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Iron in PDB 6upm: Crystal Structure of T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

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

All present enzymatic activity of Crystal Structure of T467A 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 T467A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6upm 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) 48.92 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.616, 84.718, 239.669, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.3

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 S-Malate (pdb code 6upm). 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 S-Malate, PDB code: 6upm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6upm

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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 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 T467A 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:17.2
occ:1.00
 FE1 A:SF4601 0.0 17.2 1.0
S4 A:SF4601 2.3 14.7 1.0
SG A:CYS133 2.3 19.7 1.0
S3 A:SF4601 2.3 16.8 1.0
S2 A:SF4601 2.3 18.0 1.0
FE2 A:SF4601 2.7 15.7 1.0
FE3 A:SF4601 2.8 17.4 1.0
FE4 A:SF4601 2.8 19.8 1.0
CB A:CYS133 3.5 16.3 1.0
S1 A:SF4601 3.9 17.3 1.0
CB A:ALA348 4.0 13.4 1.0
CB A:ASP135 4.3 15.6 1.0
O2 A:LMR602 4.4 20.3 1.0
O A:HOH777 4.4 17.7 1.0
NE2 A:GLN134 4.5 15.2 1.0
O A:HOH787 4.6 23.0 1.0
O A:ASP135 4.8 15.1 1.0
SG A:CYS252 4.8 18.8 1.0
CA A:CYS133 4.8 16.6 1.0
CA A:GLY515 4.9 19.9 1.0
SG A:CYS346 4.9 17.2 1.0
N A:ASP135 4.9 17.8 1.0

Iron binding site 2 out of 8 in 6upm

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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 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 T467A 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:15.7
occ:1.00
 FE2 A:SF4601 0.0 15.7 1.0
S3 A:SF4601 2.3 16.8 1.0
S4 A:SF4601 2.3 14.7 1.0
SG A:CYS346 2.3 17.2 1.0
S1 A:SF4601 2.3 17.3 1.0
FE3 A:SF4601 2.7 17.4 1.0
FE4 A:SF4601 2.7 19.8 1.0
FE1 A:SF4601 2.7 17.2 1.0
CB A:CYS346 3.3 17.4 1.0
S2 A:SF4601 3.9 18.0 1.0
CB A:ALA348 3.9 13.4 1.0
N A:ALA348 4.2 15.2 1.0
OG A:SER217 4.5 17.1 1.0
CA A:CYS346 4.6 18.7 1.0
CA A:ALA348 4.6 18.7 1.0
N A:SER347 4.6 18.8 1.0
SG A:CYS252 4.7 18.8 1.0
CB A:CYS252 4.7 17.9 1.0
O A:ALA251 4.8 15.9 1.0
O2 A:LMR602 4.8 20.3 1.0
N A:SER217 4.8 12.0 1.0
CB A:SER217 4.8 11.8 1.0
C A:CYS346 4.8 19.2 1.0
CA A:GLY214 4.9 15.4 1.0
O A:HOH834 4.9 22.4 1.0
SG A:CYS133 4.9 19.7 1.0

Iron binding site 3 out of 8 in 6upm

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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 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 T467A 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:17.4
occ:1.00
 FE3 A:SF4601 0.0 17.4 1.0
S2 A:SF4601 2.3 18.0 1.0
SG A:CYS252 2.3 18.8 1.0
S1 A:SF4601 2.3 17.3 1.0
S4 A:SF4601 2.3 14.7 1.0
FE4 A:SF4601 2.7 19.8 1.0
FE2 A:SF4601 2.7 15.7 1.0
FE1 A:SF4601 2.8 17.2 1.0
CB A:CYS252 3.2 17.9 1.0
NZ A:LYS491 3.6 16.5 1.0
S3 A:SF4601 3.9 16.8 1.0
CE A:LYS491 4.0 22.5 1.0
O1B A:LMR602 4.1 19.2 1.0
O A:HOH787 4.3 23.0 1.0
CA A:CYS252 4.4 19.8 1.0
N A:CYS252 4.4 16.7 1.0
C A:ALA251 4.5 21.2 1.0
N A:GLY515 4.5 20.9 1.0
O A:ALA251 4.6 15.9 1.0
CA A:GLY515 4.7 19.9 1.0
SG A:CYS346 4.7 17.2 1.0
SG A:CYS133 4.7 19.7 1.0
CB A:CYS346 4.8 17.4 1.0
O2 A:LMR602 4.9 20.3 1.0
C A:GLY514 4.9 19.8 1.0
CD A:LYS491 4.9 21.1 1.0

Iron binding site 4 out of 8 in 6upm

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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 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 T467A 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:19.8
occ:1.00
 FE4 A:SF4601 0.0 19.8 1.0
S1 A:SF4601 2.3 17.3 1.0
O2 A:LMR602 2.3 20.3 1.0
S2 A:SF4601 2.3 18.0 1.0
S3 A:SF4601 2.3 16.8 1.0
O1B A:LMR602 2.7 19.2 1.0
FE3 A:SF4601 2.7 17.4 1.0
FE2 A:SF4601 2.7 15.7 1.0
FE1 A:SF4601 2.8 17.2 1.0
C2 A:LMR602 3.3 27.5 1.0
C1 A:LMR602 3.4 28.0 1.0
C3 A:LMR602 3.8 20.9 1.0
N A:GLY216 3.9 19.6 1.0
S4 A:SF4601 3.9 14.7 1.0
OD2 A:ASP135 4.0 15.8 1.0
CA A:GLY216 4.0 17.3 1.0
NZ A:LYS491 4.1 16.5 1.0
CB A:ASP135 4.4 15.6 1.0
O1A A:LMR602 4.6 23.4 1.0
CG A:ASP135 4.6 19.0 1.0
SG A:CYS133 4.7 19.7 1.0
N A:SER217 4.7 12.0 1.0
SG A:CYS252 4.8 18.8 1.0
CE A:LYS491 4.8 22.5 1.0
SG A:CYS346 4.8 17.2 1.0
CA A:GLY214 4.8 15.4 1.0
N A:GLY215 4.8 15.7 1.0
C A:GLY216 4.8 18.9 1.0
C4 A:LMR602 5.0 20.8 1.0
C A:GLY214 5.0 15.8 1.0

Iron binding site 5 out of 8 in 6upm

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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 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 T467A 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:14.9
occ:1.00
 FE1 B:SF4601 0.0 14.9 1.0
S2 B:SF4601 2.3 14.0 1.0
SG B:CYS346 2.3 17.9 1.0
S4 B:SF4601 2.3 16.9 1.0
S3 B:SF4601 2.3 16.3 1.0
FE2 B:SF4601 2.7 15.7 1.0
FE3 B:SF4601 2.7 15.4 1.0
FE4 B:SF4601 2.8 17.0 1.0
CB B:CYS346 3.2 11.7 1.0
CB B:ALA348 3.8 12.1 1.0
S1 B:SF4601 3.9 16.7 1.0
N B:ALA348 4.1 12.7 1.0
OG B:SER217 4.5 15.6 1.0
CA B:ALA348 4.5 12.5 1.0
CA B:CYS346 4.6 16.2 1.0
N B:SER347 4.6 12.8 1.0
SG B:CYS252 4.7 16.3 1.0
O2 B:LMR602 4.8 17.3 1.0
O B:ALA251 4.8 18.6 1.0
C B:CYS346 4.8 20.0 1.0
CB B:CYS252 4.8 13.6 1.0
N B:SER217 4.9 14.1 1.0
CA B:GLY214 4.9 15.7 1.0
CB B:SER217 4.9 16.1 1.0
O B:HOH801 4.9 20.4 1.0
SG B:CYS133 4.9 16.1 1.0

Iron binding site 6 out of 8 in 6upm

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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 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 T467A 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:15.7
occ:1.00
 FE2 B:SF4601 0.0 15.7 1.0
S1 B:SF4601 2.3 16.7 1.0
SG B:CYS252 2.3 16.3 1.0
S4 B:SF4601 2.3 16.9 1.0
S3 B:SF4601 2.3 16.3 1.0
FE4 B:SF4601 2.7 17.0 1.0
FE1 B:SF4601 2.7 14.9 1.0
FE3 B:SF4601 2.8 15.4 1.0
CB B:CYS252 3.2 13.6 1.0
NZ B:LYS491 3.6 17.3 1.0
S2 B:SF4601 3.9 14.0 1.0
CE B:LYS491 4.0 17.9 1.0
O1B B:LMR602 4.2 18.4 1.0
O B:HOH884 4.3 20.4 1.0
CA B:CYS252 4.5 17.0 1.0
N B:CYS252 4.5 15.6 1.0
C B:ALA251 4.5 16.6 1.0
N B:GLY515 4.5 17.4 1.0
O B:ALA251 4.6 18.6 1.0
SG B:CYS346 4.6 17.9 1.0
CA B:GLY515 4.7 17.7 1.0
CB B:CYS346 4.7 11.7 1.0
SG B:CYS133 4.7 16.1 1.0
O2 B:LMR602 4.9 17.3 1.0
C B:GLY514 4.9 19.6 1.0
CD B:LYS491 4.9 15.8 1.0

Iron binding site 7 out of 8 in 6upm

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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 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 T467A 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:15.4
occ:1.00
 FE3 B:SF4601 0.0 15.4 1.0
S2 B:SF4601 2.3 14.0 1.0
S4 B:SF4601 2.3 16.9 1.0
SG B:CYS133 2.3 16.1 1.0
S1 B:SF4601 2.3 16.7 1.0
FE1 B:SF4601 2.7 14.9 1.0
FE2 B:SF4601 2.8 15.7 1.0
FE4 B:SF4601 2.8 17.0 1.0
CB B:CYS133 3.5 13.2 1.0
S3 B:SF4601 3.9 16.3 1.0
CB B:ALA348 4.0 12.1 1.0
O B:HOH857 4.3 12.8 1.0
CB B:ASP135 4.3 12.5 1.0
O2 B:LMR602 4.4 17.3 1.0
NE2 B:GLN134 4.4 14.1 1.0
O B:HOH884 4.6 20.4 1.0
O B:ASP135 4.8 14.3 1.0
SG B:CYS346 4.8 17.9 1.0
SG B:CYS252 4.8 16.3 1.0
CA B:CYS133 4.9 20.5 1.0
CA B:GLY515 4.9 17.7 1.0
N B:ASP135 4.9 14.9 1.0

Iron binding site 8 out of 8 in 6upm

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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 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 T467A 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:17.0
occ:1.00
 FE4 B:SF4601 0.0 17.0 1.0
S3 B:SF4601 2.3 16.3 1.0
S1 B:SF4601 2.3 16.7 1.0
O2 B:LMR602 2.3 17.3 1.0
S2 B:SF4601 2.3 14.0 1.0
O1B B:LMR602 2.7 18.4 1.0
FE2 B:SF4601 2.7 15.7 1.0
FE1 B:SF4601 2.8 14.9 1.0
FE3 B:SF4601 2.8 15.4 1.0
C2 B:LMR602 3.2 17.6 1.0
C1 B:LMR602 3.3 18.0 1.0
C3 B:LMR602 3.7 15.7 1.0
N B:GLY216 3.8 20.1 1.0
S4 B:SF4601 3.9 16.9 1.0
OD1 B:ASP135 4.0 14.7 1.0
CA B:GLY216 4.0 20.8 1.0
NZ B:LYS491 4.1 17.3 1.0
CB B:ASP135 4.4 12.5 1.0
O1A B:LMR602 4.6 22.9 1.0
CG B:ASP135 4.7 16.5 1.0
SG B:CYS133 4.7 16.1 1.0
CE B:LYS491 4.7 17.9 1.0
SG B:CYS252 4.7 16.3 1.0
N B:SER217 4.8 14.1 1.0
N B:GLY215 4.8 22.6 1.0
SG B:CYS346 4.8 17.9 1.0
C4 B:LMR602 4.9 20.6 1.0
C B:GLY216 4.9 19.5 1.0
CA B:GLY214 4.9 15.7 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 6 14:43:55 2025

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