Iron in PDB 5f3d: Structure of Quinolinate Synthase in Complex with Reaction Intermediate W

All present enzymatic activity of Structure of Quinolinate Synthase in Complex with Reaction Intermediate W:
2.5.1.72;

The structure of Structure of Quinolinate Synthase in Complex with Reaction Intermediate W, PDB code: 5f3d 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)	45.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.902, 49.029, 60.520, 90.00, 105.40, 90.00
R / Rfree (%)	17 / 21.1

The binding sites of Iron atom in the Structure of Quinolinate Synthase in Complex with Reaction Intermediate W (pdb code 5f3d). 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 Reaction Intermediate W, PDB code: 5f3d:
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 Reaction Intermediate W


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 Reaction Intermediate W within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:29.9 occ:1.00 FE1 A:SF4301 0.0 29.9 1.0 S4 A:SF4301 2.3 31.0 1.0 S2 A:SF4301 2.3 28.3 1.0 SG A:CYS168 2.3 28.5 1.0 S3 A:SF4301 2.4 28.4 1.0 FE3 A:SF4301 2.7 33.4 1.0 FE2 A:SF4301 2.8 30.6 1.0 FE4 A:SF4301 2.8 27.1 1.0 CB A:CYS168 3.4 33.4 1.0 CG2 A:VAL170 3.8 32.5 1.0 S1 A:SF4301 3.9 26.1 1.0 CB A:VAL170 4.2 31.1 1.0 CA A:CYS168 4.2 31.1 1.0 OE1 A:GLU195 4.3 44.4 1.0 ND1 A:HIS171 4.6 27.8 1.0 OAB A:5UK302 4.7 35.4 1.0 OAG A:5UK302 4.7 52.1 1.0 C A:CYS168 4.8 31.9 1.0 CD A:PRO169 4.8 33.8 1.0 SG A:CYS81 4.8 27.4 1.0 SG A:CYS254 4.8 23.4 1.0 N A:VAL170 4.9 29.3 1.0 CE1 A:HIS171 4.9 28.2 1.0

Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase in Complex with Reaction Intermediate W


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 Reaction Intermediate W within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:30.6 occ:1.00 FE2 A:SF4301 0.0 30.6 1.0 S3 A:SF4301 2.3 28.4 1.0 SG A:CYS254 2.3 23.4 1.0 S4 A:SF4301 2.3 31.0 1.0 S1 A:SF4301 2.4 26.1 1.0 FE1 A:SF4301 2.8 29.9 1.0 FE4 A:SF4301 2.8 27.1 1.0 FE3 A:SF4301 2.9 33.4 1.0 CB A:CYS254 3.4 22.6 1.0 O A:HOH584 4.0 40.4 1.0 S2 A:SF4301 4.0 28.3 1.0 CG2 A:VAL170 4.2 32.5 1.0 CA A:CYS254 4.5 21.9 1.0 OAB A:5UK302 4.6 35.4 1.0 CG A:MET257 4.7 23.9 1.0 SG A:CYS168 4.9 28.5 1.0 SG A:CYS81 4.9 27.4 1.0

Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase in Complex with Reaction Intermediate W


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 Reaction Intermediate W within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:33.4 occ:1.00 FE3 A:SF4301 0.0 33.4 1.0 OAB A:5UK302 2.1 35.4 1.0 S2 A:SF4301 2.3 28.3 1.0 S1 A:SF4301 2.3 26.1 1.0 S4 A:SF4301 2.4 31.0 1.0 FE4 A:SF4301 2.7 27.1 1.0 FE1 A:SF4301 2.7 29.9 1.0 FE2 A:SF4301 2.9 30.6 1.0 CAH A:5UK302 3.0 47.5 1.0 OAG A:5UK302 3.4 52.1 1.0 CAM A:5UK302 3.5 50.4 1.0 ND2 A:ASN109 3.7 41.4 1.0 S3 A:SF4301 4.0 28.4 1.0 CE2 A:TYR21 4.3 21.7 1.0 CD2 A:TYR21 4.6 21.5 1.0 SG A:CYS81 4.7 27.4 1.0 SG A:CYS168 4.8 28.5 1.0 CAI A:5UK302 4.8 47.1 1.0 SG A:CYS254 4.9 23.4 1.0 OE1 A:GLU195 4.9 44.4 1.0 CE A:MET257 4.9 21.8 1.0 CG A:ASN109 4.9 39.1 1.0

Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase in Complex with Reaction Intermediate W


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 Reaction Intermediate W within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:27.1 occ:1.00 FE4 A:SF4301 0.0 27.1 1.0 S1 A:SF4301 2.2 26.1 1.0 SG A:CYS81 2.3 27.4 1.0 S3 A:SF4301 2.4 28.4 1.0 S2 A:SF4301 2.4 28.3 1.0 FE3 A:SF4301 2.7 33.4 1.0 FE2 A:SF4301 2.8 30.6 1.0 FE1 A:SF4301 2.8 29.9 1.0 CB A:CYS81 3.1 24.5 1.0 ND2 A:ASN109 3.6 41.4 1.0 CA A:CYS81 3.8 24.3 1.0 S4 A:SF4301 4.0 31.0 1.0 OAB A:5UK302 4.5 35.4 1.0 CG A:ASN109 4.5 39.1 1.0 CD A:PRO82 4.6 36.1 1.0 C A:CYS81 4.6 27.7 1.0 CE A:MET83 4.7 53.2 0.5 N A:PRO82 4.8 32.8 1.0 SG A:CYS168 4.9 28.5 1.0 SG A:CYS254 4.9 23.4 1.0

A.Volbeda, C.Darnault, O.Renoux, D.Reichmann, P.Amara, S.Ollagnier De Choudens, J.C.Fontecilla-Camps. Crystal Structures of Quinolinate Synthase in Complex with A Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product. J.Am.Chem.Soc. V. 138 11802 2016.
ISSN: ESSN 1520-5126
PubMed: 27545412
DOI: 10.1021/JACS.6B05884