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Iron in PDB 4muy: Isph in Complex with Pyridin-4-Ylmethyl Diphosphate

Enzymatic activity of Isph in Complex with Pyridin-4-Ylmethyl Diphosphate

All present enzymatic activity of Isph in Complex with Pyridin-4-Ylmethyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with Pyridin-4-Ylmethyl Diphosphate, PDB code: 4muy was solved by I.Span, K.Wang, Y.Song, W.Eisenreich, A.Bacher, E.Oldfield, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.190, 80.460, 110.890, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.4

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with Pyridin-4-Ylmethyl Diphosphate (pdb code 4muy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Isph in Complex with Pyridin-4-Ylmethyl Diphosphate, PDB code: 4muy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4muy

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Iron binding site 1 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.7
occ:1.00
 FE1 A:F3S401 0.0 18.7 1.0
SG A:CYS197 2.3 14.7 1.0
S2 A:F3S401 2.3 19.1 1.0
S1 A:F3S401 2.3 19.8 1.0
S3 A:F3S401 2.4 17.1 1.0
FE4 A:F3S401 2.7 17.7 1.0
FE3 A:F3S401 2.7 17.8 1.0
CB A:CYS197 3.2 15.3 1.0
S4 A:F3S401 3.9 19.6 1.0
CB A:ALA199 4.2 14.7 1.0
C3 A:2E5402 4.3 28.6 1.0
OG1 A:THR200 4.5 15.6 1.0
C4 A:2E5402 4.5 30.0 1.0
CA A:CYS197 4.6 15.5 1.0
CD1 A:LEU98 4.6 16.9 1.0
SG A:CYS12 4.7 16.2 1.0
OG1 A:THR167 4.7 15.4 1.0
CB A:THR167 4.8 14.7 1.0
O A:HOH507 4.8 19.1 1.0
SG A:CYS96 4.9 17.6 1.0
N A:ALA199 4.9 15.8 1.0
N2 A:2E5402 5.0 36.5 1.0
N A:THR200 5.0 14.9 1.0

Iron binding site 2 out of 6 in 4muy

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Iron binding site 2 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.8
occ:1.00
 FE3 A:F3S401 0.0 17.8 1.0
SG A:CYS96 2.3 17.6 1.0
S1 A:F3S401 2.3 19.8 1.0
S4 A:F3S401 2.3 19.6 1.0
S3 A:F3S401 2.3 17.1 1.0
FE4 A:F3S401 2.7 17.7 1.0
FE1 A:F3S401 2.7 18.7 1.0
CB A:CYS96 3.1 16.7 1.0
S2 A:F3S401 4.0 19.1 1.0
CA A:GLY14 4.1 15.3 1.0
CB A:LEU98 4.3 16.9 1.0
N A:GLY14 4.5 16.1 1.0
CD1 A:LEU98 4.5 16.9 1.0
C3 A:2E5402 4.5 28.6 1.0
N2 A:2E5402 4.5 36.5 1.0
CA A:CYS96 4.6 17.0 1.0
SG A:CYS12 4.6 16.2 1.0
CG A:LEU98 4.7 17.0 1.0
C1 A:2E5402 4.8 31.5 1.0
C4 A:2E5402 4.8 30.0 1.0
SG A:CYS197 4.9 14.7 1.0

Iron binding site 3 out of 6 in 4muy

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Iron binding site 3 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.7
occ:1.00
 FE4 A:F3S401 0.0 17.7 1.0
SG A:CYS12 2.2 16.2 1.0
S2 A:F3S401 2.3 19.1 1.0
S4 A:F3S401 2.3 19.6 1.0
S3 A:F3S401 2.3 17.1 1.0
FE1 A:F3S401 2.7 18.7 1.0
FE3 A:F3S401 2.7 17.8 1.0
CB A:CYS12 3.2 14.7 1.0
S1 A:F3S401 4.0 19.8 1.0
C4 A:2E5402 4.1 30.0 1.0
N A:GLY14 4.2 16.1 1.0
CA A:GLY14 4.3 15.3 1.0
N A:VAL15 4.3 14.9 1.0
C5 A:2E5402 4.4 32.0 1.0
CG2 A:VAL15 4.4 14.8 1.0
CB A:ALA268 4.5 14.8 1.0
CB A:ALA199 4.6 14.7 1.0
C3 A:2E5402 4.6 28.6 1.0
CA A:CYS12 4.6 15.1 1.0
C7 A:2E5402 4.6 38.2 1.0
SG A:CYS96 4.7 17.6 1.0
SG A:CYS197 4.7 14.7 1.0
C A:GLY14 4.8 15.1 1.0
C A:CYS12 4.9 15.1 1.0
N A:ALA13 5.0 15.4 1.0

Iron binding site 4 out of 6 in 4muy

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Iron binding site 4 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:19.5
occ:1.00
 FE1 B:F3S401 0.0 19.5 1.0
S2 B:F3S401 2.3 19.9 1.0
S1 B:F3S401 2.3 20.4 1.0
SG B:CYS197 2.3 15.4 1.0
S3 B:F3S401 2.4 17.7 1.0
FE4 B:F3S401 2.7 17.7 1.0
FE3 B:F3S401 2.8 18.4 1.0
CB B:CYS197 3.2 15.6 1.0
S4 B:F3S401 3.9 19.1 1.0
C3 B:2E5402 4.1 26.0 1.0
CB B:ALA199 4.2 14.0 1.0
C4 B:2E5402 4.5 26.8 1.0
OG1 B:THR200 4.5 14.9 1.0
CA B:CYS197 4.7 15.8 1.0
CD1 B:LEU98 4.7 17.2 1.0
SG B:CYS12 4.7 16.7 1.0
CB B:THR167 4.8 14.9 1.0
N2 B:2E5402 4.8 34.5 1.0
O B:HOH512 4.8 20.5 1.0
OG1 B:THR167 4.8 15.6 1.0
SG B:CYS96 4.8 17.6 1.0
N B:ALA199 4.9 14.8 1.0
N B:THR200 5.0 14.6 1.0

Iron binding site 5 out of 6 in 4muy

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Iron binding site 5 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.4
occ:1.00
 FE3 B:F3S401 0.0 18.4 1.0
SG B:CYS96 2.2 17.6 1.0
S1 B:F3S401 2.3 20.4 1.0
S3 B:F3S401 2.3 17.7 1.0
S4 B:F3S401 2.3 19.1 1.0
FE4 B:F3S401 2.7 17.7 1.0
FE1 B:F3S401 2.8 19.5 1.0
CB B:CYS96 3.1 15.9 1.0
S2 B:F3S401 4.0 19.9 1.0
CA B:GLY14 4.1 15.4 1.0
CB B:LEU98 4.4 17.4 1.0
N2 B:2E5402 4.4 34.5 1.0
N B:GLY14 4.4 15.8 1.0
C3 B:2E5402 4.5 26.0 1.0
CD1 B:LEU98 4.5 17.2 1.0
CA B:CYS96 4.5 16.3 1.0
SG B:CYS12 4.6 16.7 1.0
CG B:LEU98 4.7 17.2 1.0
C1 B:2E5402 4.7 32.8 1.0
C4 B:2E5402 4.8 26.8 1.0
SG B:CYS197 4.9 15.4 1.0
N B:LEU98 5.0 17.7 1.0

Iron binding site 6 out of 6 in 4muy

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Iron binding site 6 out of 6 in the Isph in Complex with Pyridin-4-Ylmethyl 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 Pyridin-4-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:17.7
occ:1.00
 FE4 B:F3S401 0.0 17.7 1.0
SG B:CYS12 2.2 16.7 1.0
S2 B:F3S401 2.3 19.9 1.0
S4 B:F3S401 2.3 19.1 1.0
S3 B:F3S401 2.3 17.7 1.0
FE1 B:F3S401 2.7 19.5 1.0
FE3 B:F3S401 2.7 18.4 1.0
CB B:CYS12 3.2 15.2 1.0
S1 B:F3S401 3.9 20.4 1.0
C4 B:2E5402 4.1 26.8 1.0
N B:GLY14 4.2 15.8 1.0
CA B:GLY14 4.3 15.4 1.0
N B:VAL15 4.4 15.1 1.0
CB B:ALA268 4.4 15.2 1.0
C5 B:2E5402 4.4 32.4 1.0
C3 B:2E5402 4.5 26.0 1.0
CG2 B:VAL15 4.5 14.5 1.0
CB B:ALA199 4.5 14.0 1.0
CA B:CYS12 4.6 15.6 1.0
SG B:CYS96 4.7 17.6 1.0
SG B:CYS197 4.7 15.4 1.0
C7 B:2E5402 4.8 35.5 1.0
C B:GLY14 4.8 15.2 1.0
C B:CYS12 4.9 15.5 1.0

Reference:

I.Span, K.Wang, W.Eisenreich, A.Bacher, Y.Zhang, E.Oldfield, M.Groll. Insights Into the Binding of Pyridines to the Iron-Sulfur Enzyme Isph. J.Am.Chem.Soc. V. 136 7926 2014.
ISSN: ISSN 0002-7863
PubMed: 24813236
DOI: 10.1021/JA501127J
Page generated: Mon Aug 5 07:01:48 2024

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