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Iron in PDB 6g74: Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate

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

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

Protein crystallography data

The structure of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate, PDB code: 6g74 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) 43.43 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.140, 52.160, 58.950, 103.82, 90.63, 90.37
R / Rfree (%) 19 / 23.4

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate (pdb code 6g74). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate, PDB code: 6g74:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6g74

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Iron binding site 1 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


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 Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.7
occ:1.00
 FE1 A:SF4301 0.0 27.7 1.0
SG A:CYS168 2.3 24.9 1.0
S4 A:SF4301 2.3 29.0 1.0
S2 A:SF4301 2.3 30.6 1.0
S3 A:SF4301 2.3 31.4 1.0
FE2 A:SF4301 2.8 29.1 1.0
FE4 A:SF4301 2.8 29.6 1.0
FE3 A:SF4301 2.8 30.6 0.6
CB A:CYS168 3.4 28.1 1.0
S1 A:SF4301 4.0 32.0 1.0
CG2 A:VAL170 4.0 29.0 1.0
CB A:VAL170 4.2 27.4 1.0
OE1 A:GLU195 4.2 34.2 1.0
CA A:CYS168 4.2 28.4 1.0
CD A:PRO169 4.6 32.5 1.0
ND1 A:HIS171 4.7 23.8 1.0
SG A:CYS81 4.8 27.3 1.0
C A:CYS168 4.8 28.8 1.0
O A:HOH580 4.8 23.6 0.4
N A:VAL170 4.8 28.3 1.0
SG A:CYS254 5.0 21.8 1.0
CE1 A:HIS171 5.0 23.9 1.0
O A:HOH554 5.0 19.5 0.4

Iron binding site 2 out of 8 in 6g74

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Iron binding site 2 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


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 Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.1
occ:1.00
 FE2 A:SF4301 0.0 29.1 1.0
S3 A:SF4301 2.3 31.4 1.0
S4 A:SF4301 2.3 29.0 1.0
S1 A:SF4301 2.4 32.0 1.0
SG A:CYS254 2.4 21.8 1.0
FE1 A:SF4301 2.8 27.7 1.0
FE4 A:SF4301 2.8 29.6 1.0
FE3 A:SF4301 2.8 30.6 0.6
CB A:CYS254 3.4 22.3 1.0
S2 A:SF4301 4.0 30.6 1.0
O A:HOH548 4.2 25.6 1.0
CG2 A:VAL170 4.3 29.0 1.0
CA A:CYS254 4.6 21.9 1.0
O A:HOH580 4.6 23.6 0.4
CG A:MET257 4.7 24.5 1.0
SG A:CYS168 4.8 24.9 1.0
SG A:CYS81 4.9 27.3 1.0

Iron binding site 3 out of 8 in 6g74

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Iron binding site 3 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


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 Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.6
occ:0.59
 FE3 A:SF4301 0.0 30.6 0.6
O A:HOH580 2.1 23.6 0.4
S4 A:SF4301 2.4 29.0 1.0
S2 A:SF4301 2.4 30.6 1.0
S1 A:SF4301 2.4 32.0 1.0
FE4 A:SF4301 2.7 29.6 1.0
FE1 A:SF4301 2.8 27.7 1.0
FE2 A:SF4301 2.8 29.1 1.0
C6 A:PHT302 2.9 31.4 0.6
O A:HOH554 3.2 19.5 0.4
C5 A:PHT302 3.5 31.1 0.6
ND2 A:ASN109 4.0 42.7 1.0
S3 A:SF4301 4.0 31.4 1.0
C1 A:PHT302 4.0 32.2 0.6
CE2 A:PHE21 4.1 18.3 1.0
CD2 A:PHE21 4.4 18.2 1.0
SG A:CYS81 4.6 27.3 1.0
SG A:CYS168 4.8 24.9 1.0
C4 A:PHT302 4.8 32.3 0.6
OE1 A:GLU195 4.9 34.2 1.0
SG A:CYS254 4.9 21.8 1.0
CE A:MET257 4.9 24.0 1.0

Iron binding site 4 out of 8 in 6g74

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Iron binding site 4 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


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 Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.6
occ:1.00
 FE4 A:SF4301 0.0 29.6 1.0
SG A:CYS81 2.3 27.3 1.0
S2 A:SF4301 2.3 30.6 1.0
S1 A:SF4301 2.3 32.0 1.0
S3 A:SF4301 2.4 31.4 1.0
FE3 A:SF4301 2.7 30.6 0.6
FE2 A:SF4301 2.8 29.1 1.0
FE1 A:SF4301 2.8 27.7 1.0
CB A:CYS81 3.3 26.3 1.0
CA A:CYS81 3.9 26.9 1.0
S4 A:SF4301 3.9 29.0 1.0
C A:CYS81 4.5 26.6 1.0
ND2 A:ASN109 4.5 42.7 1.0
O A:HOH580 4.6 23.6 0.4
CD A:PRO82 4.7 31.1 1.0
CB A:MET83 4.7 36.0 1.0
N A:PRO82 4.7 28.7 1.0
N A:MET83 4.9 31.4 1.0
SG A:CYS168 4.9 24.9 1.0
SG A:CYS254 5.0 21.8 1.0

Iron binding site 5 out of 8 in 6g74

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Iron binding site 5 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.1
occ:1.00
 FE1 B:SF4301 0.0 30.1 1.0
S4 B:SF4301 2.3 29.7 1.0
S2 B:SF4301 2.3 32.5 1.0
SG B:CYS168 2.3 27.2 1.0
S3 B:SF4301 2.4 32.7 1.0
FE4 B:SF4301 2.8 32.4 1.0
FE3 B:SF4301 2.8 33.1 0.6
FE2 B:SF4301 2.8 30.1 1.0
CB B:CYS168 3.5 28.3 1.0
S1 B:SF4301 4.0 32.7 1.0
CG2 B:VAL170 4.1 32.5 1.0
CA B:CYS168 4.3 30.0 1.0
CB B:VAL170 4.3 29.9 1.0
OE1 B:GLU195 4.3 39.1 1.0
O B:HOH575 4.6 29.7 0.4
O B:HOH541 4.6 24.2 0.4
ND1 B:HIS171 4.6 25.0 1.0
CD B:PRO169 4.8 33.8 1.0
SG B:CYS81 4.8 29.9 1.0
N B:VAL170 4.9 29.7 1.0
C B:CYS168 4.9 30.0 1.0
CE1 B:HIS171 5.0 24.4 1.0

Iron binding site 6 out of 8 in 6g74

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Iron binding site 6 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.1
occ:1.00
 FE2 B:SF4301 0.0 30.1 1.0
S4 B:SF4301 2.3 29.7 1.0
S1 B:SF4301 2.3 32.7 1.0
S3 B:SF4301 2.4 32.7 1.0
SG B:CYS254 2.4 21.6 1.0
FE4 B:SF4301 2.7 32.4 1.0
FE1 B:SF4301 2.8 30.1 1.0
FE3 B:SF4301 2.8 33.1 0.6
CB B:CYS254 3.4 22.6 1.0
S2 B:SF4301 4.0 32.5 1.0
CG2 B:VAL170 4.2 32.5 1.0
O B:HOH515 4.3 25.4 1.0
CA B:CYS254 4.5 21.7 1.0
O B:HOH575 4.5 29.7 0.4
CG B:MET257 4.7 21.5 1.0
SG B:CYS81 4.8 29.9 1.0
SG B:CYS168 4.9 27.2 1.0

Iron binding site 7 out of 8 in 6g74

Go back to Iron Binding Sites List in 6g74
Iron binding site 7 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:33.1
occ:0.59
 FE3 B:SF4301 0.0 33.1 0.6
O B:HOH575 1.9 29.7 0.4
S4 B:SF4301 2.4 29.7 1.0
S2 B:SF4301 2.4 32.5 1.0
S1 B:SF4301 2.4 32.7 1.0
FE4 B:SF4301 2.8 32.4 1.0
FE1 B:SF4301 2.8 30.1 1.0
FE2 B:SF4301 2.8 30.1 1.0
C6 B:PHT302 3.0 30.6 0.6
O B:HOH541 3.2 24.2 0.4
C5 B:PHT302 3.5 30.6 0.6
ND2 B:ASN109 3.9 55.4 1.0
S3 B:SF4301 4.0 32.7 1.0
CE2 B:PHE21 4.1 17.5 1.0
C1 B:PHT302 4.2 31.2 0.6
CD2 B:PHE21 4.4 18.2 1.0
SG B:CYS81 4.7 29.9 1.0
SG B:CYS254 4.8 21.6 1.0
CE B:MET257 4.8 22.1 1.0
SG B:CYS168 4.8 27.2 1.0
C4 B:PHT302 4.8 31.7 0.6

Iron binding site 8 out of 8 in 6g74

Go back to Iron Binding Sites List in 6g74
Iron binding site 8 out of 8 in the Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Y21F Variant of Quinolinate Synthase in Complex with Phthalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.4
occ:1.00
 FE4 B:SF4301 0.0 32.4 1.0
S1 B:SF4301 2.3 32.7 1.0
SG B:CYS81 2.3 29.9 1.0
S3 B:SF4301 2.3 32.7 1.0
S2 B:SF4301 2.3 32.5 1.0
FE2 B:SF4301 2.7 30.1 1.0
FE3 B:SF4301 2.8 33.1 0.6
FE1 B:SF4301 2.8 30.1 1.0
CB B:CYS81 3.4 30.9 1.0
S4 B:SF4301 3.9 29.7 1.0
CA B:CYS81 3.9 29.2 1.0
O B:HOH575 4.2 29.7 0.4
ND2 B:ASN109 4.5 55.4 1.0
C B:CYS81 4.6 30.7 1.0
CB B:MET83 4.8 35.0 1.0
N B:PRO82 4.8 32.1 1.0
CD B:PRO82 4.8 34.3 1.0
SG B:CYS254 4.9 21.6 1.0
SG B:CYS168 4.9 27.2 1.0
N B:MET83 5.0 31.8 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: Tue Aug 6 19:12:01 2024

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