Iron in PDB 3zgn: Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Enzymatic activity of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
All present enzymatic activity of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway:
1.17.1.2;
Protein crystallography data
The structure of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway, PDB code: 3zgn
was solved by
F.Borel,
E.Barbier,
S.Kratsutsky,
K.Janthawornpong,
M.Rohmer,
C.Dalepoulter,
J.L.Ferrer,
M.Seemann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.87 /
1.95
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.390,
80.570,
70.620,
90.00,
94.46,
90.00
|
R / Rfree (%)
|
20.5 /
25.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
(pdb code 3zgn). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway, PDB code: 3zgn:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 3zgn
Go back to
Iron Binding Sites List in 3zgn
Iron binding site 1 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1311
b:15.7
occ:1.00
|
FE1
|
A:SF41311
|
0.0
|
15.7
|
1.0
|
S2
|
A:SF41311
|
2.1
|
16.7
|
1.0
|
S3
|
A:SF41311
|
2.2
|
16.4
|
1.0
|
S4
|
A:SF41311
|
2.2
|
16.1
|
1.0
|
S2
|
A:10G1310
|
2.4
|
21.8
|
1.0
|
FE2
|
A:SF41311
|
2.8
|
13.0
|
1.0
|
FE4
|
A:SF41311
|
2.8
|
14.7
|
1.0
|
FE3
|
A:SF41311
|
2.9
|
14.5
|
1.0
|
C3
|
A:10G1310
|
3.1
|
21.9
|
1.0
|
C1
|
A:10G1310
|
3.3
|
21.3
|
1.0
|
C4
|
A:10G1310
|
3.4
|
20.3
|
1.0
|
C5
|
A:10G1310
|
3.5
|
20.7
|
1.0
|
S1
|
A:SF41311
|
3.7
|
16.3
|
1.0
|
OG1
|
A:THR167
|
3.9
|
18.0
|
1.0
|
C6
|
A:10G1310
|
4.3
|
19.8
|
1.0
|
CG2
|
A:THR168
|
4.5
|
19.3
|
1.0
|
CB
|
A:CYS96
|
4.6
|
21.1
|
1.0
|
CB
|
A:THR167
|
4.7
|
15.9
|
1.0
|
CG2
|
A:VAL99
|
4.7
|
20.6
|
1.0
|
SG
|
A:CYS96
|
4.8
|
20.4
|
1.0
|
SG
|
A:CYS197
|
4.9
|
16.4
|
1.0
|
SG
|
A:CYS12
|
5.0
|
13.7
|
1.0
|
|
Iron binding site 2 out
of 8 in 3zgn
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Iron Binding Sites List in 3zgn
Iron binding site 2 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1311
b:13.0
occ:1.00
|
FE2
|
A:SF41311
|
0.0
|
13.0
|
1.0
|
S1
|
A:SF41311
|
2.1
|
16.3
|
1.0
|
S4
|
A:SF41311
|
2.2
|
16.1
|
1.0
|
S3
|
A:SF41311
|
2.2
|
16.4
|
1.0
|
SG
|
A:CYS96
|
2.3
|
20.4
|
1.0
|
FE1
|
A:SF41311
|
2.8
|
15.7
|
1.0
|
FE4
|
A:SF41311
|
2.8
|
14.7
|
1.0
|
FE3
|
A:SF41311
|
2.8
|
14.5
|
1.0
|
CB
|
A:CYS96
|
3.1
|
21.1
|
1.0
|
S2
|
A:SF41311
|
3.7
|
16.7
|
1.0
|
CA
|
A:GLY14
|
3.9
|
17.9
|
1.0
|
N
|
A:GLY14
|
4.3
|
19.1
|
1.0
|
CB
|
A:LEU98
|
4.3
|
22.7
|
1.0
|
CD1
|
A:LEU98
|
4.3
|
23.4
|
1.0
|
S2
|
A:10G1310
|
4.5
|
21.8
|
1.0
|
CA
|
A:CYS96
|
4.5
|
22.5
|
1.0
|
CG
|
A:LEU98
|
4.6
|
23.4
|
1.0
|
SG
|
A:CYS12
|
4.8
|
13.7
|
1.0
|
C
|
A:GLY14
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 3 out
of 8 in 3zgn
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Iron Binding Sites List in 3zgn
Iron binding site 3 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1311
b:14.5
occ:1.00
|
FE3
|
A:SF41311
|
0.0
|
14.5
|
1.0
|
S2
|
A:SF41311
|
2.1
|
16.7
|
1.0
|
S4
|
A:SF41311
|
2.1
|
16.1
|
1.0
|
S1
|
A:SF41311
|
2.2
|
16.3
|
1.0
|
SG
|
A:CYS197
|
2.4
|
16.4
|
1.0
|
FE4
|
A:SF41311
|
2.8
|
14.7
|
1.0
|
FE2
|
A:SF41311
|
2.8
|
13.0
|
1.0
|
FE1
|
A:SF41311
|
2.9
|
15.7
|
1.0
|
CB
|
A:CYS197
|
3.1
|
18.5
|
1.0
|
S3
|
A:SF41311
|
3.7
|
16.4
|
1.0
|
CB
|
A:ALA199
|
4.3
|
10.9
|
1.0
|
CD1
|
A:LEU98
|
4.5
|
23.4
|
1.0
|
CA
|
A:CYS197
|
4.6
|
18.2
|
1.0
|
OG1
|
A:THR200
|
4.6
|
14.4
|
1.0
|
CB
|
A:THR167
|
4.7
|
15.9
|
1.0
|
OG1
|
A:THR167
|
4.7
|
18.0
|
1.0
|
O
|
A:HOH2171
|
4.8
|
12.0
|
1.0
|
SG
|
A:CYS12
|
4.8
|
13.7
|
1.0
|
S2
|
A:10G1310
|
4.9
|
21.8
|
1.0
|
SG
|
A:CYS96
|
5.0
|
20.4
|
1.0
|
O
|
A:THR167
|
5.0
|
11.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 3zgn
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Iron Binding Sites List in 3zgn
Iron binding site 4 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1311
b:14.7
occ:1.00
|
FE4
|
A:SF41311
|
0.0
|
14.7
|
1.0
|
S3
|
A:SF41311
|
2.1
|
16.4
|
1.0
|
S1
|
A:SF41311
|
2.2
|
16.3
|
1.0
|
S2
|
A:SF41311
|
2.2
|
16.7
|
1.0
|
SG
|
A:CYS12
|
2.3
|
13.7
|
1.0
|
FE3
|
A:SF41311
|
2.8
|
14.5
|
1.0
|
FE2
|
A:SF41311
|
2.8
|
13.0
|
1.0
|
FE1
|
A:SF41311
|
2.8
|
15.7
|
1.0
|
CB
|
A:CYS12
|
3.3
|
11.5
|
1.0
|
S4
|
A:SF41311
|
3.7
|
16.1
|
1.0
|
N
|
A:GLY14
|
4.2
|
19.1
|
1.0
|
CA
|
A:GLY14
|
4.2
|
17.9
|
1.0
|
N
|
A:VAL15
|
4.2
|
14.4
|
1.0
|
CG2
|
A:VAL15
|
4.4
|
10.3
|
1.0
|
C6
|
A:10G1310
|
4.5
|
19.8
|
1.0
|
CB
|
A:ALA268
|
4.6
|
19.9
|
1.0
|
CA
|
A:CYS12
|
4.6
|
11.6
|
1.0
|
C5
|
A:10G1310
|
4.7
|
20.7
|
1.0
|
C
|
A:GLY14
|
4.7
|
16.8
|
1.0
|
CB
|
A:ALA199
|
4.8
|
10.9
|
1.0
|
C3
|
A:10G1310
|
4.8
|
21.9
|
1.0
|
SG
|
A:CYS96
|
4.9
|
20.4
|
1.0
|
C
|
A:CYS12
|
4.9
|
11.5
|
1.0
|
C4
|
A:10G1310
|
4.9
|
20.3
|
1.0
|
SG
|
A:CYS197
|
4.9
|
16.4
|
1.0
|
N
|
A:ALA13
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 5 out
of 8 in 3zgn
Go back to
Iron Binding Sites List in 3zgn
Iron binding site 5 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1310
b:16.9
occ:1.00
|
FE1
|
B:SF41310
|
0.0
|
16.9
|
1.0
|
S4
|
B:SF41310
|
2.1
|
18.7
|
1.0
|
S2
|
B:SF41310
|
2.1
|
18.8
|
1.0
|
S3
|
B:SF41310
|
2.1
|
18.4
|
1.0
|
S2
|
B:10G1311
|
2.4
|
22.2
|
1.0
|
FE2
|
B:SF41310
|
2.9
|
14.9
|
1.0
|
FE4
|
B:SF41310
|
2.9
|
16.7
|
1.0
|
FE3
|
B:SF41310
|
2.9
|
16.4
|
1.0
|
C1
|
B:10G1311
|
3.1
|
21.1
|
1.0
|
C5
|
B:10G1311
|
3.1
|
20.9
|
1.0
|
C3
|
B:10G1311
|
3.2
|
20.4
|
1.0
|
S1
|
B:SF41310
|
3.7
|
19.4
|
1.0
|
OG1
|
B:THR167
|
3.9
|
19.3
|
1.0
|
C6
|
B:10G1311
|
4.3
|
20.0
|
1.0
|
C4
|
B:10G1311
|
4.4
|
21.2
|
1.0
|
CG2
|
B:THR168
|
4.4
|
21.3
|
1.0
|
CB
|
B:THR167
|
4.6
|
18.0
|
1.0
|
CB
|
B:CYS96
|
4.7
|
17.9
|
1.0
|
SG
|
B:CYS96
|
4.8
|
18.5
|
1.0
|
CG2
|
B:VAL99
|
4.8
|
24.0
|
1.0
|
SG
|
B:CYS197
|
4.8
|
14.2
|
1.0
|
SG
|
B:CYS12
|
5.0
|
15.8
|
1.0
|
|
Iron binding site 6 out
of 8 in 3zgn
Go back to
Iron Binding Sites List in 3zgn
Iron binding site 6 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1310
b:14.9
occ:1.00
|
FE2
|
B:SF41310
|
0.0
|
14.9
|
1.0
|
S4
|
B:SF41310
|
2.1
|
18.7
|
1.0
|
S3
|
B:SF41310
|
2.1
|
18.4
|
1.0
|
S1
|
B:SF41310
|
2.1
|
19.4
|
1.0
|
SG
|
B:CYS96
|
2.3
|
18.5
|
1.0
|
FE1
|
B:SF41310
|
2.9
|
16.9
|
1.0
|
FE3
|
B:SF41310
|
2.9
|
16.4
|
1.0
|
FE4
|
B:SF41310
|
2.9
|
16.7
|
1.0
|
CB
|
B:CYS96
|
3.1
|
17.9
|
1.0
|
S2
|
B:SF41310
|
3.7
|
18.8
|
1.0
|
CA
|
B:GLY14
|
3.9
|
15.4
|
1.0
|
CB
|
B:LEU98
|
4.1
|
18.1
|
1.0
|
CD1
|
B:LEU98
|
4.2
|
18.9
|
1.0
|
N
|
B:GLY14
|
4.3
|
15.2
|
1.0
|
CG
|
B:LEU98
|
4.3
|
17.6
|
1.0
|
CA
|
B:CYS96
|
4.6
|
20.5
|
1.0
|
S2
|
B:10G1311
|
4.6
|
22.2
|
1.0
|
SG
|
B:CYS12
|
4.9
|
15.8
|
1.0
|
N
|
B:LEU98
|
4.9
|
18.3
|
1.0
|
C
|
B:GLY14
|
5.0
|
19.1
|
1.0
|
|
Iron binding site 7 out
of 8 in 3zgn
Go back to
Iron Binding Sites List in 3zgn
Iron binding site 7 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1310
b:16.4
occ:1.00
|
FE3
|
B:SF41310
|
0.0
|
16.4
|
1.0
|
S2
|
B:SF41310
|
2.1
|
18.8
|
1.0
|
S4
|
B:SF41310
|
2.1
|
18.7
|
1.0
|
S1
|
B:SF41310
|
2.1
|
19.4
|
1.0
|
SG
|
B:CYS197
|
2.4
|
14.2
|
1.0
|
FE4
|
B:SF41310
|
2.9
|
16.7
|
1.0
|
FE2
|
B:SF41310
|
2.9
|
14.9
|
1.0
|
FE1
|
B:SF41310
|
2.9
|
16.9
|
1.0
|
CB
|
B:CYS197
|
3.0
|
16.3
|
1.0
|
S3
|
B:SF41310
|
3.7
|
18.4
|
1.0
|
CD1
|
B:LEU98
|
4.3
|
18.9
|
1.0
|
CB
|
B:ALA199
|
4.4
|
12.3
|
1.0
|
CA
|
B:CYS197
|
4.5
|
14.5
|
1.0
|
OG1
|
B:THR200
|
4.5
|
19.0
|
1.0
|
CB
|
B:THR167
|
4.7
|
18.0
|
1.0
|
O
|
B:HOH2163
|
4.7
|
12.5
|
1.0
|
OG1
|
B:THR167
|
4.7
|
19.3
|
1.0
|
SG
|
B:CYS12
|
4.9
|
15.8
|
1.0
|
CB
|
B:LEU98
|
4.9
|
18.1
|
1.0
|
S2
|
B:10G1311
|
4.9
|
22.2
|
1.0
|
SG
|
B:CYS96
|
5.0
|
18.5
|
1.0
|
N
|
B:ALA199
|
5.0
|
17.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 3zgn
Go back to
Iron Binding Sites List in 3zgn
Iron binding site 8 out
of 8 in the Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structures of Escherichia Coli Isph in Complex with Tmbpp A Potent Inhibitor of the Methylerythritol Phosphate Pathway within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1310
b:16.7
occ:1.00
|
FE4
|
B:SF41310
|
0.0
|
16.7
|
1.0
|
S1
|
B:SF41310
|
2.1
|
19.4
|
1.0
|
S2
|
B:SF41310
|
2.1
|
18.8
|
1.0
|
S3
|
B:SF41310
|
2.1
|
18.4
|
1.0
|
SG
|
B:CYS12
|
2.3
|
15.8
|
1.0
|
FE3
|
B:SF41310
|
2.9
|
16.4
|
1.0
|
FE1
|
B:SF41310
|
2.9
|
16.9
|
1.0
|
FE2
|
B:SF41310
|
2.9
|
14.9
|
1.0
|
CB
|
B:CYS12
|
3.2
|
14.7
|
1.0
|
S4
|
B:SF41310
|
3.7
|
18.7
|
1.0
|
N
|
B:GLY14
|
4.2
|
15.2
|
1.0
|
N
|
B:VAL15
|
4.2
|
19.1
|
1.0
|
CA
|
B:GLY14
|
4.3
|
15.4
|
1.0
|
C5
|
B:10G1311
|
4.3
|
20.9
|
1.0
|
CG2
|
B:VAL15
|
4.4
|
12.5
|
1.0
|
C6
|
B:10G1311
|
4.5
|
20.0
|
1.0
|
CB
|
B:ALA268
|
4.6
|
15.7
|
1.0
|
CA
|
B:CYS12
|
4.6
|
14.7
|
1.0
|
C3
|
B:10G1311
|
4.7
|
20.4
|
1.0
|
C
|
B:GLY14
|
4.7
|
19.1
|
1.0
|
CB
|
B:ALA199
|
4.8
|
12.3
|
1.0
|
SG
|
B:CYS197
|
4.9
|
14.2
|
1.0
|
O
|
B:HOH2163
|
4.9
|
12.5
|
1.0
|
C
|
B:CYS12
|
4.9
|
15.4
|
1.0
|
SG
|
B:CYS96
|
4.9
|
18.5
|
1.0
|
N
|
B:ALA13
|
5.0
|
16.8
|
1.0
|
|
Reference:
F.Borel,
E.Barbier,
S.Krasutsky,
K.Janthawornpong,
P.Chaignon,
C.D.Poulter,
J.L.Ferrer,
M.Seemann.
Further Insight Into Crystal Structures of Escherichia Coli Isph/Lytb in Complex with Two Potent Inhibitors of the Mep Pathway: A Starting Point For Rational Design of New Antimicrobials. Chembiochem V. 18 2137 2017.
ISSN: ESSN 1439-7633
PubMed: 28862365
DOI: 10.1002/CBIC.201700363
Page generated: Sun Aug 4 23:04:32 2024
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