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Iron in PDB 3uv7: EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)

Enzymatic activity of EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)

All present enzymatic activity of EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300):
1.17.1.2;

Protein crystallography data

The structure of EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300), PDB code: 3uv7 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) 50.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.400, 80.510, 111.730, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21

Iron Binding Sites:

The binding sites of Iron atom in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300) (pdb code 3uv7). 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 Buta-2,3-Dienyl Diphosphate (1300), PDB code: 3uv7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3uv7

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Iron binding site 1 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:11.3
occ:1.00
 FE1 A:SF4317 0.0 11.3 1.0
S3 A:SF4317 2.3 11.5 1.0
S4 A:SF4317 2.3 13.0 1.0
S2 A:SF4317 2.3 14.4 1.0
SG A:CYS12 2.3 11.7 1.0
FE4 A:SF4317 2.6 12.9 1.0
FE2 A:SF4317 2.7 12.8 1.0
FE3 A:SF4317 2.7 15.9 1.0
CB A:CYS12 3.3 10.8 1.0
S1 A:SF4317 3.9 16.2 1.0
N A:GLY14 4.1 11.1 1.0
CA A:GLY14 4.3 12.1 1.0
N A:VAL15 4.3 10.4 1.0
C28 A:0CN318 4.3 16.3 1.0
C27 A:0CN318 4.4 14.7 1.0
CG2 A:VAL15 4.5 11.2 1.0
CB A:ALA268 4.5 11.6 1.0
CB A:ALA199 4.6 11.1 1.0
O A:HOH579 4.6 17.9 1.0
CA A:CYS12 4.7 9.8 1.0
SG A:CYS197 4.7 11.7 1.0
C A:GLY14 4.7 11.2 1.0
SG A:CYS96 4.7 12.1 1.0
C30 A:0CN318 4.8 15.8 1.0
N A:ALA13 4.9 11.5 1.0
C A:CYS12 4.9 10.2 1.0

Iron binding site 2 out of 8 in 3uv7

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Iron binding site 2 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:12.8
occ:1.00
 FE2 A:SF4317 0.0 12.8 1.0
S1 A:SF4317 2.3 16.2 1.0
S4 A:SF4317 2.3 13.0 1.0
SG A:CYS96 2.3 12.1 1.0
S3 A:SF4317 2.3 11.5 1.0
FE3 A:SF4317 2.6 15.9 1.0
FE4 A:SF4317 2.7 12.9 1.0
FE1 A:SF4317 2.7 11.3 1.0
CB A:CYS96 3.1 10.3 1.0
S2 A:SF4317 3.9 14.4 1.0
CA A:GLY14 4.0 12.1 1.0
O A:HOH579 4.2 17.9 1.0
CB A:LEU98 4.3 13.5 1.0
N A:GLY14 4.3 11.1 1.0
CD1 A:LEU98 4.5 14.7 1.0
CA A:CYS96 4.6 11.1 1.0
CG A:LEU98 4.6 15.0 1.0
SG A:CYS12 4.7 11.7 1.0
SG A:CYS197 4.9 11.7 1.0
N A:LEU98 5.0 12.9 1.0
C A:GLY14 5.0 11.2 1.0

Iron binding site 3 out of 8 in 3uv7

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Iron binding site 3 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:15.9
occ:1.00
 FE3 A:SF4317 0.0 15.9 1.0
O A:HOH579 2.0 17.9 1.0
S4 A:SF4317 2.3 13.0 1.0
S1 A:SF4317 2.3 16.2 1.0
S2 A:SF4317 2.3 14.4 1.0
FE4 A:SF4317 2.6 12.9 1.0
FE2 A:SF4317 2.6 12.8 1.0
FE1 A:SF4317 2.7 11.3 1.0
C27 A:0CN318 3.1 14.7 1.0
C30 A:0CN318 3.2 15.8 1.0
C13 A:0CN318 3.8 9.0 1.0
S3 A:SF4317 3.9 11.5 1.0
OG1 A:THR167 3.9 12.4 1.0
C28 A:0CN318 4.0 16.3 1.0
CG2 A:THR168 4.4 10.8 1.0
CB A:CYS96 4.5 10.3 1.0
SG A:CYS197 4.6 11.7 1.0
O A:HOH330 4.6 13.4 1.0
SG A:CYS96 4.6 12.1 1.0
CB A:THR167 4.7 11.2 1.0
SG A:CYS12 4.8 11.7 1.0
CG2 A:VAL99 4.9 13.0 1.0

Iron binding site 4 out of 8 in 3uv7

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Iron binding site 4 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:12.9
occ:1.00
 FE4 A:SF4317 0.0 12.9 1.0
S1 A:SF4317 2.3 16.2 1.0
S2 A:SF4317 2.3 14.4 1.0
S3 A:SF4317 2.3 11.5 1.0
SG A:CYS197 2.3 11.7 1.0
FE3 A:SF4317 2.6 15.9 1.0
FE1 A:SF4317 2.6 11.3 1.0
FE2 A:SF4317 2.7 12.8 1.0
CB A:CYS197 3.2 11.7 1.0
S4 A:SF4317 3.8 13.0 1.0
O A:HOH579 4.2 17.9 1.0
CB A:ALA199 4.2 11.1 1.0
OG1 A:THR200 4.6 11.6 1.0
OG1 A:THR167 4.7 12.4 1.0
CA A:CYS197 4.7 10.9 1.0
SG A:CYS12 4.7 11.7 1.0
CD1 A:LEU98 4.7 14.7 1.0
CB A:THR167 4.7 11.2 1.0
O A:HOH325 4.8 12.2 1.0
SG A:CYS96 4.9 12.1 1.0
N A:ALA199 4.9 11.5 1.0
CB A:CYS12 4.9 10.8 1.0

Iron binding site 5 out of 8 in 3uv7

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Iron binding site 5 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:11.6
occ:1.00
 FE1 B:SF4317 0.0 11.6 1.0
S3 B:SF4317 2.3 12.3 1.0
S2 B:SF4317 2.3 15.0 1.0
SG B:CYS12 2.3 12.1 1.0
S4 B:SF4317 2.3 12.8 1.0
FE4 B:SF4317 2.6 13.6 1.0
FE2 B:SF4317 2.7 12.5 1.0
FE3 B:SF4317 2.7 16.4 1.0
CB B:CYS12 3.3 11.1 1.0
S1 B:SF4317 3.9 15.5 1.0
N B:GLY14 4.1 11.1 1.0
N B:VAL15 4.3 11.2 1.0
C27 B:0CN318 4.3 15.6 1.0
C28 B:0CN318 4.4 15.4 1.0
CA B:GLY14 4.4 10.5 1.0
CG2 B:VAL15 4.5 11.0 1.0
CB B:ALA199 4.5 13.1 1.0
CB B:ALA268 4.6 12.9 1.0
SG B:CYS197 4.7 12.9 1.0
CA B:CYS12 4.7 10.8 1.0
O B:HOH549 4.7 16.8 1.0
SG B:CYS96 4.7 12.8 1.0
C30 B:0CN318 4.8 16.3 1.0
C B:GLY14 4.8 10.6 1.0
C B:CYS12 4.9 11.0 1.0
N B:ALA13 4.9 11.2 1.0

Iron binding site 6 out of 8 in 3uv7

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Iron binding site 6 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:12.5
occ:1.00
 FE2 B:SF4317 0.0 12.5 1.0
S1 B:SF4317 2.3 15.5 1.0
S3 B:SF4317 2.3 12.3 1.0
SG B:CYS96 2.3 12.8 1.0
S4 B:SF4317 2.3 12.8 1.0
FE3 B:SF4317 2.6 16.4 1.0
FE4 B:SF4317 2.7 13.6 1.0
FE1 B:SF4317 2.7 11.6 1.0
CB B:CYS96 3.2 10.4 1.0
S2 B:SF4317 3.9 15.0 1.0
CA B:GLY14 4.1 10.5 1.0
O B:HOH549 4.2 16.8 1.0
N B:GLY14 4.3 11.1 1.0
CB B:LEU98 4.4 11.9 1.0
CD1 B:LEU98 4.4 13.5 1.0
CA B:CYS96 4.6 11.3 1.0
CG B:LEU98 4.6 12.2 1.0
SG B:CYS12 4.6 12.1 1.0
SG B:CYS197 4.8 12.9 1.0
N B:LEU98 4.9 11.0 1.0

Iron binding site 7 out of 8 in 3uv7

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Iron binding site 7 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:16.4
occ:1.00
 FE3 B:SF4317 0.0 16.4 1.0
O B:HOH549 2.0 16.8 1.0
S4 B:SF4317 2.3 12.8 1.0
S1 B:SF4317 2.3 15.5 1.0
S2 B:SF4317 2.4 15.0 1.0
FE4 B:SF4317 2.6 13.6 1.0
FE2 B:SF4317 2.6 12.5 1.0
FE1 B:SF4317 2.7 11.6 1.0
C27 B:0CN318 3.2 15.6 1.0
C30 B:0CN318 3.2 16.3 1.0
C13 B:0CN318 3.8 8.8 1.0
S3 B:SF4317 3.8 12.3 1.0
OG1 B:THR167 4.0 12.6 1.0
C28 B:0CN318 4.1 15.4 1.0
CG2 B:THR168 4.3 10.6 1.0
CB B:CYS96 4.5 10.4 1.0
SG B:CYS96 4.5 12.8 1.0
SG B:CYS197 4.6 12.9 1.0
O B:HOH345 4.6 16.0 1.0
CB B:THR167 4.7 11.6 1.0
CG2 B:VAL99 4.8 13.4 1.0
SG B:CYS12 4.8 12.1 1.0

Iron binding site 8 out of 8 in 3uv7

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Iron binding site 8 out of 8 in the EC_ISPH in Complex with Buta-2,3-Dienyl Diphosphate (1300)


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 Buta-2,3-Dienyl Diphosphate (1300) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:13.6
occ:1.00
 FE4 B:SF4317 0.0 13.6 1.0
S1 B:SF4317 2.3 15.5 1.0
SG B:CYS197 2.3 12.9 1.0
S2 B:SF4317 2.3 15.0 1.0
S3 B:SF4317 2.3 12.3 1.0
FE3 B:SF4317 2.6 16.4 1.0
FE1 B:SF4317 2.6 11.6 1.0
FE2 B:SF4317 2.7 12.5 1.0
CB B:CYS197 3.2 12.4 1.0
S4 B:SF4317 3.8 12.8 1.0
CB B:ALA199 4.2 13.1 1.0
O B:HOH549 4.2 16.8 1.0
OG1 B:THR200 4.6 12.0 1.0
CD1 B:LEU98 4.6 13.5 1.0
CA B:CYS197 4.7 11.8 1.0
SG B:CYS12 4.7 12.1 1.0
OG1 B:THR167 4.8 12.6 1.0
O B:HOH326 4.8 13.5 1.0
CB B:THR167 4.8 11.6 1.0
SG B:CYS96 4.9 12.8 1.0
N B:ALA199 4.9 12.5 1.0
CB B:CYS12 5.0 11.1 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 21:31:04 2024

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