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Iron in PDB 3urk: Isph in Complex with Propynyl Diphosphate (1061)

Enzymatic activity of Isph in Complex with Propynyl Diphosphate (1061)

All present enzymatic activity of Isph in Complex with Propynyl Diphosphate (1061):
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with Propynyl Diphosphate (1061), PDB code: 3urk was solved by I.Span, K.Wang, W.Wang, Y.Zhang, A.Bacher, W.Eisenreich, 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) 47.98 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.630, 80.570, 111.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with Propynyl Diphosphate (1061) (pdb code 3urk). 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 Propynyl Diphosphate (1061), PDB code: 3urk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3urk

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Iron binding site 1 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:8.4
occ:1.00
 FE1 A:SF4317 0.0 8.4 1.0
S4 A:SF4317 2.2 8.6 1.0
S2 A:SF4317 2.3 10.1 1.0
S3 A:SF4317 2.3 8.5 1.0
SG A:CYS12 2.3 8.4 1.0
FE4 A:SF4317 2.6 9.0 1.0
FE3 A:SF4317 2.7 17.2 1.0
FE2 A:SF4317 2.7 8.7 1.0
CB A:CYS12 3.3 7.3 1.0
S1 A:SF4317 3.9 9.4 1.0
C28 A:0CG318 4.1 16.0 1.0
N A:GLY14 4.1 7.4 1.0
N A:VAL15 4.3 8.4 1.0
CA A:GLY14 4.3 8.8 1.0
C27 A:0CG318 4.4 11.7 1.0
CG2 A:VAL15 4.4 9.2 1.0
O A:HOH579 4.5 14.2 1.0
CB A:ALA268 4.5 8.8 1.0
CA A:CYS12 4.7 8.0 1.0
SG A:CYS197 4.7 8.8 1.0
CB A:ALA199 4.7 7.5 1.0
C A:GLY14 4.7 8.4 1.0
SG A:CYS96 4.7 8.8 1.0
C A:CYS12 4.9 8.6 1.0
N A:ALA13 4.9 8.0 1.0
C30 A:0CG318 5.0 13.6 1.0

Iron binding site 2 out of 8 in 3urk

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Iron binding site 2 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:8.7
occ:1.00
 FE2 A:SF4317 0.0 8.7 1.0
S3 A:SF4317 2.2 8.5 1.0
S1 A:SF4317 2.3 9.4 1.0
S4 A:SF4317 2.3 8.6 1.0
SG A:CYS96 2.3 8.8 1.0
FE3 A:SF4317 2.6 17.2 1.0
FE4 A:SF4317 2.7 9.0 1.0
FE1 A:SF4317 2.7 8.4 1.0
CB A:CYS96 3.2 9.2 1.0
S2 A:SF4317 3.9 10.1 1.0
CA A:GLY14 4.1 8.8 1.0
O A:HOH579 4.2 14.2 1.0
N A:GLY14 4.3 7.4 1.0
CB A:LEU98 4.4 8.3 1.0
CD1 A:LEU98 4.4 9.7 1.0
CG A:LEU98 4.7 9.8 1.0
SG A:CYS12 4.7 8.4 1.0
CA A:CYS96 4.7 8.4 1.0
SG A:CYS197 4.8 8.8 1.0
N A:LEU98 5.0 9.3 1.0

Iron binding site 3 out of 8 in 3urk

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Iron binding site 3 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:17.2
occ:1.00
 FE3 A:SF4317 0.0 17.2 1.0
O A:HOH579 1.9 14.2 1.0
S4 A:SF4317 2.3 8.6 1.0
S1 A:SF4317 2.4 9.4 1.0
S2 A:SF4317 2.4 10.1 1.0
FE4 A:SF4317 2.6 9.0 1.0
FE2 A:SF4317 2.6 8.7 1.0
FE1 A:SF4317 2.7 8.4 1.0
C27 A:0CG318 3.4 11.7 1.0
C30 A:0CG318 3.6 13.6 1.0
C28 A:0CG318 3.7 16.0 1.0
S3 A:SF4317 3.8 8.5 1.0
OG1 A:THR167 3.9 11.3 1.0
CG2 A:THR168 4.4 8.4 1.0
O A:HOH330 4.4 10.5 1.0
CB A:CYS96 4.6 9.2 1.0
SG A:CYS197 4.6 8.8 1.0
SG A:CYS96 4.6 8.8 1.0
CB A:THR167 4.7 9.8 1.0
SG A:CYS12 4.8 8.4 1.0
CG2 A:VAL99 4.8 10.6 1.0

Iron binding site 4 out of 8 in 3urk

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Iron binding site 4 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:9.0
occ:1.00
 FE4 A:SF4317 0.0 9.0 1.0
S1 A:SF4317 2.2 9.4 1.0
SG A:CYS197 2.3 8.8 1.0
S2 A:SF4317 2.3 10.1 1.0
S3 A:SF4317 2.3 8.5 1.0
FE3 A:SF4317 2.6 17.2 1.0
FE1 A:SF4317 2.6 8.4 1.0
FE2 A:SF4317 2.7 8.7 1.0
CB A:CYS197 3.2 9.1 1.0
S4 A:SF4317 3.8 8.6 1.0
O A:HOH579 4.1 14.2 1.0
CB A:ALA199 4.3 7.5 1.0
OG1 A:THR200 4.6 7.9 1.0
CA A:CYS197 4.7 7.1 1.0
OG1 A:THR167 4.7 11.3 1.0
SG A:CYS12 4.7 8.4 1.0
CD1 A:LEU98 4.7 9.7 1.0
CB A:THR167 4.7 9.8 1.0
O A:HOH325 4.8 9.9 1.0
SG A:CYS96 4.9 8.8 1.0
N A:ALA199 4.9 8.8 1.0
CB A:CYS12 5.0 7.3 1.0

Iron binding site 5 out of 8 in 3urk

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Iron binding site 5 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:9.5
occ:1.00
 FE1 B:SF4317 0.0 9.5 1.0
S4 B:SF4317 2.2 8.9 1.0
S2 B:SF4317 2.3 10.4 1.0
SG B:CYS12 2.3 9.7 1.0
S3 B:SF4317 2.3 9.3 1.0
FE3 B:SF4317 2.6 16.9 1.0
FE4 B:SF4317 2.6 10.0 1.0
FE2 B:SF4317 2.7 9.6 1.0
CB B:CYS12 3.3 9.0 1.0
S1 B:SF4317 3.9 9.9 1.0
N B:GLY14 4.1 8.3 1.0
C28 B:0CG318 4.2 12.5 1.0
CA B:GLY14 4.3 8.0 1.0
N B:VAL15 4.3 9.2 1.0
C27 B:0CG318 4.4 9.8 1.0
CG2 B:VAL15 4.4 10.2 1.0
O B:HOH549 4.5 12.3 1.0
CB B:ALA268 4.6 9.7 1.0
CB B:ALA199 4.7 10.3 1.0
SG B:CYS197 4.7 10.0 1.0
CA B:CYS12 4.7 8.3 1.0
SG B:CYS96 4.7 8.4 1.0
C B:GLY14 4.7 8.2 1.0
C B:CYS12 4.9 9.7 1.0
N B:ALA13 4.9 9.2 1.0
C30 B:0CG318 4.9 11.2 1.0

Iron binding site 6 out of 8 in 3urk

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Iron binding site 6 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:9.6
occ:1.00
 FE2 B:SF4317 0.0 9.6 1.0
S3 B:SF4317 2.2 9.3 1.0
S1 B:SF4317 2.2 9.9 1.0
S4 B:SF4317 2.3 8.9 1.0
SG B:CYS96 2.3 8.4 1.0
FE3 B:SF4317 2.6 16.9 1.0
FE4 B:SF4317 2.7 10.0 1.0
FE1 B:SF4317 2.7 9.5 1.0
CB B:CYS96 3.2 8.5 1.0
S2 B:SF4317 3.9 10.4 1.0
CA B:GLY14 4.0 8.0 1.0
O B:HOH549 4.2 12.3 1.0
N B:GLY14 4.3 8.3 1.0
CD1 B:LEU98 4.3 10.3 1.0
CB B:LEU98 4.4 9.4 1.0
CG B:LEU98 4.6 9.3 1.0
CA B:CYS96 4.6 9.0 1.0
SG B:CYS12 4.6 9.7 1.0
SG B:CYS197 4.8 10.0 1.0
N B:LEU98 4.9 8.1 1.0

Iron binding site 7 out of 8 in 3urk

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Iron binding site 7 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:16.9
occ:1.00
 FE3 B:SF4317 0.0 16.9 1.0
O B:HOH549 1.9 12.3 1.0
S4 B:SF4317 2.2 8.9 1.0
S2 B:SF4317 2.3 10.4 1.0
S1 B:SF4317 2.3 9.9 1.0
FE4 B:SF4317 2.6 10.0 1.0
FE1 B:SF4317 2.6 9.5 1.0
FE2 B:SF4317 2.6 9.6 1.0
C27 B:0CG318 3.5 9.8 1.0
C30 B:0CG318 3.6 11.2 1.0
S3 B:SF4317 3.8 9.3 1.0
C28 B:0CG318 3.8 12.5 1.0
OG1 B:THR167 3.9 9.6 1.0
CG2 B:THR168 4.4 10.3 1.0
O B:HOH348 4.5 11.4 1.0
CB B:CYS96 4.5 8.5 1.0
SG B:CYS197 4.6 10.0 1.0
SG B:CYS96 4.6 8.4 1.0
CB B:THR167 4.7 8.3 1.0
SG B:CYS12 4.8 9.7 1.0
CG2 B:VAL99 4.8 10.3 1.0

Iron binding site 8 out of 8 in 3urk

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Iron binding site 8 out of 8 in the Isph in Complex with Propynyl Diphosphate (1061)


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 Propynyl Diphosphate (1061) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:10.0
occ:1.00
 FE4 B:SF4317 0.0 10.0 1.0
S1 B:SF4317 2.2 9.9 1.0
SG B:CYS197 2.3 10.0 1.0
S2 B:SF4317 2.3 10.4 1.0
S3 B:SF4317 2.3 9.3 1.0
FE3 B:SF4317 2.6 16.9 1.0
FE1 B:SF4317 2.6 9.5 1.0
FE2 B:SF4317 2.7 9.6 1.0
CB B:CYS197 3.2 9.7 1.0
S4 B:SF4317 3.8 8.9 1.0
O B:HOH549 4.1 12.3 1.0
CB B:ALA199 4.3 10.3 1.0
CD1 B:LEU98 4.6 10.3 1.0
OG1 B:THR200 4.6 9.5 1.0
CA B:CYS197 4.7 9.2 1.0
SG B:CYS12 4.7 9.7 1.0
OG1 B:THR167 4.7 9.6 1.0
O B:HOH327 4.8 11.4 1.0
CB B:THR167 4.8 8.3 1.0
SG B:CYS96 4.9 8.4 1.0
N B:ALA199 4.9 9.7 1.0
CB B:CYS12 4.9 9.0 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 Dec 13 15:23:40 2020

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