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Iron in PDB 4h4c: Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate

Enzymatic activity of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate

All present enzymatic activity of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4c was solved by I.Span, W.Eisenreich, J.Jauch, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.360, 80.370, 111.070, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.2

Other elements in 4h4c:

The structure of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate (pdb code 4h4c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 1 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.1
occ:1.00
 FE1 A:SF4401 0.0 23.1 1.0
S2 A:SF4401 2.2 24.4 1.0
S4 A:SF4401 2.2 19.8 1.0
SG A:CYS12 2.3 19.3 1.0
S3 A:SF4401 2.3 21.5 1.0
FE4 A:SF4401 2.6 22.6 1.0
FE3 A:SF4401 2.7 39.6 1.0
FE2 A:SF4401 2.7 22.6 1.0
CB A:CYS12 3.5 18.0 1.0
C4 A:10D402 3.9 26.3 1.0
S1 A:SF4401 3.9 23.5 1.0
C3 A:10D402 4.1 24.5 1.0
N A:GLY14 4.2 16.3 1.0
C6 A:10D402 4.3 22.4 1.0
CA A:GLY14 4.3 14.3 1.0
C5 A:10D402 4.4 28.2 1.0
N A:VAL15 4.4 15.6 1.0
CG2 A:VAL15 4.4 16.4 1.0
CB A:ALA268 4.5 13.4 1.0
SG A:CYS96 4.6 19.6 1.0
SG A:CYS197 4.7 16.7 1.0
CB A:ALA199 4.7 13.8 1.0
C1 A:10D402 4.7 35.2 1.0
CA A:CYS12 4.8 15.7 1.0
C A:GLY14 4.8 13.4 1.0
F2 A:10D402 4.9 31.4 1.0
C A:CYS12 4.9 16.3 1.0
N A:ALA13 5.0 15.7 1.0

Iron binding site 2 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 2 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.6
occ:1.00
 FE2 A:SF4401 0.0 22.6 1.0
SG A:CYS96 2.2 19.6 1.0
S1 A:SF4401 2.3 23.5 1.0
S3 A:SF4401 2.3 21.5 1.0
S4 A:SF4401 2.4 19.8 1.0
FE4 A:SF4401 2.6 22.6 1.0
FE1 A:SF4401 2.7 23.1 1.0
FE3 A:SF4401 2.7 39.6 1.0
CB A:CYS96 3.1 18.4 1.0
S2 A:SF4401 3.9 24.4 1.0
CA A:GLY14 4.0 14.3 1.0
CB A:LEU98 4.2 21.0 1.0
N A:GLY14 4.3 16.3 1.0
CD1 A:LEU98 4.4 22.9 1.0
CA A:CYS96 4.5 18.3 1.0
SG A:CYS12 4.6 19.3 1.0
CG A:LEU98 4.6 21.5 1.0
F2 A:10D402 4.7 31.4 1.0
C1 A:10D402 4.8 35.2 1.0
SG A:CYS197 4.8 16.7 1.0
N A:LEU98 4.9 19.5 1.0
C A:CYS96 5.0 17.9 1.0

Iron binding site 3 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 3 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:39.6
occ:1.00
 FE3 A:SF4401 0.0 39.6 1.0
S1 A:SF4401 2.3 23.5 1.0
S4 A:SF4401 2.3 19.8 1.0
S2 A:SF4401 2.4 24.4 1.0
C1 A:10D402 2.5 35.2 1.0
C3 A:10D402 2.6 24.5 1.0
FE4 A:SF4401 2.6 22.6 1.0
FE1 A:SF4401 2.7 23.1 1.0
FE2 A:SF4401 2.7 22.6 1.0
C4 A:10D402 2.8 26.3 1.0
F2 A:10D402 3.1 31.4 1.0
C5 A:10D402 3.5 28.2 1.0
OG1 A:THR167 3.8 13.7 1.0
S3 A:SF4401 3.9 21.5 1.0
C6 A:10D402 4.2 22.4 1.0
CB A:CYS96 4.4 18.4 1.0
SG A:CYS197 4.5 16.7 1.0
SG A:CYS96 4.5 19.6 1.0
CG2 A:THR168 4.6 12.8 1.0
CB A:THR167 4.6 14.2 1.0
CG2 A:VAL99 4.8 16.1 1.0
SG A:CYS12 4.8 19.3 1.0
O A:HOH507 5.0 33.0 1.0

Iron binding site 4 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 4 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.6
occ:1.00
 FE4 A:SF4401 0.0 22.6 1.0
S3 A:SF4401 2.3 21.5 1.0
SG A:CYS197 2.3 16.7 1.0
S1 A:SF4401 2.3 23.5 1.0
S2 A:SF4401 2.3 24.4 1.0
FE3 A:SF4401 2.6 39.6 1.0
FE2 A:SF4401 2.6 22.6 1.0
FE1 A:SF4401 2.6 23.1 1.0
CB A:CYS197 3.1 18.2 1.0
S4 A:SF4401 3.9 19.8 1.0
CB A:ALA199 4.3 13.8 1.0
C4 A:10D402 4.5 26.3 1.0
CD1 A:LEU98 4.5 22.9 1.0
CA A:CYS197 4.5 16.4 1.0
OG1 A:THR200 4.6 18.5 1.0
SG A:CYS12 4.6 19.3 1.0
SG A:CYS96 4.7 19.6 1.0
OG1 A:THR167 4.8 13.7 1.0
O A:HOH504 4.8 18.5 1.0
CB A:THR167 4.9 14.2 1.0
CB A:LEU98 4.9 21.0 1.0
N A:ALA199 4.9 17.1 1.0
C3 A:10D402 5.0 24.5 1.0

Iron binding site 5 out of 8 in 4h4c

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Iron binding site 5 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:23.1
occ:1.00
 FE1 B:SF4401 0.0 23.1 1.0
S2 B:SF4401 2.2 26.8 1.0
SG B:CYS12 2.2 20.8 1.0
S4 B:SF4401 2.2 22.0 1.0
S3 B:SF4401 2.4 23.0 1.0
FE3 B:SF4401 2.7 40.8 1.0
FE4 B:SF4401 2.7 24.1 1.0
FE2 B:SF4401 2.7 24.0 1.0
CB B:CYS12 3.3 17.7 1.0
C4 B:10D402 3.8 21.9 1.0
S1 B:SF4401 3.9 22.7 1.0
C3 B:10D402 4.1 21.7 1.0
N B:GLY14 4.2 15.3 1.0
C5 B:10D402 4.3 26.5 1.0
C6 B:10D402 4.3 20.8 1.0
CG2 B:VAL15 4.4 15.7 1.0
CA B:GLY14 4.4 13.8 1.0
N B:VAL15 4.4 15.2 1.0
CB B:ALA268 4.5 14.3 1.0
SG B:CYS96 4.6 22.0 1.0
CB B:ALA199 4.6 15.6 1.0
SG B:CYS197 4.7 21.4 1.0
C1 B:10D402 4.7 27.9 1.0
CA B:CYS12 4.7 17.4 1.0
C B:GLY14 4.8 14.8 1.0
O B:HOH505 4.9 22.8 1.0
C B:CYS12 4.9 17.1 1.0

Iron binding site 6 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 6 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.0
occ:1.00
 FE2 B:SF4401 0.0 24.0 1.0
SG B:CYS96 2.1 22.0 1.0
S3 B:SF4401 2.3 23.0 1.0
S1 B:SF4401 2.3 22.7 1.0
S4 B:SF4401 2.4 22.0 1.0
FE4 B:SF4401 2.7 24.1 1.0
FE1 B:SF4401 2.7 23.1 1.0
FE3 B:SF4401 2.8 40.8 1.0
CB B:CYS96 3.0 20.6 1.0
S2 B:SF4401 3.9 26.8 1.0
CA B:GLY14 4.0 13.8 1.0
CD1 B:LEU98 4.3 20.2 1.0
N B:GLY14 4.3 15.3 1.0
CB B:LEU98 4.3 19.3 1.0
CA B:CYS96 4.4 20.5 1.0
SG B:CYS12 4.5 20.8 1.0
CG B:LEU98 4.7 20.9 1.0
N B:LEU98 4.8 17.5 1.0
C1 B:10D402 4.8 27.9 1.0
SG B:CYS197 4.9 21.4 1.0
C B:CYS96 4.9 20.1 1.0
C B:GLY14 4.9 14.8 1.0
F2 B:10D402 5.0 32.0 1.0

Iron binding site 7 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 7 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:40.8
occ:1.00
 FE3 B:SF4401 0.0 40.8 1.0
S1 B:SF4401 2.3 22.7 1.0
S4 B:SF4401 2.3 22.0 1.0
S2 B:SF4401 2.4 26.8 1.0
C1 B:10D402 2.5 27.9 1.0
C3 B:10D402 2.6 21.7 1.0
FE1 B:SF4401 2.7 23.1 1.0
FE4 B:SF4401 2.7 24.1 1.0
FE2 B:SF4401 2.8 24.0 1.0
C4 B:10D402 2.8 21.9 1.0
F2 B:10D402 3.2 32.0 1.0
C5 B:10D402 3.4 26.5 1.0
OG1 B:THR167 3.9 15.0 1.0
S3 B:SF4401 3.9 23.0 1.0
C6 B:10D402 4.2 20.8 1.0
CG2 B:THR168 4.4 14.0 1.0
CB B:CYS96 4.5 20.6 1.0
SG B:CYS197 4.5 21.4 1.0
SG B:CYS96 4.6 22.0 1.0
CB B:THR167 4.7 15.5 1.0
SG B:CYS12 4.8 20.8 1.0
CG2 B:VAL99 4.9 18.5 1.0

Iron binding site 8 out of 8 in 4h4c

Go back to Iron Binding Sites List in 4h4c
Iron binding site 8 out of 8 in the Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Isph in Complex with (E)-4-Fluoro-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.1
occ:1.00
 FE4 B:SF4401 0.0 24.1 1.0
S3 B:SF4401 2.2 23.0 1.0
SG B:CYS197 2.3 21.4 1.0
S2 B:SF4401 2.3 26.8 1.0
S1 B:SF4401 2.3 22.7 1.0
FE3 B:SF4401 2.7 40.8 1.0
FE1 B:SF4401 2.7 23.1 1.0
FE2 B:SF4401 2.7 24.0 1.0
CB B:CYS197 3.1 21.2 1.0
S4 B:SF4401 3.9 22.0 1.0
CB B:ALA199 4.2 15.6 1.0
CD1 B:LEU98 4.4 20.2 1.0
CA B:CYS197 4.5 18.5 1.0
C4 B:10D402 4.5 21.9 1.0
OG1 B:THR200 4.5 15.3 1.0
SG B:CYS12 4.6 20.8 1.0
SG B:CYS96 4.7 22.0 1.0
O B:HOH505 4.7 22.8 1.0
OG1 B:THR167 4.8 15.0 1.0
N B:ALA199 4.8 15.6 1.0
CB B:THR167 4.8 15.5 1.0
CB B:LEU98 4.9 19.3 1.0
CB B:CYS12 5.0 17.7 1.0
C B:CYS197 5.0 20.1 1.0

Reference:

I.Span, K.Wang, W.Wang, J.Jauch, W.Eisenreich, A.Bacher, E.Oldfield, M.Groll. Structures of Fluoro, Amino, and Thiol Inhibitors Bound to the [Fe(4) S(4) ] Protein Isph. Angew.Chem.Int.Ed.Engl. V. 52 2118 2013.
ISSN: ISSN 1433-7851
PubMed: 23307751
DOI: 10.1002/ANIE.201208469
Page generated: Mon Aug 5 03:09:15 2024

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