Iron in PDB 6ora: An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Enzymatic activity of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
All present enzymatic activity of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase:
2.5.1.72;
Protein crystallography data
The structure of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase, PDB code: 6ora
was solved by
O.A.Esakova,
T.L.Grove,
A.Silakov,
N.H.Yennawar,
S.J.Booker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.95 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.052,
52.134,
97.803,
90.00,
96.27,
90.00
|
R / Rfree (%)
|
19.6 /
24.3
|
Other elements in 6ora:
The structure of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
(pdb code 6ora). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase, PDB code: 6ora:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 1 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:17.4
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
17.4
|
1.0
|
S4
|
A:SF4401
|
2.2
|
16.8
|
1.0
|
S3
|
A:SF4401
|
2.2
|
18.9
|
1.0
|
S2
|
A:SF4401
|
2.2
|
18.8
|
1.0
|
SG
|
A:CYS170
|
2.3
|
15.4
|
1.0
|
FE2
|
A:SF4401
|
3.1
|
19.8
|
1.0
|
FE4
|
A:SF4401
|
3.1
|
17.1
|
1.0
|
FE3
|
A:SF4401
|
3.1
|
14.4
|
1.0
|
CB
|
A:CYS170
|
3.2
|
16.0
|
1.0
|
S1
|
A:SF4401
|
3.8
|
18.6
|
1.0
|
OE1
|
A:GLN198
|
4.0
|
19.6
|
1.0
|
CA
|
A:CYS170
|
4.2
|
17.2
|
1.0
|
CB
|
A:VAL172
|
4.3
|
15.8
|
1.0
|
CG2
|
A:VAL172
|
4.3
|
17.4
|
1.0
|
ND1
|
A:HIS173
|
4.4
|
16.0
|
1.0
|
C
|
A:CYS170
|
4.7
|
19.9
|
1.0
|
N
|
A:VAL172
|
4.8
|
16.9
|
1.0
|
CE1
|
A:HIS173
|
4.8
|
15.3
|
1.0
|
N
|
A:TYR171
|
4.9
|
18.3
|
1.0
|
|
Iron binding site 2 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 2 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:19.8
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
19.8
|
1.0
|
S3
|
A:SF4401
|
2.2
|
18.9
|
1.0
|
S4
|
A:SF4401
|
2.2
|
16.8
|
1.0
|
S1
|
A:SF4401
|
2.2
|
18.6
|
1.0
|
OAE
|
A:5XW403
|
2.5
|
20.8
|
1.0
|
FE1
|
A:SF4401
|
3.1
|
17.4
|
1.0
|
FE3
|
A:SF4401
|
3.1
|
14.4
|
1.0
|
FE4
|
A:SF4401
|
3.1
|
17.1
|
1.0
|
CAC
|
A:5XW403
|
3.1
|
20.6
|
1.0
|
OAD
|
A:5XW403
|
3.4
|
21.7
|
1.0
|
S2
|
A:SF4401
|
3.8
|
18.8
|
1.0
|
CE2
|
A:TYR23
|
3.9
|
15.9
|
1.0
|
ND2
|
A:ASN111
|
4.2
|
24.5
|
1.0
|
CD2
|
A:TYR23
|
4.3
|
14.9
|
1.0
|
CAA
|
A:5XW403
|
4.3
|
20.5
|
1.0
|
OE1
|
A:GLN198
|
4.7
|
19.6
|
1.0
|
CE
|
A:MET259
|
4.8
|
20.1
|
1.0
|
SG
|
A:CYS83
|
4.9
|
14.7
|
1.0
|
SG
|
A:CYS170
|
5.0
|
15.4
|
1.0
|
NE2
|
A:GLN198
|
5.0
|
17.7
|
1.0
|
|
Iron binding site 3 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 3 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:14.4
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
14.4
|
1.0
|
S2
|
A:SF4401
|
2.2
|
18.8
|
1.0
|
S1
|
A:SF4401
|
2.2
|
18.6
|
1.0
|
S4
|
A:SF4401
|
2.2
|
16.8
|
1.0
|
SG
|
A:CYS83
|
2.2
|
14.7
|
1.0
|
FE4
|
A:SF4401
|
3.1
|
17.1
|
1.0
|
FE1
|
A:SF4401
|
3.1
|
17.4
|
1.0
|
FE2
|
A:SF4401
|
3.1
|
19.8
|
1.0
|
CB
|
A:CYS83
|
3.1
|
12.7
|
1.0
|
CA
|
A:CYS83
|
3.5
|
13.7
|
1.0
|
S3
|
A:SF4401
|
3.8
|
18.9
|
1.0
|
N
|
A:ALA84
|
3.9
|
16.6
|
1.0
|
C
|
A:CYS83
|
4.0
|
25.5
|
1.0
|
N
|
A:MET85
|
4.2
|
18.4
|
1.0
|
ND2
|
A:ASN111
|
4.3
|
24.5
|
1.0
|
CB
|
A:MET85
|
4.5
|
21.8
|
1.0
|
CE2
|
A:PHE60
|
4.8
|
26.4
|
1.0
|
N
|
A:CYS83
|
4.9
|
13.3
|
1.0
|
O
|
A:CYS83
|
4.9
|
25.8
|
1.0
|
CA
|
A:MET85
|
5.0
|
21.6
|
1.0
|
CE
|
A:MET85
|
5.0
|
22.7
|
1.0
|
|
Iron binding site 4 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 4 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:17.1
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
17.1
|
1.0
|
S1
|
A:SF4401
|
2.2
|
18.6
|
1.0
|
S2
|
A:SF4401
|
2.2
|
18.8
|
1.0
|
S3
|
A:SF4401
|
2.2
|
18.9
|
1.0
|
SG
|
A:CYS256
|
2.2
|
13.6
|
1.0
|
FE3
|
A:SF4401
|
3.1
|
14.4
|
1.0
|
FE1
|
A:SF4401
|
3.1
|
17.4
|
1.0
|
FE2
|
A:SF4401
|
3.1
|
19.8
|
1.0
|
CB
|
A:CYS256
|
3.2
|
11.8
|
1.0
|
S4
|
A:SF4401
|
3.8
|
16.8
|
1.0
|
O
|
A:HOH630
|
4.2
|
27.4
|
1.0
|
CA
|
A:CYS256
|
4.4
|
11.9
|
1.0
|
CG
|
A:MET259
|
4.5
|
20.3
|
1.0
|
CG2
|
A:VAL172
|
4.5
|
17.4
|
1.0
|
|
Iron binding site 5 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 5 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:26.2
occ:1.00
|
FE1
|
B:SF4401
|
0.0
|
26.2
|
1.0
|
S4
|
B:SF4401
|
2.2
|
27.1
|
1.0
|
S2
|
B:SF4401
|
2.2
|
28.6
|
1.0
|
S3
|
B:SF4401
|
2.2
|
28.3
|
1.0
|
SG
|
B:CYS170
|
2.3
|
22.7
|
1.0
|
FE4
|
B:SF4401
|
3.1
|
28.4
|
1.0
|
FE3
|
B:SF4401
|
3.1
|
30.9
|
1.0
|
FE2
|
B:SF4401
|
3.1
|
28.0
|
1.0
|
CB
|
B:CYS170
|
3.3
|
22.5
|
1.0
|
S1
|
B:SF4401
|
3.8
|
28.7
|
1.0
|
CG1
|
B:VAL172
|
3.9
|
31.0
|
1.0
|
CG2
|
B:VAL172
|
4.0
|
25.8
|
1.0
|
OE1
|
B:GLN198
|
4.2
|
32.1
|
1.0
|
ND1
|
B:HIS173
|
4.3
|
17.2
|
1.0
|
CA
|
B:CYS170
|
4.3
|
24.5
|
1.0
|
CB
|
B:VAL172
|
4.6
|
27.8
|
1.0
|
CE1
|
B:HIS173
|
4.7
|
16.6
|
1.0
|
N
|
B:VAL172
|
4.8
|
27.5
|
1.0
|
C
|
B:CYS170
|
4.8
|
25.9
|
1.0
|
N
|
B:TYR171
|
4.9
|
27.7
|
1.0
|
CB
|
B:MET85
|
5.0
|
32.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 6 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:28.0
occ:1.00
|
FE2
|
B:SF4401
|
0.0
|
28.0
|
1.0
|
S3
|
B:SF4401
|
2.2
|
28.3
|
1.0
|
S1
|
B:SF4401
|
2.2
|
28.7
|
1.0
|
S4
|
B:SF4401
|
2.2
|
27.1
|
1.0
|
SG
|
B:CYS256
|
2.3
|
31.0
|
1.0
|
FE4
|
B:SF4401
|
3.1
|
28.4
|
1.0
|
FE1
|
B:SF4401
|
3.1
|
26.2
|
1.0
|
FE3
|
B:SF4401
|
3.1
|
30.9
|
1.0
|
CB
|
B:CYS256
|
3.3
|
31.6
|
1.0
|
S2
|
B:SF4401
|
3.8
|
28.6
|
1.0
|
CG1
|
B:VAL172
|
4.4
|
31.0
|
1.0
|
CA
|
B:CYS256
|
4.4
|
31.5
|
1.0
|
CG
|
B:MET259
|
4.6
|
31.5
|
1.0
|
|
Iron binding site 7 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 7 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:30.9
occ:1.00
|
FE3
|
B:SF4401
|
0.0
|
30.9
|
1.0
|
S2
|
B:SF4401
|
2.2
|
28.6
|
1.0
|
S1
|
B:SF4401
|
2.2
|
28.7
|
1.0
|
S4
|
B:SF4401
|
2.2
|
27.1
|
1.0
|
OAI
|
B:5XR403
|
2.3
|
27.9
|
1.0
|
OAJ
|
B:5XR403
|
3.0
|
27.2
|
1.0
|
FE4
|
B:SF4401
|
3.1
|
28.4
|
1.0
|
CAH
|
B:5XR403
|
3.1
|
28.5
|
1.0
|
FE1
|
B:SF4401
|
3.1
|
26.2
|
1.0
|
FE2
|
B:SF4401
|
3.1
|
28.0
|
1.0
|
S3
|
B:SF4401
|
3.8
|
28.3
|
1.0
|
CE2
|
B:TYR23
|
3.9
|
19.8
|
1.0
|
CD2
|
B:TYR23
|
4.2
|
19.6
|
1.0
|
ND2
|
B:ASN111
|
4.4
|
46.2
|
1.0
|
CAD
|
B:5XR403
|
4.5
|
29.2
|
1.0
|
OAC
|
B:5XR403
|
4.6
|
31.9
|
1.0
|
OE1
|
B:GLN198
|
4.8
|
32.1
|
1.0
|
CE
|
B:MET259
|
4.9
|
30.6
|
1.0
|
CE1
|
B:HIS173
|
4.9
|
16.6
|
1.0
|
SG
|
B:CYS170
|
5.0
|
22.7
|
1.0
|
SG
|
B:CYS83
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 6ora
Go back to
Iron Binding Sites List in 6ora
Iron binding site 8 out
of 8 in the An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of An Unexpected Intermediate in the Reaction Catalyzed By Quinolinate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:28.4
occ:1.00
|
FE4
|
B:SF4401
|
0.0
|
28.4
|
1.0
|
S1
|
B:SF4401
|
2.2
|
28.7
|
1.0
|
S3
|
B:SF4401
|
2.2
|
28.3
|
1.0
|
S2
|
B:SF4401
|
2.2
|
28.6
|
1.0
|
SG
|
B:CYS83
|
2.3
|
31.9
|
1.0
|
FE3
|
B:SF4401
|
3.1
|
30.9
|
1.0
|
FE1
|
B:SF4401
|
3.1
|
26.2
|
1.0
|
FE2
|
B:SF4401
|
3.1
|
28.0
|
1.0
|
CB
|
B:CYS83
|
3.2
|
29.2
|
1.0
|
CA
|
B:CYS83
|
3.6
|
28.6
|
1.0
|
S4
|
B:SF4401
|
3.8
|
27.1
|
1.0
|
N
|
B:ALA84
|
4.1
|
29.8
|
1.0
|
C
|
B:CYS83
|
4.1
|
29.1
|
1.0
|
N
|
B:MET85
|
4.3
|
32.2
|
1.0
|
ND2
|
B:ASN111
|
4.4
|
46.2
|
1.0
|
CB
|
B:MET85
|
4.4
|
32.2
|
1.0
|
CE2
|
B:PHE60
|
4.8
|
34.7
|
1.0
|
OAJ
|
B:5XR403
|
4.9
|
27.2
|
1.0
|
OAI
|
B:5XR403
|
4.9
|
27.9
|
1.0
|
N
|
B:CYS83
|
5.0
|
28.3
|
1.0
|
CA
|
B:MET85
|
5.0
|
33.0
|
1.0
|
|
Reference:
O.A.Esakova,
A.Silakov,
T.L.Grove,
D.M.Warui,
N.H.Yennawar,
S.J.Booker.
An Unexpected Species Determined By X-Ray Crystallography That May Represent An Intermediate in the Reaction Catalyzed By Quinolinate Synthase. J.Am.Chem.Soc. V. 141 14142 2019.
ISSN: ESSN 1520-5126
PubMed: 31390192
DOI: 10.1021/JACS.9B02513
Page generated: Wed Aug 7 05:20:03 2024
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