Iron in PDB 5f35: Structure of Quinolinate Synthase in Complex with Citrate

All present enzymatic activity of Structure of Quinolinate Synthase in Complex with Citrate:
2.5.1.72;

The structure of Structure of Quinolinate Synthase in Complex with Citrate, PDB code: 5f35 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)	27.77 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.948, 49.300, 62.701, 90.00, 104.25, 90.00
R / Rfree (%)	12.8 / 17.7

The structure of Structure of Quinolinate Synthase in Complex with Citrate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Structure of Quinolinate Synthase in Complex with Citrate (pdb code 5f35). 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 Citrate, PDB code: 5f35:
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 Citrate


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 Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.6 occ:1.00 FE1 A:SF4301 0.0 16.6 1.0 SG A:CYS168 2.3 15.5 1.0 S2 A:SF4301 2.3 16.7 1.0 S4 A:SF4301 2.3 17.3 1.0 S3 A:SF4301 2.4 17.0 1.0 FE3 A:SF4301 2.7 19.9 1.0 FE4 A:SF4301 2.7 16.4 1.0 FE2 A:SF4301 2.8 16.7 1.0 CB A:CYS168 3.5 13.8 1.0 S1 A:SF4301 3.9 17.3 1.0 OE1 A:GLU195 4.0 27.7 1.0 CG2 A:VAL170 4.1 20.4 1.0 CB A:VAL170 4.2 17.6 1.0 CA A:CYS168 4.3 14.7 1.0 OA1 A:FLC302 4.4 12.9 0.5 ND1 A:HIS171 4.5 17.7 1.0 OG1 A:FLC302 4.6 18.8 0.5 SG A:CYS81 4.8 16.1 1.0 CD A:PRO169 4.8 24.7 1.0 N A:VAL170 4.8 16.8 1.0 CE1 A:HIS171 4.9 15.7 1.0 C A:CYS168 4.9 17.5 1.0 SG A:CYS254 4.9 14.3 1.0

Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase in Complex with Citrate


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 Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.7 occ:1.00 FE2 A:SF4301 0.0 16.7 1.0 S1 A:SF4301 2.3 17.3 1.0 S3 A:SF4301 2.3 17.0 1.0 SG A:CYS254 2.4 14.3 1.0 S4 A:SF4301 2.4 17.3 1.0 FE4 A:SF4301 2.8 16.4 1.0 FE3 A:SF4301 2.8 19.9 1.0 FE1 A:SF4301 2.8 16.6 1.0 CB A:CYS254 3.4 14.2 1.0 S2 A:SF4301 4.1 16.7 1.0 O A:HOH586 4.3 19.2 1.0 CG2 A:VAL170 4.4 20.4 1.0 CA A:CYS254 4.5 12.3 1.0 OA1 A:FLC302 4.5 12.9 0.5 CG A:MET257 4.7 10.8 1.0 SG A:CYS168 4.9 15.5 1.0 SG A:CYS81 4.9 16.1 1.0

Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase in Complex with Citrate


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 Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:19.9 occ:1.00 FE3 A:SF4301 0.0 19.9 1.0 OA1 A:FLC302 2.0 12.9 0.5 S1 A:SF4301 2.3 17.3 1.0 S2 A:SF4301 2.3 16.7 1.0 S4 A:SF4301 2.4 17.3 1.0 FE1 A:SF4301 2.7 16.6 1.0 FE4 A:SF4301 2.7 16.4 1.0 FE2 A:SF4301 2.8 16.7 1.0 OG1 A:FLC302 2.9 18.8 0.5 CAC A:FLC302 3.0 14.5 0.5 OG2 A:FLC302 3.3 21.1 0.5 CGC A:FLC302 3.3 17.4 0.5 OA2 A:FLC302 3.4 13.4 0.5 ND2 A:ASN109 3.8 22.4 0.5 S3 A:SF4301 4.0 17.0 1.0 ND2 A:ASN109 4.0 21.0 0.5 CE2 A:TYR21 4.2 11.1 1.0 CA A:FLC302 4.3 15.0 0.5 CG A:FLC302 4.5 15.2 0.5 OE1 A:GLU195 4.5 27.7 1.0 CD2 A:TYR21 4.6 9.6 1.0 SG A:CYS168 4.6 15.5 1.0 SG A:CYS81 4.7 16.1 1.0 OE2 A:GLU195 4.8 20.1 1.0 SG A:CYS254 4.9 14.3 1.0 CG A:ASN109 5.0 22.6 0.5

Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase in Complex with Citrate


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 Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:16.4 occ:1.00 FE4 A:SF4301 0.0 16.4 1.0 SG A:CYS81 2.3 16.1 1.0 S2 A:SF4301 2.3 16.7 1.0 S1 A:SF4301 2.3 17.3 1.0 S3 A:SF4301 2.4 17.0 1.0 FE3 A:SF4301 2.7 19.9 1.0 FE1 A:SF4301 2.7 16.6 1.0 FE2 A:SF4301 2.8 16.7 1.0 CB A:CYS81 3.3 16.1 1.0 ND2 A:ASN109 3.9 22.4 0.5 CA A:CYS81 3.9 14.5 1.0 S4 A:SF4301 4.0 17.3 1.0 ND2 A:ASN109 4.0 21.0 0.5 CG A:ASN109 4.5 22.6 0.5 OA1 A:FLC302 4.5 12.9 0.5 C A:CYS81 4.6 14.9 1.0 CD A:PRO82 4.7 19.2 1.0 SG A:CYS168 4.8 15.5 1.0 N A:PRO82 4.8 17.3 1.0 CE A:MET83 4.8 22.9 0.4 CB A:MET83 4.9 25.2 0.4 CB A:MET83 5.0 23.9 0.6 SG A:CYS254 5.0 14.3 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