Atomistry » Iron » PDB 4m71-4n0k » 4mv5
Atomistry »
  Iron »
    PDB 4m71-4n0k »
      4mv5 »

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

Go back to Iron Binding Sites List in 4mv5
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy