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Iron in PDB 5lqs: Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate

Enzymatic activity of Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate

All present enzymatic activity of Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate:
2.5.1.72;

Protein crystallography data

The structure of Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate, PDB code: 5lqs 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) 40.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.060, 48.740, 60.250, 90.00, 103.67, 90.00
R / Rfree (%) 17.6 / 21.4

Other elements in 5lqs:

The structure of Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-Derived Quinolinate (pdb code 5lqs). 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 Y21F Mutant in Complex with Substrate-Derived Quinolinate, PDB code: 5lqs:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5lqs

Go back to Iron Binding Sites List in 5lqs
Iron binding site 1 out of 4 in the Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-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 Y21F Mutant in Complex with Substrate-Derived Quinolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:15.6
occ:1.00
 FE1 A:SF4301 0.0 15.6 1.0
S2 A:SF4301 2.3 16.6 1.0
S4 A:SF4301 2.3 16.1 1.0
SG A:CYS168 2.3 17.6 1.0
S3 A:SF4301 2.4 16.1 1.0
FE4 A:SF4301 2.7 15.5 1.0
FE2 A:SF4301 2.7 16.6 1.0
FE3 A:SF4301 2.8 17.3 1.0
CB A:CYS168 3.4 20.1 1.0
S1 A:SF4301 3.9 16.4 1.0
N1 A:NTM302 4.0 17.2 0.7
C6 A:NTM302 4.1 16.9 0.7
CG2 A:VAL170 4.2 22.4 1.0
OE1 A:GLU195 4.2 29.4 1.0
CA A:CYS168 4.2 20.6 1.0
CB A:VAL170 4.3 21.3 1.0
ND1 A:HIS171 4.7 15.6 1.0
SG A:CYS81 4.8 15.6 1.0
C A:CYS168 4.8 22.0 1.0
SG A:CYS254 4.8 14.4 1.0
O1 A:NTM302 4.9 18.1 0.7
CD A:PRO169 4.9 24.2 1.0
CE1 A:HIS171 5.0 16.8 1.0
N A:VAL170 5.0 20.5 1.0

Iron binding site 2 out of 4 in 5lqs

Go back to Iron Binding Sites List in 5lqs
Iron binding site 2 out of 4 in the Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-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 Y21F Mutant in Complex with Substrate-Derived Quinolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:16.6
occ:1.00
 FE2 A:SF4301 0.0 16.6 1.0
S1 A:SF4301 2.3 16.4 1.0
SG A:CYS254 2.3 14.4 1.0
S4 A:SF4301 2.4 16.1 1.0
S3 A:SF4301 2.4 16.1 1.0
FE4 A:SF4301 2.7 15.5 1.0
FE1 A:SF4301 2.7 15.6 1.0
FE3 A:SF4301 2.9 17.3 1.0
CB A:CYS254 3.4 14.0 1.0
S2 A:SF4301 4.0 16.6 1.0
O A:HOH559 4.3 18.8 1.0
O1 A:NTM302 4.4 18.1 0.7
CG2 A:VAL170 4.4 22.4 1.0
CA A:CYS254 4.6 14.1 1.0
CG A:MET257 4.6 11.7 1.0
N1 A:NTM302 4.7 17.2 0.7
SG A:CYS168 4.8 17.6 1.0
SG A:CYS81 4.9 15.6 1.0

Iron binding site 3 out of 4 in 5lqs

Go back to Iron Binding Sites List in 5lqs
Iron binding site 3 out of 4 in the Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-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 Y21F Mutant in Complex with Substrate-Derived Quinolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:17.3
occ:1.00
 FE3 A:SF4301 0.0 17.3 1.0
N1 A:NTM302 2.0 17.2 0.7
O1 A:NTM302 2.1 18.1 0.7
S4 A:SF4301 2.3 16.1 1.0
S2 A:SF4301 2.4 16.6 1.0
S1 A:SF4301 2.4 16.4 1.0
FE1 A:SF4301 2.8 15.6 1.0
FE4 A:SF4301 2.8 15.5 1.0
FE2 A:SF4301 2.9 16.6 1.0
C2 A:NTM302 2.9 17.5 0.7
C7 A:NTM302 3.0 17.7 0.7
C6 A:NTM302 3.0 16.9 0.7
O A:HOH595 3.3 21.2 0.3
ND2 A:ASN109 3.7 24.1 0.7
ND2 A:ASN109 3.9 18.6 0.3
S3 A:SF4301 4.1 16.1 1.0
O2 A:NTM302 4.2 18.6 0.7
C5 A:NTM302 4.3 17.2 0.7
C3 A:NTM302 4.4 17.8 0.7
CE2 A:PHE21 4.4 8.8 1.0
CD2 A:PHE21 4.6 8.6 1.0
CE A:MET257 4.7 11.3 1.0
SG A:CYS168 4.7 17.6 1.0
SG A:CYS81 4.7 15.6 1.0
OE1 A:GLU195 4.8 29.4 1.0
C4 A:NTM302 4.9 17.3 0.7
SG A:CYS254 4.9 14.4 1.0
OE2 A:GLU195 5.0 32.0 1.0
OH A:TYR107 5.0 29.3 0.7
CG A:ASN109 5.0 22.3 0.7

Iron binding site 4 out of 4 in 5lqs

Go back to Iron Binding Sites List in 5lqs
Iron binding site 4 out of 4 in the Structure of Quinolinate Synthase Y21F Mutant in Complex with Substrate-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 Y21F Mutant in Complex with Substrate-Derived Quinolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:15.5
occ:1.00
 FE4 A:SF4301 0.0 15.5 1.0
S1 A:SF4301 2.3 16.4 1.0
SG A:CYS81 2.3 15.6 1.0
S2 A:SF4301 2.3 16.6 1.0
S3 A:SF4301 2.4 16.1 1.0
FE1 A:SF4301 2.7 15.6 1.0
FE2 A:SF4301 2.7 16.6 1.0
FE3 A:SF4301 2.8 17.3 1.0
CB A:CYS81 3.3 15.9 1.0
ND2 A:ASN109 3.4 24.1 0.7
CA A:CYS81 3.9 16.5 1.0
S4 A:SF4301 3.9 16.1 1.0
O1 A:NTM302 4.1 18.1 0.7
ND2 A:ASN109 4.2 18.6 0.3
C A:CYS81 4.6 17.7 1.0
CD A:PRO82 4.6 20.5 1.0
N1 A:NTM302 4.6 17.2 0.7
CG A:ASN109 4.6 22.3 0.7
O A:HOH614 4.7 37.5 1.0
SG A:CYS168 4.8 17.6 1.0
N A:PRO82 4.8 20.1 1.0
CE A:MET83 4.9 29.4 0.5
CB A:MET83 4.9 27.5 0.5
SG A:CYS254 4.9 14.4 1.0
CB A:MET83 4.9 29.6 0.5
CE A:MET83 4.9 25.2 0.5

Reference:

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
Page generated: Tue Aug 6 04:43:11 2024

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