Iron in PDB 6i0r: Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid

All present enzymatic activity of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid:
2.5.1.72;

The structure of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid, PDB code: 6i0r was solved by A.Volbeda, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.16 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.900, 48.500, 60.500, 90.00, 107.10, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Iron atom in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid (pdb code 6i0r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid, PDB code: 6i0r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:42.8 occ:1.00 OE1 A:GLU195 2.1 36.8 1.0 S A:H2S303 2.1 46.3 1.0 S A:H2S304 2.2 43.5 1.0 SG A:CYS168 2.3 46.2 1.0 FE A:FE302 2.5 44.8 1.0 CD A:GLU195 3.0 37.3 1.0 CB A:CYS168 3.2 49.6 1.0 OE2 A:GLU195 3.2 36.5 1.0 ND1 A:HIS171 3.7 38.0 1.0 CE1 A:HIS171 3.9 38.0 1.0 S A:QAT309 4.2 43.8 0.8 C6 A:QAT309 4.2 39.8 1.0 CG A:GLU195 4.4 37.9 1.0 O A:HOH442 4.4 54.0 1.0 FE A:FE305 4.4 40.4 0.5 CA A:CYS168 4.6 49.9 1.0 S A:H2S307 4.6 48.5 1.0 FE A:FE306 4.8 45.2 0.5 C5 A:QAT309 4.8 41.4 1.0 CB A:GLU195 4.8 36.1 1.0 S A:H2S308 4.8 50.0 0.5

Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:44.8 occ:1.00 S A:QAT309 2.2 43.8 0.8 S A:H2S303 2.2 46.3 1.0 S A:H2S304 2.2 43.5 1.0 S A:H2S307 2.5 48.5 1.0 FE A:FE301 2.5 42.8 1.0 FE A:FE305 3.2 40.4 0.5 C5 A:QAT309 3.3 41.4 1.0 C6 A:QAT309 3.5 39.8 1.0 FE A:FE306 3.7 45.2 0.5 OE2 A:GLU195 4.2 36.5 1.0 OE1 A:GLU195 4.3 36.8 1.0 SG A:CYS81 4.4 42.7 1.0 SG A:CYS168 4.4 46.2 1.0 C4 A:QAT309 4.6 39.6 1.0 S A:H2S308 4.6 50.0 0.5 CD A:GLU195 4.7 37.3 1.0 N1 A:QAT309 4.8 37.1 1.0 ND2 A:ASN109 4.8 42.0 1.0 CB A:ASN109 4.9 36.2 1.0

Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe305 b:40.4 occ:0.50 S A:H2S307 2.2 48.5 1.0 SG A:CYS81 2.2 42.7 1.0 S A:H2S308 3.1 50.0 0.5 CB A:CYS81 3.1 40.3 1.0 FE A:FE302 3.2 44.8 1.0 FE A:FE306 3.2 45.2 0.5 S A:H2S303 3.4 46.3 1.0 O A:HOH488 3.5 50.5 1.0 CA A:CYS81 3.6 39.3 1.0 C A:CYS81 4.4 40.6 1.0 S A:H2S304 4.4 43.5 1.0 FE A:FE301 4.4 42.8 1.0 CD A:PRO82 4.5 42.5 1.0 S A:QAT309 4.7 43.8 0.8 N A:PRO82 4.8 41.8 1.0 N A:CYS81 4.8 37.4 1.0 SG A:CYS254 4.9 46.5 1.0 O A:THR80 4.9 32.8 1.0 SG A:CYS168 4.9 46.2 1.0

Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Quinolinate Synthase in Complex with 5-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe306 b:45.2 occ:0.50 SG A:CYS254 2.2 46.5 1.0 S A:H2S308 2.2 50.0 0.5 S A:H2S307 2.6 48.5 1.0 CB A:CYS254 3.1 44.2 1.0 FE A:FE305 3.2 40.4 0.5 S A:H2S304 3.3 43.5 1.0 FE A:FE302 3.7 44.8 1.0 CG2 A:VAL170 4.3 49.1 1.0 CA A:CYS254 4.3 41.3 1.0 CG A:MET257 4.5 32.0 1.0 FE A:FE301 4.8 42.8 1.0

J.Saez Cabodevilla, A.Volbeda, O.Hamelin, J.M.Latour, O.Gigarel, M.Clemancey, C.Darnault, D.Reichmann, P.Amara, J.C.Fontecilla-Camps, S.Ollagnier De Choudens. Design of Specific Inhibitors of Quinolinate Synthase Based on [4FE-4S] Cluster Coordination. Chem.Commun.(Camb.) V. 55 3725 2019.
ISSN: ESSN 1364-548X
PubMed: 30855610
DOI: 10.1039/C8CC09023H