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Iron in PDB 4mv5: Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate

Enzymatic activity of Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate

All present enzymatic activity of Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate, PDB code: 4mv5 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) 14.87 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.130, 80.900, 111.890, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.9

Other elements in 4mv5:

The structure of Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with 6-Chloropyridin-3-Ylmethyl Diphosphate (pdb code 4mv5). 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 6-Chloropyridin-3-Ylmethyl Diphosphate, PDB code: 4mv5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4mv5

Go back to Iron Binding Sites List in 4mv5
Iron binding site 1 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.4
occ:1.00
 FE1 A:F3S401 0.0 18.4 1.0
S1 A:F3S401 2.3 19.6 1.0
S2 A:F3S401 2.3 20.7 1.0
S3 A:F3S401 2.3 17.8 1.0
SG A:CYS197 2.3 17.4 1.0
FE4 A:F3S401 2.7 18.1 1.0
FE3 A:F3S401 2.7 17.8 1.0
CB A:CYS197 3.2 17.6 1.0
S4 A:F3S401 3.9 19.1 1.0
CB A:ALA199 4.3 18.4 1.0
OG1 A:THR200 4.5 19.5 1.0
OG1 A:THR167 4.6 19.6 1.0
CB A:THR167 4.6 19.1 1.0
CA A:CYS197 4.7 17.7 1.0
SG A:CYS12 4.7 18.1 1.0
O A:HOH510 4.7 18.4 1.0
CD1 A:LEU98 4.7 23.1 1.0
C4 A:2E7402 4.8 33.0 1.0
SG A:CYS96 4.9 19.1 1.0
N3 A:2E7402 4.9 33.7 1.0

Iron binding site 2 out of 6 in 4mv5

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Iron binding site 2 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-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
S3 A:F3S401 2.3 17.8 1.0
S1 A:F3S401 2.3 19.6 1.0
S4 A:F3S401 2.3 19.1 1.0
SG A:CYS96 2.3 19.1 1.0
FE4 A:F3S401 2.7 18.1 1.0
FE1 A:F3S401 2.7 18.4 1.0
CB A:CYS96 3.2 18.8 1.0
S2 A:F3S401 4.0 20.7 1.0
CA A:GLY14 4.0 19.0 1.0
N A:GLY14 4.4 19.4 1.0
CB A:LEU98 4.4 21.8 1.0
CD1 A:LEU98 4.6 23.1 1.0
SG A:CYS12 4.6 18.1 1.0
CA A:CYS96 4.7 18.9 1.0
CG A:LEU98 4.8 22.5 1.0
SG A:CYS197 4.9 17.4 1.0

Iron binding site 3 out of 6 in 4mv5

Go back to Iron Binding Sites List in 4mv5
Iron binding site 3 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.1
occ:1.00
 FE4 A:F3S401 0.0 18.1 1.0
SG A:CYS12 2.2 18.1 1.0
S4 A:F3S401 2.2 19.1 1.0
S2 A:F3S401 2.3 20.7 1.0
S3 A:F3S401 2.3 17.8 1.0
FE1 A:F3S401 2.7 18.4 1.0
FE3 A:F3S401 2.7 17.8 1.0
CB A:CYS12 3.3 18.9 1.0
S1 A:F3S401 3.9 19.6 1.0
N A:GLY14 4.2 19.4 1.0
C7 A:2E7402 4.2 30.7 1.0
C5 A:2E7402 4.2 30.3 1.0
CA A:GLY14 4.3 19.0 1.0
N A:VAL15 4.3 19.4 1.0
C4 A:2E7402 4.4 33.0 1.0
CG2 A:VAL15 4.5 20.4 1.0
CB A:ALA268 4.5 20.6 1.0
CB A:ALA199 4.7 18.4 1.0
CA A:CYS12 4.7 18.4 1.0
SG A:CYS96 4.7 19.1 1.0
SG A:CYS197 4.7 17.4 1.0
C A:GLY14 4.7 19.2 1.0
C6 A:2E7402 4.7 31.3 1.0
C A:CYS12 5.0 19.0 1.0

Iron binding site 4 out of 6 in 4mv5

Go back to Iron Binding Sites List in 4mv5
Iron binding site 4 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:19.7
occ:1.00
 FE1 B:F3S401 0.0 19.7 1.0
S2 B:F3S401 2.3 20.4 1.0
S1 B:F3S401 2.3 20.6 1.0
SG B:CYS197 2.3 18.3 1.0
S3 B:F3S401 2.3 18.2 1.0
FE4 B:F3S401 2.7 18.6 1.0
FE3 B:F3S401 2.8 17.9 1.0
CB B:CYS197 3.2 19.2 1.0
S4 B:F3S401 3.9 18.8 1.0
CB B:ALA199 4.3 18.3 1.0
OG1 B:THR200 4.5 17.6 1.0
OG1 B:THR167 4.6 21.2 1.0
CB B:THR167 4.6 20.8 1.0
O B:HOH513 4.7 20.9 1.0
CA B:CYS197 4.7 19.1 1.0
CD1 B:LEU98 4.7 23.8 1.0
SG B:CYS12 4.7 18.0 1.0
C4 B:2E7402 4.7 31.9 1.0
N3 B:2E7402 4.8 32.5 1.0
SG B:CYS96 4.9 19.7 1.0
O B:THR167 5.0 19.5 1.0
CB B:CYS12 5.0 18.3 1.0

Iron binding site 5 out of 6 in 4mv5

Go back to Iron Binding Sites List in 4mv5
Iron binding site 5 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:17.9
occ:1.00
 FE3 B:F3S401 0.0 17.9 1.0
SG B:CYS96 2.2 19.7 1.0
S1 B:F3S401 2.3 20.6 1.0
S4 B:F3S401 2.3 18.8 1.0
S3 B:F3S401 2.3 18.2 1.0
FE4 B:F3S401 2.8 18.6 1.0
FE1 B:F3S401 2.8 19.7 1.0
CB B:CYS96 3.1 19.1 1.0
S2 B:F3S401 4.0 20.4 1.0
CA B:GLY14 4.1 18.9 1.0
CB B:LEU98 4.4 23.0 1.0
N B:GLY14 4.4 18.9 1.0
CA B:CYS96 4.5 19.6 1.0
CD1 B:LEU98 4.5 23.8 1.0
SG B:CYS12 4.6 18.0 1.0
CG B:LEU98 4.7 23.4 1.0
SG B:CYS197 4.9 18.3 1.0
C2 B:2E7402 5.0 33.2 1.0

Iron binding site 6 out of 6 in 4mv5

Go back to Iron Binding Sites List in 4mv5
Iron binding site 6 out of 6 in the Isph in Complex with 6-Chloropyridin-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 6-Chloropyridin-3-Ylmethyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:18.6
occ:1.00
 FE4 B:F3S401 0.0 18.6 1.0
SG B:CYS12 2.2 18.0 1.0
S4 B:F3S401 2.2 18.8 1.0
S2 B:F3S401 2.3 20.4 1.0
S3 B:F3S401 2.3 18.2 1.0
FE1 B:F3S401 2.7 19.7 1.0
FE3 B:F3S401 2.8 17.9 1.0
CB B:CYS12 3.2 18.3 1.0
S1 B:F3S401 3.9 20.6 1.0
N B:GLY14 4.2 18.9 1.0
C5 B:2E7402 4.3 29.3 1.0
C7 B:2E7402 4.3 28.5 1.0
N B:VAL15 4.3 19.1 1.0
CA B:GLY14 4.4 18.9 1.0
CG2 B:VAL15 4.4 18.1 1.0
C4 B:2E7402 4.4 31.9 1.0
CB B:ALA268 4.4 20.8 1.0
CA B:CYS12 4.6 18.5 1.0
CB B:ALA199 4.6 18.3 1.0
SG B:CYS96 4.7 19.7 1.0
SG B:CYS197 4.7 18.3 1.0
C6 B:2E7402 4.8 31.4 1.0
C B:GLY14 4.8 19.4 1.0
C B:CYS12 4.9 18.6 1.0
N3 B:2E7402 5.0 32.5 1.0
N B:ALA13 5.0 19.2 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 07:02:27 2024

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