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Iron in PDB 7p4m: Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form

Enzymatic activity of Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form

All present enzymatic activity of Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form:
2.5.1.72;

Protein crystallography data

The structure of Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form, PDB code: 7p4m was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.48 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.442, 49.051, 60.809, 90, 106.83, 90
R / Rfree (%) 13.3 / 17.8

Other elements in 7p4m:

The structure of Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form (pdb code 7p4m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form, PDB code: 7p4m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 7p4m

Go back to Iron Binding Sites List in 7p4m
Iron binding site 1 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.0
occ:0.55
 FE1 A:SF4301 0.0 29.0 0.6
FE1 A:F3S302 0.1 38.1 0.5
S3 A:F3S302 2.2 38.2 0.5
S2 A:SF4301 2.3 29.0 0.6
S2 A:F3S302 2.3 39.0 0.5
S4 A:SF4301 2.3 27.1 0.6
S3 A:SF4301 2.3 29.0 0.6
S1 A:F3S302 2.3 38.2 0.5
SG A:CYS168 2.4 31.8 1.0
FE4 A:F3S302 2.7 36.0 0.5
FE3 A:F3S302 2.7 36.2 0.5
FE3 A:SF4301 2.7 29.4 0.6
FE2 A:SF4301 2.7 27.2 0.6
FE4 A:SF4301 2.8 28.5 0.6
CB A:CYS168 3.5 31.5 1.0
S1 A:SF4301 3.9 28.2 0.6
S4 A:F3S302 4.0 36.3 0.5
CG2 A:VAL170 4.1 38.6 1.0
CA A:CYS168 4.3 32.9 1.0
CB A:VAL170 4.3 34.9 1.0
CD A:PRO169 4.7 38.0 1.0
ND1 A:HIS171 4.8 31.8 1.0
SG A:CYS81 4.8 29.0 1.0
C A:CYS168 4.8 33.4 1.0
SG A:CYS254 4.9 25.6 1.0
N A:VAL170 4.9 33.5 1.0
CL A:CL303 4.9 34.2 0.6
N A:PRO169 5.0 35.5 1.0

Iron binding site 2 out of 7 in 7p4m

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Iron binding site 2 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.2
occ:0.55
 FE2 A:SF4301 0.0 27.2 0.6
FE3 A:F3S302 0.3 36.2 0.5
S4 A:F3S302 2.1 36.3 0.5
S1 A:F3S302 2.2 38.2 0.5
S3 A:SF4301 2.3 29.0 0.6
S1 A:SF4301 2.3 28.2 0.6
S4 A:SF4301 2.3 27.1 0.6
SG A:CYS254 2.4 25.6 1.0
S3 A:F3S302 2.5 38.2 0.5
FE3 A:SF4301 2.7 29.4 0.6
FE4 A:F3S302 2.7 36.0 0.5
FE1 A:SF4301 2.7 29.0 0.6
FE1 A:F3S302 2.8 38.1 0.5
FE4 A:SF4301 2.8 28.5 0.6
CB A:CYS254 3.5 23.7 1.0
S2 A:F3S302 3.9 39.0 0.5
S2 A:SF4301 3.9 29.0 0.6
O A:HOH571 4.4 33.4 1.0
CG2 A:VAL170 4.4 38.6 1.0
CG A:MET257 4.6 23.6 1.0
CA A:CYS254 4.6 23.0 1.0
CL A:CL303 4.7 34.2 0.6
SG A:CYS81 4.9 29.0 1.0
SG A:CYS168 4.9 31.8 1.0

Iron binding site 3 out of 7 in 7p4m

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Iron binding site 3 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.4
occ:0.55
 FE3 A:SF4301 0.0 29.4 0.6
S2 A:F3S302 2.2 39.0 0.5
S1 A:SF4301 2.3 28.2 0.6
S2 A:SF4301 2.3 29.0 0.6
S4 A:SF4301 2.3 27.1 0.6
CL A:CL303 2.3 34.2 0.6
S1 A:F3S302 2.6 38.2 0.5
FE4 A:F3S302 2.7 36.0 0.5
S4 A:F3S302 2.7 36.3 0.5
FE1 A:F3S302 2.7 38.1 0.5
FE4 A:SF4301 2.7 28.5 0.6
FE2 A:SF4301 2.7 27.2 0.6
FE1 A:SF4301 2.7 29.0 0.6
FE3 A:F3S302 2.9 36.2 0.5
O A:HOH651 3.5 38.4 0.5
ND2 A:ASN109 3.7 38.3 1.0
S3 A:SF4301 3.8 29.0 0.6
S3 A:F3S302 3.9 38.2 0.5
CE2 A:TYR21 4.3 22.5 1.0
CD2 A:TYR21 4.5 21.7 1.0
SG A:CYS81 4.6 29.0 1.0
SG A:CYS168 4.7 31.8 1.0
SG A:CYS254 4.9 25.6 1.0
CE A:MET257 4.9 33.4 1.0

Iron binding site 4 out of 7 in 7p4m

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Iron binding site 4 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:28.5
occ:0.55
 FE4 A:SF4301 0.0 28.5 0.6
FE4 A:F3S302 0.1 36.0 0.5
S1 A:SF4301 2.3 28.2 0.6
SG A:CYS81 2.3 29.0 1.0
S4 A:F3S302 2.3 36.3 0.5
S3 A:SF4301 2.3 29.0 0.6
S2 A:SF4301 2.3 29.0 0.6
S2 A:F3S302 2.3 39.0 0.5
S3 A:F3S302 2.3 38.2 0.5
FE3 A:SF4301 2.7 29.4 0.6
FE1 A:SF4301 2.8 29.0 0.6
FE2 A:SF4301 2.8 27.2 0.6
FE1 A:F3S302 2.8 38.1 0.5
FE3 A:F3S302 2.8 36.2 0.5
CB A:CYS81 3.3 26.9 1.0
CA A:CYS81 3.9 23.8 1.0
S4 A:SF4301 3.9 27.1 0.6
S1 A:F3S302 4.0 38.2 0.5
ND2 A:ASN109 4.3 38.3 1.0
C A:CYS81 4.5 24.7 1.0
CD A:PRO82 4.6 27.0 1.0
CL A:CL303 4.7 34.2 0.6
N A:PRO82 4.7 26.4 1.0
CB A:MET83 4.8 32.1 0.3
CB A:MET83 4.8 31.8 0.7
CE A:MET83 4.8 36.6 0.7
N A:MET83 4.9 30.2 1.0
SG A:CYS168 4.9 31.8 1.0
CE A:MET83 4.9 35.3 0.3
SG A:CYS254 5.0 25.6 1.0

Iron binding site 5 out of 7 in 7p4m

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Iron binding site 5 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:38.1
occ:0.45
 FE1 A:F3S302 0.0 38.1 0.5
FE1 A:SF4301 0.1 29.0 0.6
S4 A:SF4301 2.2 27.1 0.6
S1 A:F3S302 2.2 38.2 0.5
S2 A:SF4301 2.3 29.0 0.6
S2 A:F3S302 2.3 39.0 0.5
S3 A:F3S302 2.3 38.2 0.5
SG A:CYS168 2.3 31.8 1.0
S3 A:SF4301 2.4 29.0 0.6
FE3 A:SF4301 2.7 29.4 0.6
FE3 A:F3S302 2.7 36.2 0.5
FE2 A:SF4301 2.8 27.2 0.6
FE4 A:F3S302 2.8 36.0 0.5
FE4 A:SF4301 2.8 28.5 0.6
CB A:CYS168 3.5 31.5 1.0
S1 A:SF4301 3.9 28.2 0.6
S4 A:F3S302 4.0 36.3 0.5
CG2 A:VAL170 4.0 38.6 1.0
CB A:VAL170 4.3 34.9 1.0
CA A:CYS168 4.3 32.9 1.0
ND1 A:HIS171 4.7 31.8 1.0
CD A:PRO169 4.8 38.0 1.0
CL A:CL303 4.8 34.2 0.6
N A:VAL170 4.8 33.5 1.0
C A:CYS168 4.9 33.4 1.0
SG A:CYS254 4.9 25.6 1.0
SG A:CYS81 4.9 29.0 1.0

Iron binding site 6 out of 7 in 7p4m

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Iron binding site 6 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:36.2
occ:0.45
 FE3 A:F3S302 0.0 36.2 0.5
FE2 A:SF4301 0.3 27.2 0.6
S3 A:SF4301 2.1 29.0 0.6
S1 A:F3S302 2.2 38.2 0.5
S4 A:F3S302 2.3 36.3 0.5
S3 A:F3S302 2.3 38.2 0.5
SG A:CYS254 2.3 25.6 1.0
S4 A:SF4301 2.4 27.1 0.6
S1 A:SF4301 2.5 28.2 0.6
FE1 A:SF4301 2.7 29.0 0.6
FE1 A:F3S302 2.7 38.1 0.5
FE4 A:F3S302 2.8 36.0 0.5
FE4 A:SF4301 2.8 28.5 0.6
FE3 A:SF4301 2.9 29.4 0.6
CB A:CYS254 3.4 23.7 1.0
S2 A:F3S302 3.9 39.0 0.5
S2 A:SF4301 4.0 29.0 0.6
O A:HOH571 4.2 33.4 1.0
CG2 A:VAL170 4.2 38.6 1.0
CA A:CYS254 4.5 23.0 1.0
CG A:MET257 4.7 23.6 1.0
SG A:CYS168 4.9 31.8 1.0
SG A:CYS81 5.0 29.0 1.0
CL A:CL303 5.0 34.2 0.6

Iron binding site 7 out of 7 in 7p4m

Go back to Iron Binding Sites List in 7p4m
Iron binding site 7 out of 7 in the Structure of the Quinolinate Synthase Y107F Variant in An Empty Open Form


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 Quinolinate Synthase Y107F Variant in An Empty Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:36.0
occ:0.45
 FE4 A:F3S302 0.0 36.0 0.5
FE4 A:SF4301 0.1 28.5 0.6
S1 A:SF4301 2.2 28.2 0.6
S4 A:F3S302 2.3 36.3 0.5
S2 A:SF4301 2.3 29.0 0.6
S3 A:SF4301 2.3 29.0 0.6
S2 A:F3S302 2.3 39.0 0.5
S3 A:F3S302 2.3 38.2 0.5
SG A:CYS81 2.3 29.0 1.0
FE3 A:SF4301 2.7 29.4 0.6
FE1 A:SF4301 2.7 29.0 0.6
FE2 A:SF4301 2.7 27.2 0.6
FE1 A:F3S302 2.8 38.1 0.5
FE3 A:F3S302 2.8 36.2 0.5
CB A:CYS81 3.4 26.9 1.0
S4 A:SF4301 3.8 27.1 0.6
CA A:CYS81 3.9 23.8 1.0
S1 A:F3S302 3.9 38.2 0.5
ND2 A:ASN109 4.3 38.3 1.0
C A:CYS81 4.6 24.7 1.0
CD A:PRO82 4.6 27.0 1.0
CL A:CL303 4.6 34.2 0.6
N A:PRO82 4.8 26.4 1.0
CB A:MET83 4.8 32.1 0.3
CE A:MET83 4.8 36.6 0.7
CB A:MET83 4.8 31.8 0.7
SG A:CYS168 4.9 31.8 1.0
CE A:MET83 4.9 35.3 0.3
SG A:CYS254 4.9 25.6 1.0
N A:MET83 4.9 30.2 1.0

Reference:

H.Basbous, A.Volbeda, P.Amara, R.Rohac, L.Martin, S.Ollagnier De Choudens, J.C.Fontecilla-Camps. Essential Transient Extension of the Active Site Cavity During Quinolinic Acid Synthesis By Nada To Be Published.
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