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Iron in PDB 6i0p: Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid

Enzymatic activity of Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid

All present enzymatic activity of Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid:
2.5.1.72;

Protein crystallography data

The structure of Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid, PDB code: 6i0p 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) 46.49 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.500, 48.700, 60.600, 90.00, 107.00, 90.00
R / Rfree (%) 17 / 20

Other elements in 6i0p:

The structure of Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Quinolinate Synthase in Complex with 6-Mercaptopyridine- 2,3-Dicarboxylic Acid (pdb code 6i0p). 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 6-Mercaptopyridine- 2,3-Dicarboxylic Acid, PDB code: 6i0p:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6i0p

Go back to Iron Binding Sites List in 6i0p
Iron binding site 1 out of 4 in the Structure of Quinolinate Synthase in Complex with 6-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 6-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.3
occ:1.00
 FE1 A:SF4301 0.0 27.3 1.0
S2 A:SF4301 2.2 26.9 1.0
SG A:CYS168 2.3 27.8 1.0
S4 A:SF4301 2.4 27.6 1.0
S3 A:SF4301 2.4 28.6 1.0
FE3 A:SF4301 2.7 25.3 1.0
FE4 A:SF4301 2.8 23.7 1.0
FE2 A:SF4301 3.0 25.7 1.0
CB A:CYS168 3.4 28.9 1.0
S1 A:SF4301 4.0 24.8 1.0
CA A:CYS168 4.2 29.3 1.0
CG2 A:VAL170 4.2 30.1 1.0
CB A:VAL170 4.3 27.7 1.0
ND1 A:HIS171 4.7 25.2 1.0
C A:CYS168 4.8 29.8 1.0
CD A:PRO169 4.9 31.3 1.0
SG A:CYS81 4.9 26.8 1.0
OE1 A:GLU195 4.9 31.2 1.0
CE1 A:HIS171 5.0 24.1 1.0
S A:QAS302 5.0 28.6 1.0
N A:VAL170 5.0 28.7 1.0
SG A:CYS254 5.0 26.0 1.0

Iron binding site 2 out of 4 in 6i0p

Go back to Iron Binding Sites List in 6i0p
Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase in Complex with 6-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 6-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:25.7
occ:1.00
 FE2 A:SF4301 0.0 25.7 1.0
S1 A:SF4301 2.3 24.8 1.0
SG A:CYS254 2.3 26.0 1.0
S4 A:SF4301 2.4 27.6 1.0
S3 A:SF4301 2.5 28.6 1.0
FE3 A:SF4301 2.8 25.3 1.0
FE4 A:SF4301 2.9 23.7 1.0
FE1 A:SF4301 3.0 27.3 1.0
CB A:CYS254 3.4 22.6 1.0
S2 A:SF4301 4.0 26.9 1.0
CG2 A:VAL170 4.4 30.1 1.0
O A:HOH564 4.5 29.2 1.0
CA A:CYS254 4.6 23.2 1.0
CG A:MET257 4.6 20.6 1.0
S A:QAS302 4.7 28.6 1.0
SG A:CYS81 5.0 26.8 1.0

Iron binding site 3 out of 4 in 6i0p

Go back to Iron Binding Sites List in 6i0p
Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase in Complex with 6-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 6-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:25.3
occ:1.00
 FE3 A:SF4301 0.0 25.3 1.0
S4 A:SF4301 2.2 27.6 1.0
S2 A:SF4301 2.3 26.9 1.0
S A:QAS302 2.3 28.6 1.0
S1 A:SF4301 2.4 24.8 1.0
FE1 A:SF4301 2.7 27.3 1.0
FE2 A:SF4301 2.8 25.7 1.0
FE4 A:SF4301 2.9 23.7 1.0
C6 A:QAS302 3.4 27.5 1.0
C5 A:QAS302 3.6 26.8 1.0
ND2 A:ASN109 3.8 32.9 1.0
S3 A:SF4301 3.9 28.6 1.0
CE2 A:PHE21 4.3 19.6 1.0
CD2 A:PHE21 4.6 20.2 1.0
N1 A:QAS302 4.6 27.3 1.0
SG A:CYS81 4.7 26.8 1.0
SG A:CYS168 4.7 27.8 1.0
SG A:CYS254 4.8 26.0 1.0
CE A:MET257 4.9 20.5 1.0
C4 A:QAS302 5.0 26.9 1.0

Iron binding site 4 out of 4 in 6i0p

Go back to Iron Binding Sites List in 6i0p
Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase in Complex with 6-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 6-Mercaptopyridine- 2,3-Dicarboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:23.7
occ:1.00
 FE4 A:SF4301 0.0 23.7 1.0
SG A:CYS81 2.2 26.8 1.0
S3 A:SF4301 2.3 28.6 1.0
S1 A:SF4301 2.4 24.8 1.0
S2 A:SF4301 2.5 26.9 1.0
FE1 A:SF4301 2.8 27.3 1.0
FE2 A:SF4301 2.9 25.7 1.0
FE3 A:SF4301 2.9 25.3 1.0
CB A:CYS81 3.2 24.3 1.0
CA A:CYS81 3.7 23.2 1.0
S4 A:SF4301 4.0 27.6 1.0
C A:CYS81 4.4 24.7 1.0
CD A:PRO82 4.4 29.4 1.0
CB A:MET83 4.5 29.9 1.0
N A:PRO82 4.6 28.0 1.0
S A:QAS302 4.7 28.6 1.0
N A:MET83 4.7 29.2 1.0
ND2 A:ASN109 4.7 32.9 1.0
CE A:MET83 4.7 32.7 1.0
SG A:CYS168 4.9 27.8 1.0

Reference:

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
Page generated: Tue Aug 6 21:58:37 2024

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