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Iron in PDB 4mux: Isph in Complex with Pyridin-3-Ylmethyl Diphosphate

Enzymatic activity of Isph in Complex with Pyridin-3-Ylmethyl Diphosphate

All present enzymatic activity of Isph in Complex with Pyridin-3-Ylmethyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with Pyridin-3-Ylmethyl Diphosphate, PDB code: 4mux was solved by I.Span, 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.780, 80.820, 111.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.1

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 4mux

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Iron binding site 1 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:38.5
occ:0.50
 FE1 A:SF4401 0.0 38.5 0.5
S4 A:SF4401 2.3 24.4 1.0
N3 A:2E4402 2.3 30.4 1.0
C4 A:2E4402 2.3 31.5 1.0
S2 A:SF4401 2.3 24.9 1.0
S3 A:SF4401 2.4 26.6 1.0
FE2 A:SF4401 2.4 25.2 1.0
FE3 A:SF4401 2.5 24.3 1.0
FE4 A:SF4401 2.6 23.7 1.0
C2 A:2E4402 2.8 28.7 1.0
C5 A:2E4402 2.9 28.5 1.0
C1 A:2E4402 3.3 26.6 1.0
C6 A:2E4402 3.4 26.6 1.0
S1 A:SF4401 3.7 23.3 1.0
C7 A:2E4402 3.9 27.9 1.0
OG1 A:THR167 4.1 26.1 1.0
SG A:CYS197 4.4 24.0 1.0
SG A:CYS96 4.5 27.0 1.0
CG2 A:THR168 4.6 26.1 1.0
SG A:CYS12 4.7 24.8 1.0
CB A:CYS96 4.7 25.3 1.0
CB A:THR167 4.8 25.8 1.0
O8 A:2E4402 4.9 27.9 1.0

Iron binding site 2 out of 8 in 4mux

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Iron binding site 2 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:25.2
occ:1.00
 FE2 A:SF4401 0.0 25.2 1.0
S4 A:SF4401 2.2 24.4 1.0
S3 A:SF4401 2.3 26.6 1.0
SG A:CYS197 2.3 24.0 1.0
S1 A:SF4401 2.3 23.3 1.0
FE1 A:SF4401 2.4 38.5 0.5
FE3 A:SF4401 2.6 24.3 1.0
FE4 A:SF4401 2.7 23.7 1.0
CB A:CYS197 3.2 23.8 1.0
S2 A:SF4401 3.8 24.9 1.0
CB A:ALA199 4.2 23.4 1.0
N3 A:2E4402 4.3 30.4 1.0
C4 A:2E4402 4.4 31.5 1.0
OG1 A:THR200 4.5 23.3 1.0
CA A:CYS197 4.6 23.4 1.0
OG1 A:THR167 4.6 26.1 1.0
CD1 A:LEU98 4.6 28.7 1.0
CB A:THR167 4.7 25.8 1.0
SG A:CYS96 4.7 27.0 1.0
SG A:CYS12 4.7 24.8 1.0
O A:HOH506 4.8 27.2 1.0

Iron binding site 3 out of 8 in 4mux

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Iron binding site 3 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.3
occ:1.00
 FE3 A:SF4401 0.0 24.3 1.0
SG A:CYS96 2.2 27.0 1.0
S1 A:SF4401 2.3 23.3 1.0
S4 A:SF4401 2.3 24.4 1.0
S2 A:SF4401 2.3 24.9 1.0
FE1 A:SF4401 2.5 38.5 0.5
FE4 A:SF4401 2.6 23.7 1.0
FE2 A:SF4401 2.6 25.2 1.0
CB A:CYS96 3.2 25.3 1.0
S3 A:SF4401 3.9 26.6 1.0
CA A:GLY14 4.1 25.2 1.0
CB A:LEU98 4.4 27.5 1.0
N A:GLY14 4.4 25.0 1.0
CD1 A:LEU98 4.5 28.7 1.0
N3 A:2E4402 4.6 30.4 1.0
SG A:CYS12 4.6 24.8 1.0
C2 A:2E4402 4.6 28.7 1.0
CG A:LEU98 4.7 28.1 1.0
CA A:CYS96 4.7 25.2 1.0
C4 A:2E4402 4.8 31.5 1.0
SG A:CYS197 4.8 24.0 1.0
C1 A:2E4402 4.9 26.6 1.0
CB A:CYS197 5.0 23.8 1.0

Iron binding site 4 out of 8 in 4mux

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Iron binding site 4 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.7
occ:1.00
 FE4 A:SF4401 0.0 23.7 1.0
S2 A:SF4401 2.2 24.9 1.0
S3 A:SF4401 2.3 26.6 1.0
S1 A:SF4401 2.3 23.3 1.0
SG A:CYS12 2.3 24.8 1.0
FE3 A:SF4401 2.6 24.3 1.0
FE1 A:SF4401 2.6 38.5 0.5
FE2 A:SF4401 2.7 25.2 1.0
CB A:CYS12 3.3 25.4 1.0
S4 A:SF4401 3.9 24.4 1.0
N A:GLY14 4.1 25.0 1.0
C4 A:2E4402 4.2 31.5 1.0
CA A:GLY14 4.2 25.2 1.0
N A:VAL15 4.3 25.7 1.0
C5 A:2E4402 4.3 28.5 1.0
CG2 A:VAL15 4.4 24.7 1.0
C7 A:2E4402 4.4 27.9 1.0
SG A:CYS96 4.5 27.0 1.0
CB A:ALA268 4.5 26.2 1.0
CB A:ALA199 4.6 23.4 1.0
CA A:CYS12 4.7 24.9 1.0
SG A:CYS197 4.7 24.0 1.0
C A:GLY14 4.7 24.8 1.0
N3 A:2E4402 4.7 30.4 1.0
C A:CYS12 4.9 25.1 1.0
C6 A:2E4402 4.9 26.6 1.0
N A:ALA13 5.0 25.1 1.0

Iron binding site 5 out of 8 in 4mux

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Iron binding site 5 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:37.8
occ:0.50
 FE1 B:SF4401 0.0 37.8 0.5
N3 B:2E4402 2.2 29.6 1.0
S4 B:SF4401 2.3 25.2 1.0
C4 B:2E4402 2.3 29.4 1.0
S3 B:SF4401 2.3 28.1 1.0
S2 B:SF4401 2.4 25.5 1.0
FE2 B:SF4401 2.4 25.2 1.0
FE3 B:SF4401 2.6 24.0 1.0
FE4 B:SF4401 2.6 23.9 1.0
C2 B:2E4402 2.8 27.1 1.0
C5 B:2E4402 2.9 26.2 1.0
C1 B:2E4402 3.3 26.7 1.0
C6 B:2E4402 3.3 28.2 1.0
S1 B:SF4401 3.8 24.4 1.0
C7 B:2E4402 4.0 26.0 1.0
OG1 B:THR167 4.0 24.6 1.0
SG B:CYS197 4.4 24.5 1.0
SG B:CYS96 4.6 25.9 1.0
CG2 B:THR168 4.6 26.0 1.0
SG B:CYS12 4.8 25.3 1.0
CB B:CYS96 4.8 24.2 1.0
CB B:THR167 4.8 25.4 1.0

Iron binding site 6 out of 8 in 4mux

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Iron binding site 6 out of 8 in the Isph in Complex with Pyridin-3-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-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:25.2
occ:1.00
 FE2 B:SF4401 0.0 25.2 1.0
S4 B:SF4401 2.2 25.2 1.0
S3 B:SF4401 2.3 28.1 1.0
SG B:CYS197 2.3 24.5 1.0
S1 B:SF4401 2.3 24.4 1.0
FE1 B:SF4401 2.4 37.8 0.5
FE3 B:SF4401 2.6 24.0 1.0
FE4 B:SF4401 2.6 23.9 1.0
CB B:CYS197 3.2 24.2 1.0
S2 B:SF4401 3.8 25.5 1.0
N3 B:2E4402 4.2 29.6 1.0
CB B:ALA199 4.3 24.0 1.0
C4 B:2E4402 4.4 29.4 1.0
OG1 B:THR200 4.6 23.5 1.0
CA B:CYS197 4.7 23.8 1.0
OG1 B:THR167 4.7 24.6 1.0
SG B:CYS96 4.7 25.9 1.0
CD1 B:LEU98 4.7 26.8 1.0
SG B:CYS12 4.7 25.3 1.0
CB B:THR167 4.7 25.4 1.0
C2 B:2E4402 4.9 27.1 1.0

Iron binding site 7 out of 8 in 4mux

Go back to Iron Binding Sites List in 4mux
Iron binding site 7 out of 8 in the Isph in Complex with Pyridin-3-Ylmethyl Diphosphate


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 Pyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:24.0
occ:1.00
 FE3 B:SF4401 0.0 24.0 1.0
SG B:CYS96 2.2 25.9 1.0
S1 B:SF4401 2.3 24.4 1.0
S4 B:SF4401 2.3 25.2 1.0
S2 B:SF4401 2.3 25.5 1.0
FE4 B:SF4401 2.6 23.9 1.0
FE1 B:SF4401 2.6 37.8 0.5
FE2 B:SF4401 2.6 25.2 1.0
CB B:CYS96 3.2 24.2 1.0
S3 B:SF4401 3.9 28.1 1.0
CA B:GLY14 4.1 26.1 1.0
CB B:LEU98 4.3 26.9 1.0
N B:GLY14 4.4 25.8 1.0
CD1 B:LEU98 4.5 26.8 1.0
N3 B:2E4402 4.6 29.6 1.0
C2 B:2E4402 4.6 27.1 1.0
SG B:CYS12 4.6 25.3 1.0
CA B:CYS96 4.7 24.6 1.0
CG B:LEU98 4.7 26.3 1.0
SG B:CYS197 4.8 24.5 1.0
C4 B:2E4402 4.8 29.4 1.0
C1 B:2E4402 4.8 26.7 1.0

Iron binding site 8 out of 8 in 4mux

Go back to Iron Binding Sites List in 4mux
Iron binding site 8 out of 8 in the Isph in Complex with Pyridin-3-Ylmethyl Diphosphate


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 Pyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:23.9
occ:1.00
 FE4 B:SF4401 0.0 23.9 1.0
S2 B:SF4401 2.2 25.5 1.0
S1 B:SF4401 2.3 24.4 1.0
S3 B:SF4401 2.3 28.1 1.0
SG B:CYS12 2.3 25.3 1.0
FE3 B:SF4401 2.6 24.0 1.0
FE1 B:SF4401 2.6 37.8 0.5
FE2 B:SF4401 2.6 25.2 1.0
CB B:CYS12 3.4 26.5 1.0
S4 B:SF4401 3.9 25.2 1.0
C4 B:2E4402 4.2 29.4 1.0
N B:GLY14 4.2 25.8 1.0
C5 B:2E4402 4.3 26.2 1.0
CA B:GLY14 4.3 26.1 1.0
N B:VAL15 4.3 26.8 1.0
CG2 B:VAL15 4.3 25.1 1.0
CB B:ALA268 4.5 26.6 1.0
SG B:CYS96 4.5 25.9 1.0
C7 B:2E4402 4.5 26.0 1.0
CB B:ALA199 4.6 24.0 1.0
N3 B:2E4402 4.7 29.6 1.0
CA B:CYS12 4.7 26.8 1.0
SG B:CYS197 4.7 24.5 1.0
C B:GLY14 4.7 26.6 1.0
C6 B:2E4402 4.9 28.2 1.0
C B:CYS12 4.9 25.9 1.0
N B:ALA13 4.9 26.3 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: Sun Dec 13 15:42:03 2020

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