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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

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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

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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

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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

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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

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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

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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

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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

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