Iron in PDB 6f48: Structure of Quinolinate Synthase with Reaction Intermediates X and Y

All present enzymatic activity of Structure of Quinolinate Synthase with Reaction Intermediates X and Y:
2.5.1.72;

The structure of Structure of Quinolinate Synthase with Reaction Intermediates X and Y, PDB code: 6f48 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)	37.50 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.500, 48.950, 61.250, 90.00, 107.27, 90.00
R / Rfree (%)	13.4 / 17.9

The structure of Structure of Quinolinate Synthase with Reaction Intermediates X and Y also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Structure of Quinolinate Synthase with Reaction Intermediates X and Y (pdb code 6f48). 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 Reaction Intermediates X and Y, PDB code: 6f48:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Quinolinate Synthase with Reaction Intermediates X and Y


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 Reaction Intermediates X and Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:23.0 occ:1.00 FE1 A:SF4301 0.0 23.0 1.0 S2 A:SF4301 2.3 24.1 1.0 S4 A:SF4301 2.3 22.7 1.0 SG A:CYS168 2.3 22.7 1.0 S3 A:SF4301 2.3 24.7 1.0 FE3 A:SF4301 2.7 24.1 1.0 FE4 A:SF4301 2.7 22.5 1.0 FE2 A:SF4301 2.8 22.6 1.0 CB A:CYS168 3.4 21.5 1.0 S1 A:SF4301 4.0 23.5 1.0 OAB A:XQB302 4.1 20.1 0.4 CG2 A:VAL170 4.2 30.2 1.0 CA A:CYS168 4.2 21.6 1.0 CB A:VAL170 4.3 25.4 1.0 O9 A:YQA305 4.4 24.9 0.4 OE1 A:GLU195 4.5 36.6 1.0 ND1 A:HIS171 4.7 23.0 1.0 OAG A:XQB302 4.7 26.0 0.4 CD A:PRO169 4.8 29.5 1.0 SG A:CYS81 4.8 21.9 1.0 C A:CYS168 4.8 22.8 1.0 CAH A:XQB302 4.9 23.1 0.4 SG A:CYS254 4.9 19.2 1.0 N A:VAL170 4.9 22.0 1.0

Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase with Reaction Intermediates X and Y


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 Reaction Intermediates X and Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.6 occ:1.00 FE2 A:SF4301 0.0 22.6 1.0 S1 A:SF4301 2.3 23.5 1.0 S4 A:SF4301 2.3 22.7 1.0 SG A:CYS254 2.3 19.2 1.0 S3 A:SF4301 2.4 24.7 1.0 FE3 A:SF4301 2.7 24.1 1.0 FE4 A:SF4301 2.8 22.5 1.0 FE1 A:SF4301 2.8 23.0 1.0 CB A:CYS254 3.5 16.3 1.0 S2 A:SF4301 4.0 24.1 1.0 CG2 A:VAL170 4.4 30.2 1.0 O A:HOH589 4.4 26.0 1.0 CA A:CYS254 4.6 15.9 1.0 OAG A:XQB302 4.6 26.0 0.4 O9 A:YQA305 4.6 24.9 0.4 CG A:MET257 4.8 16.4 1.0 SG A:CYS168 4.9 22.7 1.0 SG A:CYS81 4.9 21.9 1.0

Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase with Reaction Intermediates X and Y


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 Reaction Intermediates X and Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.1 occ:1.00 FE3 A:SF4301 0.0 24.1 1.0 O9 A:YQA305 2.0 24.9 0.4 OAG A:XQB302 2.1 26.0 0.4 S4 A:SF4301 2.3 22.7 1.0 S2 A:SF4301 2.4 24.1 1.0 S1 A:SF4301 2.4 23.5 1.0 O A:HOH630 2.6 25.0 0.2 FE4 A:SF4301 2.7 22.5 1.0 FE1 A:SF4301 2.7 23.0 1.0 FE2 A:SF4301 2.7 22.6 1.0 CAM A:XQB302 3.0 25.6 0.4 OAB A:XQB302 3.0 20.1 0.4 CAH A:XQB302 3.2 23.1 0.4 C5 A:YQA305 3.3 25.7 0.4 S3 A:SF4301 3.9 24.7 1.0 ND2 A:ASN109 3.9 34.9 1.0 C6 A:YQA305 4.2 26.4 0.4 C4 A:YQA305 4.3 26.4 0.4 CAI A:XQB302 4.3 26.6 0.4 CE2 A:PHE21 4.4 17.6 1.0 SG A:CYS81 4.6 21.9 1.0 CD2 A:PHE21 4.6 17.0 1.0 SG A:CYS168 4.7 22.7 1.0 SG A:CYS254 4.8 19.2 1.0 CE A:MET257 4.9 17.6 1.0 O A:HOH652 5.0 10.7 0.2

Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase with Reaction Intermediates X and Y


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 Reaction Intermediates X and Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.5 occ:1.00 FE4 A:SF4301 0.0 22.5 1.0 SG A:CYS81 2.3 21.9 1.0 S1 A:SF4301 2.3 23.5 1.0 S3 A:SF4301 2.3 24.7 1.0 S2 A:SF4301 2.3 24.1 1.0 FE3 A:SF4301 2.7 24.1 1.0 FE1 A:SF4301 2.7 23.0 1.0 FE2 A:SF4301 2.8 22.6 1.0 CB A:CYS81 3.3 21.5 1.0 CA A:CYS81 3.8 17.9 1.0 S4 A:SF4301 3.9 22.7 1.0 OAG A:XQB302 4.2 26.0 0.4 C A:CYS81 4.4 18.2 1.0 CD A:PRO82 4.5 21.8 1.0 N A:PRO82 4.5 19.0 1.0 O9 A:YQA305 4.5 24.9 0.4 ND2 A:ASN109 4.6 34.9 1.0 CB A:MET83 4.6 24.3 1.0 N A:MET83 4.7 21.9 1.0 O A:HOH630 4.8 25.0 0.2 SG A:CYS168 4.9 22.7 1.0 SG A:CYS254 5.0 19.2 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