Atomistry » Iron » PDB 4gl7-4h9l » 4h4d
Atomistry »
  Iron »
    PDB 4gl7-4h9l »
      4h4d »

Iron in PDB 4h4d: Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate

Enzymatic activity of Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate

All present enzymatic activity of Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate:
1.17.1.2;

Protein crystallography data

The structure of Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4d was solved by I.Span, W.Eisenreich, J.Jauch, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.320, 80.710, 112.110, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.4

Iron Binding Sites:

The binding sites of Iron atom in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate (pdb code 4h4d). 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate, PDB code: 4h4d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 1 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.1
occ:1.00
 FE1 A:SF4401 0.0 17.1 1.0
N2 A:10E402 2.0 18.3 1.0
S4 A:SF4401 2.3 11.8 1.0
S2 A:SF4401 2.3 10.1 1.0
S3 A:SF4401 2.4 10.7 1.0
FE3 A:SF4401 2.6 9.9 1.0
FE2 A:SF4401 2.6 10.3 1.0
FE4 A:SF4401 2.7 9.3 1.0
C1 A:10E402 3.1 13.2 1.0
C3 A:10E402 3.1 12.0 1.0
C5 A:10E402 3.2 10.7 1.0
C4 A:10E402 3.7 11.8 1.0
S1 A:SF4401 3.8 9.7 1.0
OG1 A:THR167 3.9 10.7 1.0
C6 A:10E402 4.1 12.3 1.0
SG A:CYS96 4.5 9.2 1.0
SG A:CYS197 4.5 9.6 1.0
CB A:CYS96 4.6 9.0 1.0
CG2 A:THR168 4.6 10.8 1.0
CB A:THR167 4.7 9.9 1.0
CG2 A:VAL99 4.8 10.4 1.0
SG A:CYS12 4.9 8.8 1.0

Iron binding site 2 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 2 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:10.3
occ:1.00
 FE2 A:SF4401 0.0 10.3 1.0
S4 A:SF4401 2.3 11.8 1.0
SG A:CYS197 2.3 9.6 1.0
S3 A:SF4401 2.3 10.7 1.0
S1 A:SF4401 2.3 9.7 1.0
FE1 A:SF4401 2.6 17.1 1.0
FE4 A:SF4401 2.7 9.3 1.0
FE3 A:SF4401 2.7 9.9 1.0
CB A:CYS197 3.3 9.8 1.0
S2 A:SF4401 3.8 10.1 1.0
N2 A:10E402 4.2 18.3 1.0
CB A:ALA199 4.3 10.3 1.0
OG1 A:THR167 4.7 10.7 1.0
OG1 A:THR200 4.7 9.6 1.0
CA A:CYS197 4.7 9.5 1.0
CD1 A:LEU98 4.7 11.2 1.0
SG A:CYS12 4.7 8.8 1.0
CB A:THR167 4.7 9.9 1.0
O A:HOH504 4.8 12.0 1.0
SG A:CYS96 4.8 9.2 1.0
N A:ALA199 4.9 9.7 1.0

Iron binding site 3 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 3 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:9.9
occ:1.00
 FE3 A:SF4401 0.0 9.9 1.0
S1 A:SF4401 2.2 9.7 1.0
S2 A:SF4401 2.3 10.1 1.0
S4 A:SF4401 2.3 11.8 1.0
SG A:CYS96 2.3 9.2 1.0
FE1 A:SF4401 2.6 17.1 1.0
FE2 A:SF4401 2.7 10.3 1.0
FE4 A:SF4401 2.7 9.3 1.0
CB A:CYS96 3.2 9.0 1.0
S3 A:SF4401 4.0 10.7 1.0
CA A:GLY14 4.1 9.4 1.0
N2 A:10E402 4.1 18.3 1.0
CB A:LEU98 4.3 10.7 1.0
N A:GLY14 4.3 9.2 1.0
CD1 A:LEU98 4.5 11.2 1.0
CA A:CYS96 4.6 9.1 1.0
SG A:CYS12 4.7 8.8 1.0
CG A:LEU98 4.7 11.2 1.0
SG A:CYS197 4.8 9.6 1.0
N A:LEU98 4.9 9.9 1.0

Iron binding site 4 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 4 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:9.3
occ:1.00
 FE4 A:SF4401 0.0 9.3 1.0
S2 A:SF4401 2.2 10.1 1.0
SG A:CYS12 2.3 8.8 1.0
S1 A:SF4401 2.3 9.7 1.0
S3 A:SF4401 2.3 10.7 1.0
FE2 A:SF4401 2.7 10.3 1.0
FE3 A:SF4401 2.7 9.9 1.0
FE1 A:SF4401 2.7 17.1 1.0
CB A:CYS12 3.3 9.1 1.0
S4 A:SF4401 3.9 11.8 1.0
N A:GLY14 4.2 9.2 1.0
C6 A:10E402 4.3 12.3 1.0
C5 A:10E402 4.3 10.7 1.0
CA A:GLY14 4.4 9.4 1.0
N A:VAL15 4.4 8.8 1.0
CG2 A:VAL15 4.5 9.4 1.0
CB A:ALA199 4.6 10.3 1.0
N2 A:10E402 4.6 18.3 1.0
CB A:ALA268 4.6 9.6 1.0
CA A:CYS12 4.7 9.4 1.0
SG A:CYS197 4.7 9.6 1.0
SG A:CYS96 4.7 9.2 1.0
C3 A:10E402 4.8 12.0 1.0
C A:GLY14 4.8 9.1 1.0
C A:CYS12 4.9 9.6 1.0
N A:ALA13 5.0 9.4 1.0

Iron binding site 5 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 5 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:17.7
occ:1.00
 FE1 B:SF4401 0.0 17.7 1.0
N2 B:10E402 2.0 18.0 1.0
S2 B:SF4401 2.3 10.8 1.0
S4 B:SF4401 2.3 11.7 1.0
S3 B:SF4401 2.4 11.3 1.0
FE2 B:SF4401 2.6 10.7 1.0
FE3 B:SF4401 2.6 10.1 1.0
FE4 B:SF4401 2.7 9.7 1.0
C1 B:10E402 3.0 14.4 1.0
C3 B:10E402 3.1 10.8 1.0
C5 B:10E402 3.2 10.5 1.0
C4 B:10E402 3.8 14.8 1.0
S1 B:SF4401 3.8 9.9 1.0
OG1 B:THR167 3.9 11.2 1.0
C6 B:10E402 4.1 12.8 1.0
CB B:CYS96 4.5 10.1 1.0
SG B:CYS197 4.6 10.0 1.0
SG B:CYS96 4.6 10.4 1.0
CG2 B:THR168 4.6 11.6 1.0
CB B:THR167 4.7 10.8 1.0
CG2 B:VAL99 4.8 11.5 1.0
SG B:CYS12 4.8 10.0 1.0

Iron binding site 6 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 6 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:10.7
occ:1.00
 FE2 B:SF4401 0.0 10.7 1.0
S4 B:SF4401 2.3 11.7 1.0
SG B:CYS197 2.3 10.0 1.0
S1 B:SF4401 2.3 9.9 1.0
S3 B:SF4401 2.3 11.3 1.0
FE1 B:SF4401 2.6 17.7 1.0
FE4 B:SF4401 2.6 9.7 1.0
FE3 B:SF4401 2.7 10.1 1.0
CB B:CYS197 3.2 10.5 1.0
S2 B:SF4401 3.8 10.8 1.0
N2 B:10E402 4.3 18.0 1.0
CB B:ALA199 4.3 9.6 1.0
OG1 B:THR200 4.6 10.0 1.0
CD1 B:LEU98 4.7 11.6 1.0
OG1 B:THR167 4.7 11.2 1.0
CA B:CYS197 4.7 10.0 1.0
SG B:CYS12 4.7 10.0 1.0
CB B:THR167 4.7 10.8 1.0
O B:HOH506 4.7 13.2 1.0
SG B:CYS96 4.9 10.4 1.0
N B:ALA199 4.9 9.3 1.0

Iron binding site 7 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 7 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:10.1
occ:1.00
 FE3 B:SF4401 0.0 10.1 1.0
S4 B:SF4401 2.2 11.7 1.0
S1 B:SF4401 2.3 9.9 1.0
SG B:CYS96 2.3 10.4 1.0
S2 B:SF4401 2.3 10.8 1.0
FE1 B:SF4401 2.6 17.7 1.0
FE2 B:SF4401 2.7 10.7 1.0
FE4 B:SF4401 2.7 9.7 1.0
CB B:CYS96 3.1 10.1 1.0
S3 B:SF4401 4.0 11.3 1.0
CA B:GLY14 4.1 9.6 1.0
N2 B:10E402 4.1 18.0 1.0
CB B:LEU98 4.3 11.5 1.0
N B:GLY14 4.3 9.6 1.0
CD1 B:LEU98 4.4 11.6 1.0
CA B:CYS96 4.6 9.9 1.0
SG B:CYS12 4.7 10.0 1.0
CG B:LEU98 4.7 11.5 1.0
SG B:CYS197 4.8 10.0 1.0
N B:LEU98 5.0 11.1 1.0

Iron binding site 8 out of 8 in 4h4d

Go back to Iron Binding Sites List in 4h4d
Iron binding site 8 out of 8 in the Isph in Complex with (E)-4-Amino-3-Methylbut-2-Enyl 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 (E)-4-Amino-3-Methylbut-2-Enyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:9.7
occ:1.00
 FE4 B:SF4401 0.0 9.7 1.0
S2 B:SF4401 2.2 10.8 1.0
S1 B:SF4401 2.3 9.9 1.0
S3 B:SF4401 2.3 11.3 1.0
SG B:CYS12 2.3 10.0 1.0
FE2 B:SF4401 2.6 10.7 1.0
FE1 B:SF4401 2.7 17.7 1.0
FE3 B:SF4401 2.7 10.1 1.0
CB B:CYS12 3.4 10.5 1.0
S4 B:SF4401 3.9 11.7 1.0
N B:GLY14 4.2 9.6 1.0
CA B:GLY14 4.3 9.6 1.0
N B:VAL15 4.4 9.7 1.0
C6 B:10E402 4.4 12.8 1.0
C5 B:10E402 4.4 10.5 1.0
CG2 B:VAL15 4.5 10.4 1.0
CB B:ALA268 4.5 10.1 1.0
CB B:ALA199 4.6 9.6 1.0
N2 B:10E402 4.7 18.0 1.0
CA B:CYS12 4.7 10.1 1.0
SG B:CYS197 4.7 10.0 1.0
C3 B:10E402 4.7 10.8 1.0
SG B:CYS96 4.7 10.4 1.0
C B:GLY14 4.9 9.4 1.0
C B:CYS12 4.9 10.0 1.0
N B:ALA13 4.9 10.2 1.0

Reference:

I.Span, K.Wang, W.Wang, J.Jauch, W.Eisenreich, A.Bacher, E.Oldfield, M.Groll. Structures of Fluoro, Amino, and Thiol Inhibitors Bound to the [Fe(4) S(4) ] Protein Isph. Angew.Chem.Int.Ed.Engl. V. 52 2118 2013.
ISSN: ISSN 1433-7851
PubMed: 23307751
DOI: 10.1002/ANIE.201208469
Page generated: Mon Aug 5 03:10:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy