Atomistry » Iron » PDB 6u97-6uw2 » 6up9
Atomistry »
  Iron »
    PDB 6u97-6uw2 »
      6up9 »

Iron in PDB 6up9: Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate

Enzymatic activity of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate

All present enzymatic activity of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate:
4.2.1.2;

Protein crystallography data

The structure of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate, PDB code: 6up9 was solved by P.R.Feliciano, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.03 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.653, 84.937, 240.205, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate (pdb code 6up9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate, PDB code: 6up9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 1 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:20.0
occ:1.00
 FE1 A:SF4604 0.0 20.0 1.0
S4 A:SF4604 2.3 21.5 1.0
SG A:CYS133 2.3 19.4 1.0
S3 A:SF4604 2.3 25.0 1.0
S2 A:SF4604 2.3 19.8 1.0
FE3 A:SF4604 2.7 19.6 1.0
FE2 A:SF4604 2.8 19.7 1.0
FE4 A:SF4604 2.8 24.2 1.0
CB A:CYS133 3.4 17.1 1.0
S1 A:SF4604 3.9 21.9 1.0
CB A:ALA348 4.0 18.6 1.0
O A:HOH839 4.2 21.2 1.0
O A:HOH719 4.3 21.8 1.0
CB A:ASP135 4.4 21.4 1.0
NE2 A:GLN134 4.6 17.8 1.0
O A:HOH782 4.6 28.4 1.0
CA A:CYS133 4.8 17.7 1.0
O A:ASP135 4.8 18.1 1.0
CA A:GLY515 4.8 21.3 1.0
SG A:CYS252 4.8 20.1 1.0
SG A:CYS346 4.9 20.9 1.0
N A:ALA348 5.0 17.7 1.0
N A:ASP135 5.0 22.5 1.0

Iron binding site 2 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 2 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:19.7
occ:1.00
 FE2 A:SF4604 0.0 19.7 1.0
S3 A:SF4604 2.3 25.0 1.0
S1 A:SF4604 2.3 21.9 1.0
SG A:CYS346 2.3 20.9 1.0
S4 A:SF4604 2.3 21.5 1.0
FE4 A:SF4604 2.7 24.2 1.0
FE3 A:SF4604 2.7 19.6 1.0
FE1 A:SF4604 2.8 20.0 1.0
CB A:CYS346 3.2 19.3 1.0
CB A:ALA348 3.8 18.6 1.0
S2 A:SF4604 3.9 19.8 1.0
N A:ALA348 4.0 17.7 1.0
OG A:SER217 4.4 22.1 1.0
CA A:ALA348 4.5 21.4 1.0
O A:HOH719 4.5 21.8 1.0
N A:SER347 4.5 18.7 1.0
CA A:CYS346 4.6 23.4 1.0
O A:HOH856 4.6 23.4 1.0
SG A:CYS252 4.7 20.1 1.0
O A:ALA251 4.7 17.7 1.0
CB A:SER217 4.7 17.7 1.0
C A:CYS346 4.8 20.5 1.0
CB A:CYS252 4.8 22.9 1.0
O A:ALA348 4.9 20.1 1.0
N A:SER217 4.9 18.5 1.0
CA A:GLY214 5.0 14.8 1.0
SG A:CYS133 5.0 19.4 1.0

Iron binding site 3 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 3 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:19.6
occ:1.00
 FE3 A:SF4604 0.0 19.6 1.0
S2 A:SF4604 2.3 19.8 1.0
SG A:CYS252 2.3 20.1 1.0
S4 A:SF4604 2.3 21.5 1.0
S1 A:SF4604 2.3 21.9 1.0
FE2 A:SF4604 2.7 19.7 1.0
FE4 A:SF4604 2.7 24.2 1.0
FE1 A:SF4604 2.7 20.0 1.0
CB A:CYS252 3.2 22.9 1.0
NZ A:LYS491 3.5 22.8 1.0
S3 A:SF4604 3.9 25.0 1.0
CE A:LYS491 4.1 25.6 1.0
O A:HOH782 4.2 28.4 1.0
C A:ALA251 4.4 20.6 1.0
N A:CYS252 4.5 18.1 1.0
CA A:CYS252 4.5 23.0 1.0
N A:GLY515 4.5 26.9 1.0
O A:ALA251 4.5 17.7 1.0
O A:HOH703 4.5 20.3 1.0
O A:HOH719 4.6 21.8 1.0
CA A:GLY515 4.7 21.3 1.0
SG A:CYS346 4.7 20.9 1.0
SG A:CYS133 4.7 19.4 1.0
CB A:CYS346 4.8 19.3 1.0
C A:GLY514 4.9 20.6 1.0
CA A:ALA251 5.0 19.3 1.0

Iron binding site 4 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 4 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:24.2
occ:1.00
 FE4 A:SF4604 0.0 24.2 1.0
O A:HOH719 2.0 21.8 1.0
S1 A:SF4604 2.3 21.9 1.0
S3 A:SF4604 2.3 25.0 1.0
S2 A:SF4604 2.3 19.8 1.0
FE2 A:SF4604 2.7 19.7 1.0
FE3 A:SF4604 2.7 19.6 1.0
FE1 A:SF4604 2.8 20.0 1.0
O A:HOH703 3.2 20.3 1.0
S4 A:SF4604 3.9 21.5 1.0
OD2 A:ASP135 4.0 19.8 1.0
N A:GLY216 4.0 22.9 1.0
NZ A:LYS491 4.2 22.8 1.0
CA A:GLY216 4.2 19.6 1.0
C2 A:MLA601 4.3 23.1 1.0
CB A:ASP135 4.3 21.4 1.0
CG A:ASP135 4.6 22.1 1.0
N A:SER217 4.6 18.5 1.0
CA A:GLY214 4.6 14.8 1.0
SG A:CYS133 4.6 19.4 1.0
SG A:CYS346 4.8 20.9 1.0
N A:GLY215 4.8 18.0 1.0
SG A:CYS252 4.8 20.1 1.0
C A:GLY214 4.9 14.7 1.0
C A:GLY216 4.9 20.2 1.0
CE A:LYS491 5.0 25.6 1.0

Iron binding site 5 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 5 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:18.7
occ:1.00
 FE1 B:SF4604 0.0 18.7 1.0
S3 B:SF4604 2.3 18.4 1.0
SG B:CYS252 2.3 17.6 1.0
S4 B:SF4604 2.3 20.2 1.0
S2 B:SF4604 2.3 19.5 1.0
FE3 B:SF4604 2.7 18.2 1.0
FE2 B:SF4604 2.7 18.8 1.0
FE4 B:SF4604 2.7 20.8 1.0
CB B:CYS252 3.2 15.5 1.0
NZ B:LYS491 3.5 22.0 1.0
S1 B:SF4604 3.9 20.7 1.0
CE B:LYS491 4.1 20.4 1.0
O B:HOH804 4.2 23.7 1.0
O B:HOH704 4.4 24.2 1.0
C B:ALA251 4.4 18.5 1.0
N B:CYS252 4.4 17.6 1.0
O B:ALA251 4.4 21.2 1.0
CA B:CYS252 4.5 21.0 1.0
N B:GLY515 4.5 21.8 1.0
O B:HOH727 4.6 20.1 1.0
CA B:GLY515 4.7 25.4 1.0
SG B:CYS133 4.7 18.6 1.0
SG B:CYS346 4.7 19.5 1.0
CB B:CYS346 4.8 17.1 1.0
CA B:ALA251 4.9 19.6 1.0
C B:GLY514 4.9 22.9 1.0
CD B:LYS491 5.0 20.2 1.0

Iron binding site 6 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 6 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:18.8
occ:1.00
 FE2 B:SF4604 0.0 18.8 1.0
S4 B:SF4604 2.3 20.2 1.0
S3 B:SF4604 2.3 18.4 1.0
S1 B:SF4604 2.3 20.7 1.0
SG B:CYS133 2.3 18.6 1.0
FE4 B:SF4604 2.7 20.8 1.0
FE1 B:SF4604 2.7 18.7 1.0
FE3 B:SF4604 2.7 18.2 1.0
CB B:CYS133 3.4 17.3 1.0
CB B:ALA348 3.9 15.6 1.0
S2 B:SF4604 3.9 19.5 1.0
O B:HOH887 4.2 20.3 1.0
CB B:ASP135 4.4 19.5 1.0
O B:HOH727 4.4 20.1 1.0
NE2 B:GLN134 4.5 15.6 1.0
O B:HOH761 4.6 44.3 1.0
O B:HOH804 4.7 23.7 1.0
O B:ASP135 4.7 16.5 1.0
SG B:CYS252 4.8 17.6 1.0
CA B:CYS133 4.8 22.1 1.0
CA B:GLY515 4.9 25.4 1.0
SG B:CYS346 4.9 19.5 1.0
N B:ASP135 5.0 17.0 1.0
N B:ALA348 5.0 14.6 1.0

Iron binding site 7 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 7 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:18.2
occ:1.00
 FE3 B:SF4604 0.0 18.2 1.0
S2 B:SF4604 2.3 19.5 1.0
S1 B:SF4604 2.3 20.7 1.0
S4 B:SF4604 2.3 20.2 1.0
SG B:CYS346 2.3 19.5 1.0
FE4 B:SF4604 2.7 20.8 1.0
FE1 B:SF4604 2.7 18.7 1.0
FE2 B:SF4604 2.7 18.8 1.0
CB B:CYS346 3.2 17.1 1.0
CB B:ALA348 3.7 15.6 1.0
S3 B:SF4604 3.9 18.4 1.0
N B:ALA348 3.9 14.6 1.0
OG B:SER217 4.3 23.8 1.0
CA B:ALA348 4.4 17.0 1.0
O B:HOH796 4.5 25.0 1.0
O B:HOH727 4.5 20.1 1.0
N B:SER347 4.5 17.6 1.0
CA B:CYS346 4.5 19.6 1.0
O B:ALA251 4.6 21.2 1.0
CB B:SER217 4.7 20.1 1.0
SG B:CYS252 4.7 17.6 1.0
CB B:CYS252 4.7 15.5 1.0
C B:CYS346 4.8 18.3 1.0
O B:ALA348 4.8 16.1 1.0
C B:ALA348 5.0 16.4 1.0
SG B:CYS133 5.0 18.6 1.0

Iron binding site 8 out of 8 in 6up9

Go back to Iron Binding Sites List in 6up9
Iron binding site 8 out of 8 in the Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:20.8
occ:1.00
 FE4 B:SF4604 0.0 20.8 1.0
O B:HOH727 2.0 20.1 1.0
S1 B:SF4604 2.3 20.7 1.0
S2 B:SF4604 2.3 19.5 1.0
S3 B:SF4604 2.3 18.4 1.0
FE3 B:SF4604 2.7 18.2 1.0
FE2 B:SF4604 2.7 18.8 1.0
FE1 B:SF4604 2.7 18.7 1.0
O B:HOH704 3.2 24.2 1.0
S4 B:SF4604 3.9 20.2 1.0
OD2 B:ASP135 3.9 17.1 1.0
N B:GLY216 4.1 18.7 1.0
C2 B:MLA601 4.2 19.3 1.0
NZ B:LYS491 4.2 22.0 1.0
CB B:ASP135 4.3 19.5 1.0
CA B:GLY216 4.3 23.2 1.0
CA B:GLY214 4.5 19.3 1.0
N B:SER217 4.5 18.4 1.0
CG B:ASP135 4.5 20.7 1.0
SG B:CYS133 4.6 18.6 1.0
SG B:CYS346 4.7 19.5 1.0
C B:GLY214 4.8 18.3 1.0
N B:GLY215 4.8 16.8 1.0
SG B:CYS252 4.9 17.6 1.0
C B:GLY216 4.9 23.0 1.0

Reference:

P.R.Feliciano, C.L.Drennan. Structural and Biochemical Investigations of the [4FE-4S] Cluster-Containing Fumarate Hydratase Fromleishmania Major. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31743022
DOI: 10.1021/ACS.BIOCHEM.9B00923
Page generated: Wed Aug 7 12:23:47 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