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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

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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 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 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 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

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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

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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

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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

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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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