2 B:TRP28 4.6 53.1 1.0 C A:CO2603 4.7 65.7 1.0 CZ2 B:TRP28 4.7 53.5 1.0 CA A:CYS198 4.8 58.1 1.0 CD1 B:TRP28 4.9 53.8 1.0 CB A:GLU89 5.0 63.3 1.0

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


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:67.9 occ:1.00 FE2 A:FES601 0.0 67.9 1.0 S1 A:FES601 2.2 63.9 1.0 S2 A:FES601 2.2 76.1 1.0 SG A:CYS57 2.8 66.2 1.0 SG A:CYS125 2.9 73.6 1.0 FE1 A:FES601 3.0 77.1 1.0 CB A:CYS125 3.7 59.9 1.0 CB A:CYS57 3.7 58.2 1.0 CA A:CYS125 3.9 64.9 1.0 OD1 A:ASP126 4.0 69.2 1.0 N A:ASP126 4.1 67.4 1.0 CB A:HIS197 4.5 54.6 1.0 C A:CYS125 4.6 67.7 1.0 N A:CYS198 4.6 52.4 1.0 CA A:HIS197 4.6 58.1 1.0 NE1 B:TRP28 4.7 49.6 1.0 CD1 B:TRP28 4.7 53.8 1.0 CG A:ASP126 4.8 67.2 1.0 N A:GLU89 4.9 50.1 1.0 CB A:ALA204 4.9 53.4 1.0 SG A:CYS198 5.0 56.8 1.0 CB A:GLU89 5.0 63.3 1.0

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


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:62.4 occ:0.83 FE1 B:FES702 0.0 62.4 0.8 S2 B:FES702 2.2 72.2 0.8 S1 B:FES702 2.2 59.1 0.8 SG B:CYS57 2.6 52.6 1.0 SG B:CYS125 2.6 66.5 1.0 FE2 B:FES702 3.0 65.0 0.8 CB B:CYS57 3.3 56.9 1.0 CB B:CYS125 3.7 65.1 1.0 CA B:CYS125 3.8 64.6 1.0 N B:ASP126 4.2 56.5 1.0 NE1 A:TRP28 4.3 62.5 1.0 CD1 A:TRP28 4.4 61.3 1.0 C B:CYS125 4.4 63.8 1.0 CB B:HIS197 4.6 54.3 1.0 CA B:CYS57 4.6 51.4 1.0 N B:CYS198 4.7 52.4 1.0 CA B:HIS197 4.8 53.9 1.0 N B:CYS57 4.8 59.4 1.0 SG B:CYS198 4.8 57.3 1.0 OD2 B:ASP126 4.9 53.6 1.0 N B:GLU89 4.9 56.3 1.0 CB B:GLU89 5.0 59.3 1.0 CB B:ASP126 5.0 53.8 1.0

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


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 Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:65.0 occ:0.83 FE2 B:FES702 0.0 65.0 0.8 S2 B:FES702 2.2 72.2 0.8 S1 B:FES702 2.2 59.1 0.8 SG B:CYS198 2.6 57.3 1.0 FE1 B:FES702 3.0 62.4 0.8 O B:HOH807 3.5 59.7 1.0 OD2 B:ASP126 3.5 53.6 1.0 CB B:CYS198 3.6 58.5 1.0 NE1 A:TRP28 3.9 62.5 1.0 CG B:ASP126 4.0 62.1 1.0 OD1 B:ASP126 4.4 81.3 1.0 CE2 A:TRP28 4.4 64.4 1.0 N B:CYS198 4.4 52.4 1.0 CZ2 A:TRP28 4.5 72.6 1.0 CA B:CYS198 4.5 59.0 1.0 CB B:ASP126 4.7 53.8 1.0 SG B:CYS57 4.7 52.6 1.0 O1 B:CO2704 4.7 70.2 1.0 OE2 B:GLU89 4.8 71.4 1.0 CD1 A:TRP28 4.8 61.3 1.0 O2 A:CO2604 4.8 64.6 1.0 CB B:GLU89 4.8 59.3 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.