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Iron in PDB 6f4d: Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh

Enzymatic activity of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh

All present enzymatic activity of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh:
2.5.1.72;

Protein crystallography data

The structure of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh, PDB code: 6f4d 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) 39.15 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.970, 49.170, 69.390, 90.00, 107.79, 90.00
R / Rfree (%) 19.2 / 24.1

Other elements in 6f4d:

The structure of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh (pdb code 6f4d). 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 the Y21F Variant of Quinolinate Synthase in Complex with Pgh, PDB code: 6f4d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f4d

Go back to Iron Binding Sites List in 6f4d
Iron binding site 1 out of 4 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:32.2
occ:1.00
 FE1 A:SF4301 0.0 32.2 1.0
SG A:CYS168 2.2 29.9 1.0
S4 A:SF4301 2.3 32.8 1.0
S3 A:SF4301 2.3 34.0 1.0
S2 A:SF4301 2.3 32.1 1.0
FE4 A:SF4301 2.8 32.7 1.0
FE2 A:SF4301 2.8 34.4 1.0
FE3 A:SF4301 2.8 34.4 1.0
O2 A:PGH302 3.2 33.3 0.7
CB A:CYS168 3.4 32.0 1.0
S1 A:SF4301 3.9 33.7 1.0
OE1 A:GLU195 3.9 32.3 1.0
CG2 A:VAL170 4.2 33.8 1.0
CB A:VAL170 4.2 32.3 1.0
CA A:CYS168 4.3 33.3 1.0
N2 A:PGH302 4.4 32.4 0.7
ND1 A:HIS171 4.4 25.4 1.0
CE1 A:HIS171 4.8 26.5 1.0
SG A:CYS81 4.8 30.8 1.0
C A:CYS168 4.8 32.4 1.0
SG A:CYS254 4.9 30.1 1.0
N A:VAL170 4.9 32.2 1.0
CD A:PRO169 4.9 33.4 1.0

Iron binding site 2 out of 4 in 6f4d

Go back to Iron Binding Sites List in 6f4d
Iron binding site 2 out of 4 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:34.4
occ:1.00
 FE2 A:SF4301 0.0 34.4 1.0
S1 A:SF4301 2.3 33.7 1.0
S4 A:SF4301 2.4 32.8 1.0
S3 A:SF4301 2.4 34.0 1.0
SG A:CYS254 2.4 30.1 1.0
FE4 A:SF4301 2.8 32.7 1.0
FE1 A:SF4301 2.8 32.2 1.0
FE3 A:SF4301 2.9 34.4 1.0
CB A:CYS254 3.5 30.6 1.0
S2 A:SF4301 4.0 32.1 1.0
CG2 A:VAL170 4.4 33.8 1.0
O2 A:PGH302 4.6 33.3 0.7
CG A:MET257 4.6 31.0 1.0
CA A:CYS254 4.6 30.6 1.0
O A:HOH539 4.7 32.1 0.3
SG A:CYS168 4.8 29.9 1.0
SG A:CYS81 4.9 30.8 1.0

Iron binding site 3 out of 4 in 6f4d

Go back to Iron Binding Sites List in 6f4d
Iron binding site 3 out of 4 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:34.4
occ:1.00
 FE3 A:SF4301 0.0 34.4 1.0
O2 A:PGH302 2.0 33.3 0.7
S2 A:SF4301 2.3 32.1 1.0
O A:HOH539 2.4 32.1 0.3
S4 A:SF4301 2.4 32.8 1.0
S1 A:SF4301 2.4 33.7 1.0
N2 A:PGH302 2.7 32.4 0.7
FE1 A:SF4301 2.8 32.2 1.0
FE4 A:SF4301 2.8 32.7 1.0
FE2 A:SF4301 2.9 34.4 1.0
O1 A:PGH302 2.9 34.1 0.7
C1 A:PGH302 3.1 32.9 0.7
ND2 A:ASN109 3.8 38.1 1.0
S3 A:SF4301 4.1 34.0 1.0
CE2 A:PHE21 4.2 22.6 1.0
OE1 A:GLU195 4.3 32.3 1.0
OE2 A:GLU195 4.6 31.0 1.0
CD2 A:PHE21 4.6 23.3 1.0
C2 A:PGH302 4.6 33.3 0.7
SG A:CYS168 4.7 29.9 1.0
SG A:CYS81 4.7 30.8 1.0
CD A:GLU195 4.9 30.8 1.0

Iron binding site 4 out of 4 in 6f4d

Go back to Iron Binding Sites List in 6f4d
Iron binding site 4 out of 4 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Pgh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:32.7
occ:1.00
 FE4 A:SF4301 0.0 32.7 1.0
S1 A:SF4301 2.3 33.7 1.0
SG A:CYS81 2.3 30.8 1.0
S2 A:SF4301 2.4 32.1 1.0
S3 A:SF4301 2.4 34.0 1.0
FE1 A:SF4301 2.8 32.2 1.0
FE2 A:SF4301 2.8 34.4 1.0
FE3 A:SF4301 2.8 34.4 1.0
CB A:CYS81 3.3 31.2 1.0
ND2 A:ASN109 3.8 38.1 1.0
CA A:CYS81 3.9 32.7 1.0
S4 A:SF4301 3.9 32.8 1.0
O2 A:PGH302 4.2 33.3 0.7
O A:HOH539 4.3 32.1 0.3
C A:CYS81 4.5 33.8 1.0
CD A:PRO82 4.6 38.2 1.0
SG A:CYS168 4.7 29.9 1.0
N A:PRO82 4.8 37.2 1.0
CB A:MET83 4.9 42.9 1.0
SG A:CYS254 4.9 30.1 1.0
CG A:ASN109 5.0 39.3 1.0

Reference:

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
Page generated: Wed Aug 6 05:57:04 2025

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