Iron in PDB 6f4l: Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate

All present enzymatic activity of Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate:
2.5.1.72;

The structure of Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate, PDB code: 6f4l 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)	46.95 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.440, 49.310, 61.900, 90.00, 107.21, 90.00
R / Rfree (%)	20.2 / 22

The structure of Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate (pdb code 6f4l). 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 with Inhibitor-Derived Quinolinate, PDB code: 6f4l:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate


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 with Inhibitor-Derived Quinolinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:79.1 occ:1.00 FE1 A:SF4301 0.0 79.1 1.0 S2 A:SF4301 2.3 74.0 1.0 SG A:CYS168 2.3 70.5 1.0 S4 A:SF4301 2.4 78.6 1.0 S3 A:SF4301 2.4 77.4 1.0 FE4 A:SF4301 2.7 76.4 1.0 FE3 A:SF4301 2.8 78.2 1.0 FE2 A:SF4301 2.8 76.8 1.0 CB A:CYS168 3.3 63.3 1.0 S1 A:SF4301 4.0 77.7 1.0 OE1 A:GLU195 4.1 65.9 1.0 CA A:CYS168 4.2 61.8 1.0 CG2 A:VAL170 4.4 50.5 1.0 CB A:VAL170 4.4 48.9 1.0 CD A:PRO169 4.6 58.2 1.0 ND1 A:HIS171 4.6 49.2 1.0 C A:CYS168 4.8 60.6 1.0 SG A:CYS254 4.8 54.4 1.0 CE1 A:HIS171 4.9 49.0 1.0 SG A:CYS81 5.0 70.7 1.0 N A:PRO169 5.0 58.3 1.0 N A:VAL170 5.0 50.7 1.0

Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate


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 with Inhibitor-Derived Quinolinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:76.8 occ:1.00 FE2 A:SF4301 0.0 76.8 1.0 S1 A:SF4301 2.3 77.7 1.0 S4 A:SF4301 2.3 78.6 1.0 SG A:CYS254 2.4 54.4 1.0 S3 A:SF4301 2.4 77.4 1.0 FE4 A:SF4301 2.8 76.4 1.0 FE3 A:SF4301 2.8 78.2 1.0 FE1 A:SF4301 2.8 79.1 1.0 CB A:CYS254 3.8 47.8 1.0 S2 A:SF4301 4.1 74.0 1.0 CG2 A:VAL170 4.5 50.5 1.0 SG A:CYS81 4.7 70.7 1.0 CA A:CYS254 4.9 48.3 1.0 SG A:CYS168 4.9 70.5 1.0 CG A:MET257 5.0 43.5 1.0

Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate


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 with Inhibitor-Derived Quinolinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:78.2 occ:1.00 FE3 A:SF4301 0.0 78.2 1.0 S4 A:SF4301 2.3 78.6 1.0 S2 A:SF4301 2.4 74.0 1.0 S1 A:SF4301 2.4 77.7 1.0 FE1 A:SF4301 2.8 79.1 1.0 FE2 A:SF4301 2.8 76.8 1.0 FE4 A:SF4301 2.8 76.4 1.0 C5 A:NTM302 3.5 75.6 1.0 S3 A:SF4301 4.0 77.4 1.0 C6 A:NTM302 4.1 74.7 1.0 CE2 A:TYR21 4.3 36.8 1.0 C4 A:NTM302 4.4 75.3 1.0 CD2 A:TYR21 4.5 36.0 1.0 SG A:CYS81 4.7 70.7 1.0 SG A:CYS254 4.7 54.4 1.0 SG A:CYS168 4.9 70.5 1.0 CE A:MET257 4.9 40.2 1.0

Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase with Inhibitor-Derived Quinolinate


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 with Inhibitor-Derived Quinolinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:76.4 occ:1.00 FE4 A:SF4301 0.0 76.4 1.0 S3 A:SF4301 2.3 77.4 1.0 SG A:CYS81 2.3 70.7 1.0 S1 A:SF4301 2.4 77.7 1.0 S2 A:SF4301 2.5 74.0 1.0 FE1 A:SF4301 2.7 79.1 1.0 FE2 A:SF4301 2.8 76.8 1.0 FE3 A:SF4301 2.8 78.2 1.0 CB A:CYS81 3.6 62.9 1.0 S4 A:SF4301 4.0 78.6 1.0 CE A:MET83 4.2 72.3 1.0 CA A:CYS81 4.3 60.6 1.0 CB A:MET83 4.5 67.3 1.0 SG A:CYS168 4.7 70.5 1.0 C A:CYS81 4.9 61.9 1.0 CB A:CYS168 4.9 63.3 1.0

A.Volbeda, J.Saez Cabodevilla, C.Darnault, O.Gigarel, T.H.Han, O.Renoux, O.Hamelin, S.Ollagnier-De-Choudens, P.Amara, J.C.Fontecilla-Camps. Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis By Nada. Acs Chem. Biol. V. 13 1209 2018.
ISSN: ESSN 1554-8937
PubMed: 29641168
DOI: 10.1021/ACSCHEMBIO.7B01104