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Iron in PDB 3utc: EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate

Enzymatic activity of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate

All present enzymatic activity of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate, PDB code: 3utc was solved by I.Span, K.Wang, W.Wang, Y.Zhang, A.Bacher, W.Eisenreich, K.Li, C.Schulz, E.Oldfield, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.120, 80.790, 112.560, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 22.7

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 3utc

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Iron binding site 1 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:18.8
occ:1.00
 FE1 A:SF4317 0.0 18.8 1.0
SG A:CYS12 2.2 17.7 1.0
S4 A:SF4317 2.3 20.7 1.0
S3 A:SF4317 2.3 20.3 1.0
S2 A:SF4317 2.3 21.1 1.0
FE4 A:SF4317 2.7 20.5 1.0
FE2 A:SF4317 2.8 20.9 1.0
FE3 A:SF4317 2.8 26.2 1.0
CB A:CYS12 3.2 16.9 1.0
S1 A:SF4317 3.9 20.9 1.0
N A:GLY14 4.1 16.8 1.0
CA A:GLY14 4.3 17.7 1.0
N A:VAL15 4.3 17.6 1.0
CG2 A:VAL15 4.5 17.7 1.0
C30 A:0JX318 4.5 20.4 1.0
CB A:ALA199 4.6 16.0 1.0
CA A:CYS12 4.6 20.9 1.0
CB A:ALA268 4.6 16.4 1.0
SG A:CYS197 4.7 19.5 1.0
SG A:CYS96 4.7 19.4 1.0
C A:GLY14 4.8 19.5 1.0
C A:CYS12 4.8 18.2 1.0
N A:ALA13 4.8 19.4 1.0
O33 A:0JX318 4.9 14.9 1.0
C28 A:0JX318 4.9 24.5 1.0

Iron binding site 2 out of 8 in 3utc

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Iron binding site 2 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:20.9
occ:1.00
 FE2 A:SF4317 0.0 20.9 1.0
S1 A:SF4317 2.3 20.9 1.0
SG A:CYS96 2.3 19.4 1.0
S3 A:SF4317 2.3 20.3 1.0
S4 A:SF4317 2.3 20.7 1.0
FE4 A:SF4317 2.7 20.5 1.0
FE3 A:SF4317 2.7 26.2 1.0
FE1 A:SF4317 2.8 18.8 1.0
CB A:CYS96 3.1 21.4 1.0
S2 A:SF4317 3.9 21.1 1.0
CA A:GLY14 4.0 17.7 1.0
CB A:LEU98 4.1 24.5 1.0
N A:GLY14 4.3 16.8 1.0
O33 A:0JX318 4.5 14.9 1.0
CD1 A:LEU98 4.6 17.0 1.0
CA A:CYS96 4.6 18.8 1.0
CG A:LEU98 4.6 21.9 1.0
SG A:CYS12 4.7 17.7 1.0
SG A:CYS197 4.9 19.5 1.0
N A:LEU98 4.9 23.5 1.0
CE1 A:PHE302 5.0 19.3 1.0

Iron binding site 3 out of 8 in 3utc

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Iron binding site 3 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:26.2
occ:1.00
 FE3 A:SF4317 0.0 26.2 1.0
O33 A:0JX318 2.1 14.9 1.0
S2 A:SF4317 2.3 21.1 1.0
S1 A:SF4317 2.3 20.9 1.0
S4 A:SF4317 2.3 20.7 1.0
FE4 A:SF4317 2.7 20.5 1.0
FE2 A:SF4317 2.7 20.9 1.0
C13 A:0JX318 2.8 22.5 1.0
C30 A:0JX318 2.8 20.4 1.0
FE1 A:SF4317 2.8 18.8 1.0
OG1 A:THR167 3.8 24.0 1.0
S3 A:SF4317 3.9 20.3 1.0
C27 A:0JX318 4.0 28.4 1.0
CG2 A:THR168 4.3 16.3 1.0
C28 A:0JX318 4.6 24.5 1.0
SG A:CYS197 4.6 19.5 1.0
CB A:THR167 4.6 20.4 1.0
CB A:CYS96 4.7 21.4 1.0
SG A:CYS96 4.7 19.4 1.0
CG2 A:VAL99 4.7 20.4 1.0
SG A:CYS12 4.9 17.7 1.0

Iron binding site 4 out of 8 in 3utc

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Iron binding site 4 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:20.5
occ:1.00
 FE4 A:SF4317 0.0 20.5 1.0
S1 A:SF4317 2.3 20.9 1.0
SG A:CYS197 2.3 19.5 1.0
S2 A:SF4317 2.3 21.1 1.0
S3 A:SF4317 2.3 20.3 1.0
FE1 A:SF4317 2.7 18.8 1.0
FE3 A:SF4317 2.7 26.2 1.0
FE2 A:SF4317 2.7 20.9 1.0
CB A:CYS197 3.2 19.7 1.0
S4 A:SF4317 3.8 20.7 1.0
CB A:ALA199 4.2 16.0 1.0
OG1 A:THR200 4.5 19.1 1.0
O33 A:0JX318 4.6 14.9 1.0
CD1 A:LEU98 4.6 17.0 1.0
CA A:CYS197 4.7 19.3 1.0
SG A:CYS12 4.7 17.7 1.0
CB A:THR167 4.7 20.4 1.0
OG1 A:THR167 4.8 24.0 1.0
SG A:CYS96 4.9 19.4 1.0
N A:ALA199 4.9 17.9 1.0
O A:HOH323 4.9 25.9 1.0
CB A:LEU98 4.9 24.5 1.0
CB A:CYS12 5.0 16.9 1.0

Iron binding site 5 out of 8 in 3utc

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Iron binding site 5 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:20.3
occ:1.00
 FE1 B:SF4317 0.0 20.3 1.0
S4 B:SF4317 2.2 19.8 1.0
SG B:CYS12 2.2 17.6 1.0
S2 B:SF4317 2.3 22.9 1.0
S3 B:SF4317 2.3 19.4 1.0
FE4 B:SF4317 2.7 21.3 1.0
FE2 B:SF4317 2.8 20.2 1.0
FE3 B:SF4317 2.8 26.4 1.0
CB B:CYS12 3.2 15.7 1.0
S1 B:SF4317 3.9 21.1 1.0
N B:GLY14 4.1 16.7 1.0
CA B:GLY14 4.3 18.3 1.0
N B:VAL15 4.4 19.3 1.0
CG2 B:VAL15 4.5 17.1 1.0
CB B:ALA268 4.6 18.3 1.0
C30 B:0JX318 4.6 22.8 1.0
CA B:CYS12 4.6 19.1 1.0
CB B:ALA199 4.7 17.6 1.0
SG B:CYS197 4.7 19.9 1.0
SG B:CYS96 4.8 21.4 1.0
C B:GLY14 4.8 21.7 1.0
C13 B:0JX318 4.8 23.6 1.0
C B:CYS12 4.9 19.2 1.0
C28 B:0JX318 4.9 24.1 1.0
O33 B:0JX318 4.9 14.4 1.0
N B:ALA13 4.9 20.4 1.0

Iron binding site 6 out of 8 in 3utc

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Iron binding site 6 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:20.2
occ:1.00
 FE2 B:SF4317 0.0 20.2 1.0
S3 B:SF4317 2.3 19.4 1.0
S1 B:SF4317 2.3 21.1 1.0
SG B:CYS96 2.3 21.4 1.0
S4 B:SF4317 2.3 19.8 1.0
FE4 B:SF4317 2.7 21.3 1.0
FE3 B:SF4317 2.7 26.4 1.0
FE1 B:SF4317 2.8 20.3 1.0
CB B:CYS96 3.2 19.1 1.0
S2 B:SF4317 3.9 22.9 1.0
CA B:GLY14 4.0 18.3 1.0
CB B:LEU98 4.2 19.7 1.0
N B:GLY14 4.3 16.7 1.0
CD1 B:LEU98 4.4 19.4 1.0
CG B:LEU98 4.5 18.9 1.0
CA B:CYS96 4.6 20.7 1.0
O33 B:0JX318 4.6 14.4 1.0
SG B:CYS12 4.7 17.6 1.0
C13 B:0JX318 4.9 23.6 1.0
SG B:CYS197 4.9 19.9 1.0
N B:LEU98 4.9 21.6 1.0

Iron binding site 7 out of 8 in 3utc

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Iron binding site 7 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:26.4
occ:1.00
 FE3 B:SF4317 0.0 26.4 1.0
O33 B:0JX318 2.2 14.4 1.0
S1 B:SF4317 2.3 21.1 1.0
S2 B:SF4317 2.3 22.9 1.0
S4 B:SF4317 2.4 19.8 1.0
C13 B:0JX318 2.7 23.6 1.0
FE4 B:SF4317 2.7 21.3 1.0
FE2 B:SF4317 2.7 20.2 1.0
FE1 B:SF4317 2.8 20.3 1.0
C30 B:0JX318 3.0 22.8 1.0
OG1 B:THR167 3.8 23.3 1.0
S3 B:SF4317 3.9 19.4 1.0
C27 B:0JX318 4.0 28.2 1.0
CG2 B:THR168 4.3 17.5 1.0
CB B:THR167 4.5 22.6 1.0
SG B:CYS197 4.6 19.9 1.0
C28 B:0JX318 4.7 24.1 1.0
CB B:CYS96 4.7 19.1 1.0
SG B:CYS96 4.7 21.4 1.0
CG2 B:VAL99 4.7 21.7 1.0
SG B:CYS12 4.9 17.6 1.0

Iron binding site 8 out of 8 in 3utc

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Iron binding site 8 out of 8 in the EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of EC_ISPH in Complex with (E)-4-Hydroxybut-3-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:21.3
occ:1.00
 FE4 B:SF4317 0.0 21.3 1.0
SG B:CYS197 2.3 19.9 1.0
S1 B:SF4317 2.3 21.1 1.0
S2 B:SF4317 2.3 22.9 1.0
S3 B:SF4317 2.3 19.4 1.0
FE1 B:SF4317 2.7 20.3 1.0
FE3 B:SF4317 2.7 26.4 1.0
FE2 B:SF4317 2.7 20.2 1.0
CB B:CYS197 3.2 17.1 1.0
S4 B:SF4317 3.9 19.8 1.0
CB B:ALA199 4.3 17.6 1.0
CD1 B:LEU98 4.4 19.4 1.0
OG1 B:THR200 4.6 18.1 1.0
CA B:CYS197 4.6 19.1 1.0
CB B:THR167 4.7 22.6 1.0
O33 B:0JX318 4.7 14.4 1.0
SG B:CYS12 4.7 17.6 1.0
OG1 B:THR167 4.8 23.3 1.0
O B:HOH327 4.9 23.8 1.0
SG B:CYS96 4.9 21.4 1.0
N B:ALA199 4.9 19.8 1.0
CB B:CYS12 5.0 15.7 1.0

Reference:

I.Span, K.Wang, W.Wang, Y.Zhang, A.Bacher, W.Eisenreich, K.Li, C.Schulz, E.Oldfield, M.Groll. Discovery of Acetylene Hydratase Activity of the Iron-Sulphur Protein Isph. Nat Commun V. 3 1042 2012.
ISSN: ESSN 2041-1723
PubMed: 22948824
DOI: 10.1038/NCOMMS2052
Page generated: Sun Aug 4 21:21:44 2024

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