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Iron in PDB 3uv6: EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)

Enzymatic activity of EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)

All present enzymatic activity of EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301):
1.17.1.2;

Protein crystallography data

The structure of EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301), PDB code: 3uv6 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.760, 80.470, 111.660, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 20.4

Iron Binding Sites:

The binding sites of Iron atom in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301) (pdb code 3uv6). 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 4-Hydroxybutyl Diphosphate (1301), PDB code: 3uv6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3uv6

Go back to Iron Binding Sites List in 3uv6
Iron binding site 1 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:17.5
occ:1.00
 FE1 A:SF4317 0.0 17.5 1.0
S4 A:SF4317 2.2 18.4 1.0
S2 A:SF4317 2.3 20.2 1.0
SG A:CYS12 2.3 16.8 1.0
S3 A:SF4317 2.3 17.6 1.0
FE4 A:SF4317 2.6 18.2 1.0
FE2 A:SF4317 2.7 18.6 1.0
FE3 A:SF4317 2.8 27.6 1.0
CB A:CYS12 3.3 16.6 1.0
S1 A:SF4317 3.9 20.9 1.0
N A:GLY14 4.1 15.8 1.0
N A:VAL15 4.3 13.7 1.0
CA A:GLY14 4.3 15.6 1.0
C27 A:0CH318 4.4 25.2 1.0
C28 A:0CH318 4.4 22.8 1.0
CG2 A:VAL15 4.5 16.5 1.0
CB A:ALA199 4.5 14.6 1.0
CB A:ALA268 4.6 15.8 1.0
O33 A:0CH318 4.6 24.8 1.0
CA A:CYS12 4.7 15.9 1.0
SG A:CYS197 4.7 17.6 1.0
SG A:CYS96 4.7 18.0 1.0
C A:GLY14 4.8 14.0 1.0
C30 A:0CH318 4.9 28.8 1.0
C A:CYS12 4.9 15.6 1.0
N A:ALA13 4.9 15.5 1.0

Iron binding site 2 out of 8 in 3uv6

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Iron binding site 2 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:18.6
occ:1.00
 FE2 A:SF4317 0.0 18.6 1.0
S3 A:SF4317 2.3 17.6 1.0
S1 A:SF4317 2.3 20.9 1.0
SG A:CYS96 2.3 18.0 1.0
S4 A:SF4317 2.3 18.4 1.0
FE3 A:SF4317 2.6 27.6 1.0
FE1 A:SF4317 2.7 17.5 1.0
FE4 A:SF4317 2.7 18.2 1.0
CB A:CYS96 3.2 17.2 1.0
S2 A:SF4317 3.8 20.2 1.0
CA A:GLY14 4.1 15.6 1.0
O33 A:0CH318 4.2 24.8 1.0
CB A:LEU98 4.4 18.8 1.0
N A:GLY14 4.5 15.8 1.0
CD1 A:LEU98 4.5 18.9 1.0
CA A:CYS96 4.6 16.9 1.0
C13 A:0CH318 4.6 31.5 1.0
SG A:CYS12 4.7 16.8 1.0
CG A:LEU98 4.7 18.6 1.0
SG A:CYS197 4.8 17.6 1.0
N A:LEU98 5.0 18.8 1.0

Iron binding site 3 out of 8 in 3uv6

Go back to Iron Binding Sites List in 3uv6
Iron binding site 3 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:27.6
occ:1.00
 FE3 A:SF4317 0.0 27.6 1.0
O33 A:0CH318 2.0 24.8 1.0
S1 A:SF4317 2.3 20.9 1.0
S4 A:SF4317 2.3 18.4 1.0
S2 A:SF4317 2.4 20.2 1.0
FE2 A:SF4317 2.6 18.6 1.0
FE4 A:SF4317 2.6 18.2 1.0
FE1 A:SF4317 2.8 17.5 1.0
C13 A:0CH318 2.9 31.5 1.0
C27 A:0CH318 3.0 25.2 1.0
C30 A:0CH318 3.3 28.8 1.0
S3 A:SF4317 3.9 17.6 1.0
OG1 A:THR167 4.0 14.8 1.0
C28 A:0CH318 4.0 22.8 1.0
CG2 A:THR168 4.2 16.1 1.0
O A:HOH594 4.5 23.2 1.0
CB A:CYS96 4.5 17.2 1.0
SG A:CYS96 4.5 18.0 1.0
SG A:CYS197 4.7 17.6 1.0
CG2 A:VAL99 4.8 16.6 1.0
SG A:CYS12 4.9 16.8 1.0
CB A:THR167 5.0 15.4 1.0

Iron binding site 4 out of 8 in 3uv6

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Iron binding site 4 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe317

b:18.2
occ:1.00
 FE4 A:SF4317 0.0 18.2 1.0
S2 A:SF4317 2.2 20.2 1.0
S1 A:SF4317 2.3 20.9 1.0
SG A:CYS197 2.3 17.6 1.0
S3 A:SF4317 2.3 17.6 1.0
FE1 A:SF4317 2.6 17.5 1.0
FE3 A:SF4317 2.6 27.6 1.0
FE2 A:SF4317 2.7 18.6 1.0
CB A:CYS197 3.2 17.9 1.0
S4 A:SF4317 3.8 18.4 1.0
CB A:ALA199 4.2 14.6 1.0
OG1 A:THR167 4.4 14.8 1.0
O33 A:0CH318 4.5 24.8 1.0
OG1 A:THR200 4.5 16.0 1.0
CA A:CYS197 4.7 16.3 1.0
SG A:CYS12 4.7 16.8 1.0
CD1 A:LEU98 4.7 18.9 1.0
CB A:THR167 4.7 15.4 1.0
O A:HOH325 4.7 17.3 1.0
SG A:CYS96 4.8 18.0 1.0
CG2 A:THR168 4.8 16.1 1.0

Iron binding site 5 out of 8 in 3uv6

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Iron binding site 5 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:18.5
occ:1.00
 FE1 B:SF4317 0.0 18.5 1.0
S4 B:SF4317 2.2 19.5 1.0
SG B:CYS12 2.3 16.8 1.0
S2 B:SF4317 2.3 22.7 1.0
S3 B:SF4317 2.3 18.1 1.0
FE4 B:SF4317 2.6 20.5 1.0
FE2 B:SF4317 2.7 19.7 1.0
FE3 B:SF4317 2.8 29.5 1.0
CB B:CYS12 3.3 17.0 1.0
S1 B:SF4317 3.9 22.5 1.0
N B:GLY14 4.2 15.1 1.0
CA B:GLY14 4.3 13.9 1.0
N B:VAL15 4.3 16.1 1.0
CG2 B:VAL15 4.4 14.1 1.0
C28 B:0CH318 4.4 21.4 1.0
CB B:ALA199 4.5 17.3 1.0
CB B:ALA268 4.5 15.9 1.0
C27 B:0CH318 4.5 27.2 1.0
CA B:CYS12 4.6 16.1 1.0
SG B:CYS197 4.7 19.1 1.0
SG B:CYS96 4.7 18.8 1.0
C30 B:0CH318 4.7 35.5 1.0
O33 B:0CH318 4.7 27.4 1.0
C B:GLY14 4.8 14.7 1.0
C B:CYS12 4.9 15.5 1.0
N B:ALA13 4.9 15.3 1.0

Iron binding site 6 out of 8 in 3uv6

Go back to Iron Binding Sites List in 3uv6
Iron binding site 6 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:19.7
occ:1.00
 FE2 B:SF4317 0.0 19.7 1.0
S4 B:SF4317 2.3 19.5 1.0
S3 B:SF4317 2.3 18.1 1.0
S1 B:SF4317 2.3 22.5 1.0
SG B:CYS96 2.3 18.8 1.0
FE3 B:SF4317 2.6 29.5 1.0
FE4 B:SF4317 2.7 20.5 1.0
FE1 B:SF4317 2.7 18.5 1.0
CB B:CYS96 3.2 16.5 1.0
S2 B:SF4317 3.9 22.7 1.0
CA B:GLY14 4.1 13.9 1.0
O33 B:0CH318 4.2 27.4 1.0
CB B:LEU98 4.3 19.7 1.0
N B:GLY14 4.5 15.1 1.0
CD1 B:LEU98 4.5 20.5 1.0
CA B:CYS96 4.5 16.2 1.0
SG B:CYS12 4.6 16.8 1.0
CG B:LEU98 4.7 18.8 1.0
SG B:CYS197 4.8 19.1 1.0
C13 B:0CH318 4.8 31.7 1.0
C30 B:0CH318 5.0 35.5 1.0
N B:LEU98 5.0 18.6 1.0

Iron binding site 7 out of 8 in 3uv6

Go back to Iron Binding Sites List in 3uv6
Iron binding site 7 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:29.5
occ:1.00
 FE3 B:SF4317 0.0 29.5 1.0
O33 B:0CH318 2.1 27.4 1.0
S1 B:SF4317 2.3 22.5 1.0
S4 B:SF4317 2.3 19.5 1.0
S2 B:SF4317 2.4 22.7 1.0
FE2 B:SF4317 2.6 19.7 1.0
FE4 B:SF4317 2.6 20.5 1.0
FE1 B:SF4317 2.8 18.5 1.0
C13 B:0CH318 3.0 31.7 1.0
C30 B:0CH318 3.1 35.5 1.0
C27 B:0CH318 3.2 27.2 1.0
S3 B:SF4317 3.9 18.1 1.0
OG1 B:THR167 3.9 15.6 1.0
C28 B:0CH318 4.0 21.4 1.0
CG2 B:THR168 4.1 13.0 1.0
CB B:CYS96 4.5 16.5 1.0
O B:HOH605 4.5 25.2 1.0
SG B:CYS96 4.5 18.8 1.0
SG B:CYS197 4.7 19.1 1.0
CG2 B:VAL99 4.8 16.8 1.0
SG B:CYS12 4.9 16.8 1.0
CB B:THR167 4.9 16.2 1.0

Iron binding site 8 out of 8 in 3uv6

Go back to Iron Binding Sites List in 3uv6
Iron binding site 8 out of 8 in the EC_ISPH in Complex with 4-Hydroxybutyl Diphosphate (1301)


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 4-Hydroxybutyl Diphosphate (1301) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe317

b:20.5
occ:1.00
 FE4 B:SF4317 0.0 20.5 1.0
S2 B:SF4317 2.3 22.7 1.0
S1 B:SF4317 2.3 22.5 1.0
SG B:CYS197 2.3 19.1 1.0
S3 B:SF4317 2.3 18.1 1.0
FE3 B:SF4317 2.6 29.5 1.0
FE1 B:SF4317 2.6 18.5 1.0
FE2 B:SF4317 2.7 19.7 1.0
CB B:CYS197 3.2 18.2 1.0
S4 B:SF4317 3.8 19.5 1.0
CB B:ALA199 4.2 17.3 1.0
OG1 B:THR167 4.4 15.6 1.0
O33 B:0CH318 4.5 27.4 1.0
OG1 B:THR200 4.5 16.0 1.0
CB B:THR167 4.7 16.2 1.0
CA B:CYS197 4.7 15.6 1.0
SG B:CYS12 4.7 16.8 1.0
O B:HOH327 4.7 22.3 1.0
CD1 B:LEU98 4.8 20.5 1.0
CG2 B:THR168 4.8 13.0 1.0
SG B:CYS96 4.8 18.8 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 21:30:48 2024

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