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Iron in PDB 6upo: Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

Enzymatic activity of Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

All present enzymatic activity of Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate:
4.2.1.2;

Protein crystallography data

The structure of Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6upo 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) 48.99 / 3.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.929, 84.590, 240.354, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate (pdb code 6upo). 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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6upo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6upo

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Iron binding site 1 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:39.1
occ:1.00
 FE1 A:SF4601 0.0 39.1 1.0
S4 A:SF4601 2.3 38.4 1.0
SG A:CYS346 2.3 37.0 1.0
S3 A:SF4601 2.3 42.0 1.0
S2 A:SF4601 2.3 40.8 1.0
FE4 A:SF4601 2.7 54.3 1.0
FE2 A:SF4601 2.7 44.4 1.0
FE3 A:SF4601 2.7 44.7 1.0
CB A:CYS346 3.0 37.1 1.0
S1 A:SF4601 3.9 47.4 1.0
CB A:ALA348 3.9 33.8 1.0
N A:ALA348 4.2 38.2 1.0
CA A:CYS346 4.4 35.8 1.0
OG A:SER217 4.6 40.4 1.0
N A:SER347 4.6 39.6 1.0
CA A:ALA348 4.6 36.7 1.0
O2 A:LMR602 4.7 41.1 1.0
SG A:CYS252 4.7 47.1 1.0
O A:ALA251 4.8 41.9 1.0
CB A:CYS252 4.8 44.2 1.0
C A:CYS346 4.8 35.7 1.0
CA A:GLY214 4.8 36.5 1.0
SG A:CYS133 4.8 41.3 1.0
N A:SER217 4.8 37.3 1.0
O1B A:LMR602 4.8 43.4 1.0
CB A:SER217 4.9 37.5 1.0

Iron binding site 2 out of 8 in 6upo

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Iron binding site 2 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:44.4
occ:1.00
 FE2 A:SF4601 0.0 44.4 1.0
S3 A:SF4601 2.3 42.0 1.0
S4 A:SF4601 2.3 38.4 1.0
SG A:CYS133 2.3 41.3 1.0
S1 A:SF4601 2.3 47.4 1.0
FE1 A:SF4601 2.7 39.1 1.0
FE4 A:SF4601 2.7 54.3 1.0
FE3 A:SF4601 2.7 44.7 1.0
CB A:CYS133 3.5 44.0 1.0
S2 A:SF4601 3.9 40.8 1.0
CB A:ALA348 4.2 33.8 1.0
O2 A:LMR602 4.2 41.1 1.0
CB A:ASP135 4.4 40.5 1.0
OE1 A:GLN134 4.8 39.3 1.0
SG A:CYS252 4.8 47.1 1.0
O1B A:LMR602 4.8 43.4 1.0
SG A:CYS346 4.8 37.0 1.0
NE2 A:GLN134 4.9 41.9 1.0
CA A:CYS133 4.9 44.9 1.0
C3 A:LMR602 4.9 45.9 1.0
N A:ASP135 4.9 39.7 1.0
O A:ASP135 5.0 38.4 1.0
CA A:GLY515 5.0 48.5 1.0

Iron binding site 3 out of 8 in 6upo

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Iron binding site 3 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:44.7
occ:1.00
 FE3 A:SF4601 0.0 44.7 1.0
S2 A:SF4601 2.3 40.8 1.0
S1 A:SF4601 2.3 47.4 1.0
S4 A:SF4601 2.3 38.4 1.0
O2 A:LMR602 2.3 41.1 1.0
O1B A:LMR602 2.4 43.4 1.0
FE4 A:SF4601 2.7 54.3 1.0
FE1 A:SF4601 2.7 39.1 1.0
FE2 A:SF4601 2.7 44.4 1.0
C1 A:LMR602 3.1 42.3 1.0
C2 A:LMR602 3.2 42.3 1.0
N A:GLY216 3.7 36.4 1.0
C3 A:LMR602 3.7 45.9 1.0
S3 A:SF4601 3.9 42.0 1.0
CA A:GLY216 4.0 35.9 1.0
OD2 A:ASP135 4.1 38.2 1.0
O1A A:LMR602 4.3 39.8 1.0
N A:GLY215 4.6 35.4 1.0
CB A:ASP135 4.6 40.5 1.0
SG A:CYS133 4.7 41.3 1.0
SG A:CYS346 4.8 37.0 1.0
N A:SER217 4.8 37.3 1.0
SG A:CYS252 4.8 47.1 1.0
NZ A:LYS491 4.8 41.0 1.0
CG A:ASP135 4.9 38.2 1.0
C A:GLY215 4.9 38.1 1.0
C A:GLY216 4.9 39.3 1.0
CA A:GLY214 5.0 36.5 1.0
C A:GLY214 5.0 34.0 1.0

Iron binding site 4 out of 8 in 6upo

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Iron binding site 4 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:54.3
occ:1.00
 FE4 A:SF4601 0.0 54.3 1.0
S1 A:SF4601 2.3 47.4 1.0
SG A:CYS252 2.3 47.1 1.0
S2 A:SF4601 2.3 40.8 1.0
S3 A:SF4601 2.3 42.0 1.0
FE1 A:SF4601 2.7 39.1 1.0
FE3 A:SF4601 2.7 44.7 1.0
FE2 A:SF4601 2.7 44.4 1.0
CB A:CYS252 3.2 44.2 1.0
S4 A:SF4601 3.9 38.4 1.0
O1B A:LMR602 4.0 43.4 1.0
NZ A:LYS491 4.4 41.0 1.0
CE A:LYS491 4.5 43.0 1.0
CD A:LYS491 4.5 45.3 1.0
CA A:CYS252 4.5 43.1 1.0
N A:GLY515 4.5 48.9 1.0
CB A:CYS346 4.5 37.1 1.0
N A:CYS252 4.5 46.4 1.0
C A:ALA251 4.5 46.3 1.0
O A:ALA251 4.5 41.9 1.0
CA A:GLY515 4.7 48.5 1.0
SG A:CYS346 4.7 37.0 1.0
C A:GLY514 4.8 43.7 1.0
SG A:CYS133 4.8 41.3 1.0
O2 A:LMR602 4.9 41.1 1.0

Iron binding site 5 out of 8 in 6upo

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Iron binding site 5 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:51.9
occ:1.00
 FE1 B:SF4601 0.0 51.9 1.0
S4 B:SF4601 2.3 43.5 1.0
SG B:CYS133 2.3 49.1 1.0
S3 B:SF4601 2.3 44.5 1.0
S2 B:SF4601 2.3 50.0 1.0
FE2 B:SF4601 2.7 44.1 1.0
FE3 B:SF4601 2.7 46.8 1.0
FE4 B:SF4601 2.7 40.9 1.0
CB B:CYS133 3.5 51.6 1.0
S1 B:SF4601 3.9 45.5 1.0
CB B:ALA348 4.2 38.8 1.0
CB B:ASP135 4.3 46.9 1.0
O2 B:LMR602 4.4 43.1 1.0
NE2 B:GLN134 4.6 51.8 1.0
OE1 B:GLN134 4.6 44.8 1.0
O1B B:LMR602 4.7 50.9 1.0
SG B:CYS252 4.8 36.9 1.0
N B:ASP135 4.8 46.1 1.0
CA B:CYS133 4.8 49.6 1.0
C3 B:LMR602 4.8 44.5 1.0
O B:ASP135 4.8 43.7 1.0
SG B:CYS346 4.8 54.5 1.0
CD B:GLN134 4.9 47.8 1.0

Iron binding site 6 out of 8 in 6upo

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Iron binding site 6 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:44.1
occ:1.00
 FE2 B:SF4601 0.0 44.1 1.0
SG B:CYS346 2.3 54.5 1.0
S4 B:SF4601 2.3 43.5 1.0
S3 B:SF4601 2.3 44.5 1.0
S1 B:SF4601 2.3 45.5 1.0
FE3 B:SF4601 2.7 46.8 1.0
FE1 B:SF4601 2.7 51.9 1.0
FE4 B:SF4601 2.7 40.9 1.0
CB B:CYS346 3.1 36.9 1.0
S2 B:SF4601 3.9 50.0 1.0
CB B:ALA348 3.9 38.8 1.0
N B:ALA348 4.2 42.4 1.0
CA B:CYS346 4.5 39.5 1.0
OG B:SER217 4.5 46.5 1.0
N B:SER347 4.6 40.9 1.0
O1B B:LMR602 4.6 50.9 1.0
CA B:ALA348 4.6 38.7 1.0
SG B:CYS252 4.7 36.9 1.0
O2 B:LMR602 4.7 43.1 1.0
CB B:CYS252 4.8 41.6 1.0
N B:SER217 4.8 42.3 1.0
O B:ALA251 4.8 40.5 1.0
C B:CYS346 4.8 40.6 1.0
SG B:CYS133 4.8 49.1 1.0
CB B:SER217 4.9 43.9 1.0
CA B:GLY214 4.9 42.8 1.0

Iron binding site 7 out of 8 in 6upo

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Iron binding site 7 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:46.8
occ:1.00
 FE3 B:SF4601 0.0 46.8 1.0
SG B:CYS252 2.3 36.9 1.0
S1 B:SF4601 2.3 45.5 1.0
S2 B:SF4601 2.3 50.0 1.0
S4 B:SF4601 2.3 43.5 1.0
FE2 B:SF4601 2.7 44.1 1.0
FE1 B:SF4601 2.7 51.9 1.0
FE4 B:SF4601 2.7 40.9 1.0
CB B:CYS252 3.2 41.6 1.0
O1B B:LMR602 3.7 50.9 1.0
S3 B:SF4601 3.9 44.5 1.0
CE B:LYS491 4.1 43.9 1.0
NZ B:LYS491 4.4 45.6 1.0
CA B:CYS252 4.5 42.5 1.0
N B:GLY515 4.5 48.2 1.0
N B:CYS252 4.5 44.3 1.0
CB B:CYS346 4.5 36.9 1.0
C B:ALA251 4.5 42.5 1.0
CD B:LYS491 4.6 45.0 1.0
CA B:GLY515 4.6 50.0 1.0
O B:ALA251 4.6 40.5 1.0
SG B:CYS346 4.7 54.5 1.0
SG B:CYS133 4.8 49.1 1.0
C B:GLY514 4.8 45.3 1.0
C1 B:LMR602 4.8 49.3 1.0
O2 B:LMR602 5.0 43.1 1.0

Iron binding site 8 out of 8 in 6upo

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Iron binding site 8 out of 8 in the Crystal Structure of H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate


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 H334A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:40.9
occ:1.00
 FE4 B:SF4601 0.0 40.9 1.0
O1B B:LMR602 2.2 50.9 1.0
S1 B:SF4601 2.3 45.5 1.0
S2 B:SF4601 2.3 50.0 1.0
S3 B:SF4601 2.3 44.5 1.0
O2 B:LMR602 2.3 43.1 1.0
FE3 B:SF4601 2.7 46.8 1.0
FE2 B:SF4601 2.7 44.1 1.0
FE1 B:SF4601 2.7 51.9 1.0
C1 B:LMR602 3.0 49.3 1.0
C2 B:LMR602 3.0 43.6 1.0
C3 B:LMR602 3.5 44.5 1.0
N B:GLY216 3.8 41.7 1.0
S4 B:SF4601 3.9 43.5 1.0
CA B:GLY216 4.1 43.8 1.0
OD2 B:ASP135 4.1 50.3 1.0
O1A B:LMR602 4.2 49.0 1.0
CB B:ASP135 4.4 46.9 1.0
NZ B:LYS491 4.5 45.6 1.0
SG B:CYS133 4.7 49.1 1.0
N B:GLY215 4.7 42.3 1.0
CG B:ASP135 4.8 45.9 1.0
N B:SER217 4.8 42.3 1.0
SG B:CYS346 4.8 54.5 1.0
SG B:CYS252 4.8 36.9 1.0
C4 B:LMR602 4.9 49.8 1.0
C B:GLY216 4.9 42.6 1.0
C B:GLY215 5.0 42.5 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 12:25:31 2024

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