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Iron in PDB 4h4e: Isph in Complex with (E)-4-Mercapto-3-Methylbut-2-Enyl Diphosphate

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

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

Protein crystallography data

The structure of Isph in Complex with (E)-4-Mercapto-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4e 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.700, 80.670, 111.460, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with (E)-4-Mercapto-3-Methylbut-2-Enyl Diphosphate (pdb code 4h4e). 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-Mercapto-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4h4e

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Iron binding site 1 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:15.3
occ:1.00
 FE1 A:SF4401 0.0 15.3 1.0
S4 A:SF4401 2.2 16.5 1.0
SG A:CYS12 2.3 15.3 1.0
S2 A:SF4401 2.3 16.6 1.0
S3 A:SF4401 2.3 15.7 1.0
FE4 A:SF4401 2.7 16.0 1.0
FE2 A:SF4401 2.7 15.9 1.0
FE3 A:SF4401 2.7 18.0 1.0
CB A:CYS12 3.4 15.6 1.0
S1 A:SF4401 3.9 16.7 1.0
N A:GLY14 4.1 14.8 1.0
CA A:GLY14 4.3 15.1 1.0
N A:VAL15 4.4 15.0 1.0
C6 A:10G402 4.4 16.3 1.0
CG2 A:VAL15 4.5 15.6 1.0
C5 A:10G402 4.5 17.9 1.0
CB A:ALA268 4.6 15.9 1.0
SG A:CYS197 4.7 15.9 1.0
CA A:CYS12 4.7 15.4 1.0
SG A:CYS96 4.7 15.2 1.0
C A:GLY14 4.7 15.0 1.0
CB A:ALA199 4.8 15.1 1.0
N A:ALA13 4.8 15.4 1.0
C3 A:10G402 4.9 24.8 1.0
C A:CYS12 4.9 15.3 1.0
S2 A:10G402 4.9 23.1 1.0

Iron binding site 2 out of 8 in 4h4e

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Iron binding site 2 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:15.9
occ:1.00
 FE2 A:SF4401 0.0 15.9 1.0
S3 A:SF4401 2.3 15.7 1.0
SG A:CYS96 2.3 15.2 1.0
S1 A:SF4401 2.3 16.7 1.0
S4 A:SF4401 2.3 16.5 1.0
FE3 A:SF4401 2.7 18.0 1.0
FE4 A:SF4401 2.7 16.0 1.0
FE1 A:SF4401 2.7 15.3 1.0
CB A:CYS96 3.2 15.1 1.0
S2 A:SF4401 3.9 16.6 1.0
CA A:GLY14 4.0 15.1 1.0
N A:GLY14 4.3 14.8 1.0
CB A:LEU98 4.3 18.3 1.0
CD1 A:LEU98 4.4 18.1 1.0
S2 A:10G402 4.4 23.1 1.0
CG A:LEU98 4.6 18.3 1.0
CA A:CYS96 4.6 15.7 1.0
SG A:CYS12 4.7 15.3 1.0
SG A:CYS197 4.9 15.9 1.0

Iron binding site 3 out of 8 in 4h4e

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Iron binding site 3 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.0
occ:1.00
 FE3 A:SF4401 0.0 18.0 1.0
S2 A:10G402 2.3 23.1 1.0
S1 A:SF4401 2.3 16.7 1.0
S2 A:SF4401 2.3 16.6 1.0
S4 A:SF4401 2.3 16.5 1.0
FE2 A:SF4401 2.7 15.9 1.0
FE4 A:SF4401 2.7 16.0 1.0
FE1 A:SF4401 2.7 15.3 1.0
C3 A:10G402 3.3 24.8 1.0
C1 A:10G402 3.4 26.4 1.0
C5 A:10G402 3.4 17.9 1.0
C4 A:10G402 3.8 24.5 1.0
S3 A:SF4401 3.9 15.7 1.0
OG1 A:THR167 3.9 20.1 1.0
C6 A:10G402 4.2 16.3 1.0
CG2 A:THR168 4.5 17.5 1.0
CB A:CYS96 4.6 15.1 1.0
SG A:CYS96 4.6 15.2 1.0
SG A:CYS197 4.6 15.9 1.0
CB A:THR167 4.7 17.8 1.0
CG2 A:VAL99 4.7 17.4 1.0
SG A:CYS12 4.9 15.3 1.0

Iron binding site 4 out of 8 in 4h4e

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Iron binding site 4 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:16.0
occ:1.00
 FE4 A:SF4401 0.0 16.0 1.0
S1 A:SF4401 2.2 16.7 1.0
SG A:CYS197 2.3 15.9 1.0
S2 A:SF4401 2.3 16.6 1.0
S3 A:SF4401 2.4 15.7 1.0
FE3 A:SF4401 2.7 18.0 1.0
FE1 A:SF4401 2.7 15.3 1.0
FE2 A:SF4401 2.7 15.9 1.0
CB A:CYS197 3.2 15.7 1.0
S4 A:SF4401 3.9 16.5 1.0
CB A:ALA199 4.4 15.1 1.0
CD1 A:LEU98 4.6 18.1 1.0
OG1 A:THR200 4.6 15.8 1.0
CA A:CYS197 4.7 15.2 1.0
OG1 A:THR167 4.7 20.1 1.0
SG A:CYS12 4.7 15.3 1.0
CB A:THR167 4.7 17.8 1.0
S2 A:10G402 4.7 23.1 1.0
O A:HOH508 4.8 16.4 1.0
SG A:CYS96 4.8 15.2 1.0

Iron binding site 5 out of 8 in 4h4e

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Iron binding site 5 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.3
occ:1.00
 FE1 B:SF4401 0.0 16.3 1.0
S4 B:SF4401 2.2 16.8 1.0
SG B:CYS12 2.2 16.5 1.0
S2 B:SF4401 2.3 17.1 1.0
S3 B:SF4401 2.3 15.8 1.0
FE4 B:SF4401 2.7 16.8 1.0
FE2 B:SF4401 2.7 16.2 1.0
FE3 B:SF4401 2.7 18.4 1.0
CB B:CYS12 3.3 15.7 1.0
S1 B:SF4401 3.9 17.3 1.0
N B:GLY14 4.1 15.6 1.0
CA B:GLY14 4.3 15.6 1.0
N B:VAL15 4.4 15.9 1.0
CG2 B:VAL15 4.4 15.7 1.0
C6 B:10G402 4.4 18.3 1.0
C5 B:10G402 4.5 18.5 1.0
CB B:ALA268 4.6 16.5 1.0
CA B:CYS12 4.7 15.9 1.0
CB B:ALA199 4.7 16.1 1.0
SG B:CYS96 4.7 16.6 1.0
SG B:CYS197 4.7 16.1 1.0
C B:GLY14 4.8 15.8 1.0
C3 B:10G402 4.8 26.8 1.0
C B:CYS12 4.9 15.7 1.0
N B:ALA13 4.9 15.7 1.0
S2 B:10G402 4.9 24.3 1.0

Iron binding site 6 out of 8 in 4h4e

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Iron binding site 6 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.2
occ:1.00
 FE2 B:SF4401 0.0 16.2 1.0
S3 B:SF4401 2.2 15.8 1.0
S1 B:SF4401 2.3 17.3 1.0
SG B:CYS96 2.3 16.6 1.0
S4 B:SF4401 2.3 16.8 1.0
FE3 B:SF4401 2.7 18.4 1.0
FE4 B:SF4401 2.7 16.8 1.0
FE1 B:SF4401 2.7 16.3 1.0
CB B:CYS96 3.2 15.7 1.0
S2 B:SF4401 3.9 17.1 1.0
CA B:GLY14 4.0 15.6 1.0
CD1 B:LEU98 4.3 18.1 1.0
N B:GLY14 4.3 15.6 1.0
CB B:LEU98 4.3 18.3 1.0
S2 B:10G402 4.4 24.3 1.0
CG B:LEU98 4.6 18.7 1.0
CA B:CYS96 4.6 16.1 1.0
SG B:CYS12 4.6 16.5 1.0
SG B:CYS197 4.9 16.1 1.0

Iron binding site 7 out of 8 in 4h4e

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Iron binding site 7 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.4
occ:1.00
 FE3 B:SF4401 0.0 18.4 1.0
S2 B:10G402 2.3 24.3 1.0
S1 B:SF4401 2.3 17.3 1.0
S4 B:SF4401 2.3 16.8 1.0
S2 B:SF4401 2.3 17.1 1.0
FE2 B:SF4401 2.7 16.2 1.0
FE4 B:SF4401 2.7 16.8 1.0
FE1 B:SF4401 2.7 16.3 1.0
C3 B:10G402 3.3 26.8 1.0
C1 B:10G402 3.4 28.6 1.0
C5 B:10G402 3.5 18.5 1.0
C4 B:10G402 3.7 25.2 1.0
S3 B:SF4401 3.9 15.8 1.0
OG1 B:THR167 3.9 21.0 1.0
C6 B:10G402 4.3 18.3 1.0
CG2 B:THR168 4.5 19.2 1.0
CB B:CYS96 4.5 15.7 1.0
SG B:CYS96 4.6 16.6 1.0
SG B:CYS197 4.7 16.1 1.0
CB B:THR167 4.7 19.2 1.0
CG2 B:VAL99 4.7 17.7 1.0
SG B:CYS12 4.8 16.5 1.0

Iron binding site 8 out of 8 in 4h4e

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Iron binding site 8 out of 8 in the Isph in Complex with (E)-4-Mercapto-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-Mercapto-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.8
occ:1.00
 FE4 B:SF4401 0.0 16.8 1.0
S1 B:SF4401 2.3 17.3 1.0
SG B:CYS197 2.3 16.1 1.0
S2 B:SF4401 2.3 17.1 1.0
S3 B:SF4401 2.3 15.8 1.0
FE3 B:SF4401 2.7 18.4 1.0
FE1 B:SF4401 2.7 16.3 1.0
FE2 B:SF4401 2.7 16.2 1.0
CB B:CYS197 3.2 16.5 1.0
S4 B:SF4401 3.8 16.8 1.0
CB B:ALA199 4.3 16.1 1.0
CD1 B:LEU98 4.5 18.1 1.0
OG1 B:THR200 4.6 17.3 1.0
OG1 B:THR167 4.7 21.0 1.0
CA B:CYS197 4.7 16.3 1.0
S2 B:10G402 4.7 24.3 1.0
SG B:CYS12 4.7 16.5 1.0
CB B:THR167 4.7 19.2 1.0
O B:HOH503 4.8 16.5 1.0
SG B:CYS96 4.9 16.6 1.0
CB B:CYS12 5.0 15.7 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 03:11:01 2024

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