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Iron in PDB 6uqm: Crystal Structure of R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

Enzymatic activity of Crystal Structure of R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

All present enzymatic activity of Crystal Structure of R173A 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 R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6uqm 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) 49.09 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.624, 85.072, 240.423, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate (pdb code 6uqm). 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 R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6uqm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6uqm

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Iron binding site 1 out of 8 in the Crystal Structure of R173A 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 R173A 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:18.2
occ:1.00
 FE1 A:SF4601 0.0 18.2 1.0
S4 A:SF4601 2.3 17.7 1.0
SG A:CYS133 2.3 20.6 1.0
S3 A:SF4601 2.3 16.7 1.0
S2 A:SF4601 2.3 20.7 1.0
FE2 A:SF4601 2.7 18.2 1.0
FE3 A:SF4601 2.7 17.3 1.0
FE4 A:SF4601 2.8 20.0 1.0
CB A:CYS133 3.4 19.7 1.0
S1 A:SF4601 3.9 18.1 1.0
CB A:ALA348 4.0 14.8 1.0
O A:HOH805 4.3 18.6 1.0
CB A:ASP135 4.4 16.5 1.0
NE2 A:GLN134 4.4 16.3 1.0
O2 A:LMR602 4.4 18.0 1.0
O A:ASP135 4.8 18.9 1.0
O A:HOH772 4.8 23.5 1.0
SG A:CYS346 4.8 18.8 1.0
CA A:CYS133 4.8 21.8 1.0
SG A:CYS252 4.8 18.3 1.0
O1B A:LMR602 4.9 19.9 1.0
CA A:GLY515 4.9 16.4 1.0
N A:ASP135 5.0 18.5 1.0

Iron binding site 2 out of 8 in 6uqm

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Iron binding site 2 out of 8 in the Crystal Structure of R173A 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 R173A 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:18.2
occ:1.00
 FE2 A:SF4601 0.0 18.2 1.0
S3 A:SF4601 2.3 16.7 1.0
S4 A:SF4601 2.3 17.7 1.0
SG A:CYS346 2.3 18.8 1.0
S1 A:SF4601 2.3 18.1 1.0
FE3 A:SF4601 2.7 17.3 1.0
FE1 A:SF4601 2.7 18.2 1.0
FE4 A:SF4601 2.8 20.0 1.0
CB A:CYS346 3.3 14.8 1.0
S2 A:SF4601 3.9 20.7 1.0
CB A:ALA348 3.9 14.8 1.0
N A:ALA348 4.2 18.7 1.0
OG A:SER217 4.6 19.8 1.0
CA A:CYS346 4.6 19.8 1.0
CA A:ALA348 4.6 21.1 1.0
N A:SER347 4.7 17.4 1.0
SG A:CYS252 4.7 18.3 1.0
O2 A:LMR602 4.7 18.0 1.0
N A:SER217 4.7 21.1 1.0
O A:ALA251 4.8 18.5 1.0
CB A:CYS252 4.8 20.0 1.0
O1B A:LMR602 4.9 19.9 1.0
C A:CYS346 4.9 23.0 1.0
CA A:GLY214 4.9 15.4 1.0
O A:HOH822 4.9 20.6 1.0
SG A:CYS133 4.9 20.6 1.0

Iron binding site 3 out of 8 in 6uqm

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Iron binding site 3 out of 8 in the Crystal Structure of R173A 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 R173A 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:17.3
occ:1.00
 FE3 A:SF4601 0.0 17.3 1.0
S2 A:SF4601 2.3 20.7 1.0
SG A:CYS252 2.3 18.3 1.0
S4 A:SF4601 2.3 17.7 1.0
S1 A:SF4601 2.3 18.1 1.0
FE2 A:SF4601 2.7 18.2 1.0
FE4 A:SF4601 2.7 20.0 1.0
FE1 A:SF4601 2.7 18.2 1.0
CB A:CYS252 3.2 20.0 1.0
NZ A:LYS491 3.6 18.0 1.0
S3 A:SF4601 3.9 16.7 1.0
O1B A:LMR602 4.0 19.9 1.0
CE A:LYS491 4.0 16.7 1.0
O A:HOH772 4.3 23.5 1.0
N A:GLY515 4.4 16.8 1.0
CA A:CYS252 4.5 15.6 1.0
N A:CYS252 4.5 16.1 1.0
C A:ALA251 4.5 21.3 1.0
CA A:GLY515 4.5 16.4 1.0
O A:ALA251 4.6 18.5 1.0
SG A:CYS346 4.6 18.8 1.0
SG A:CYS133 4.7 20.6 1.0
CB A:CYS346 4.7 14.8 1.0
C A:GLY514 4.9 19.5 1.0
O2 A:LMR602 4.9 18.0 1.0
CD A:LYS491 4.9 15.7 1.0

Iron binding site 4 out of 8 in 6uqm

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Iron binding site 4 out of 8 in the Crystal Structure of R173A 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 R173A 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:20.0
occ:1.00
 FE4 A:SF4601 0.0 20.0 1.0
O2 A:LMR602 2.3 18.0 1.0
S1 A:SF4601 2.3 18.1 1.0
S2 A:SF4601 2.3 20.7 1.0
S3 A:SF4601 2.3 16.7 1.0
O1B A:LMR602 2.4 19.9 1.0
FE3 A:SF4601 2.7 17.3 1.0
FE2 A:SF4601 2.8 18.2 1.0
FE1 A:SF4601 2.8 18.2 1.0
C1 A:LMR602 3.2 18.3 1.0
C2 A:LMR602 3.3 15.2 1.0
N A:GLY216 3.8 18.0 1.0
CA A:GLY216 3.9 21.7 1.0
S4 A:SF4601 3.9 17.7 1.0
NZ A:LYS491 4.0 18.0 1.0
OD1 A:ASP135 4.1 18.8 1.0
O4B A:LMR602 4.3 21.5 1.0
C4 A:LMR602 4.4 26.1 1.0
O1A A:LMR602 4.4 22.4 1.0
C3 A:LMR602 4.4 21.0 1.0
CB A:ASP135 4.5 16.5 1.0
SG A:CYS133 4.6 20.6 1.0
CE A:LYS491 4.7 16.7 1.0
CG A:ASP135 4.7 20.1 1.0
SG A:CYS252 4.8 18.3 1.0
C A:GLY216 4.8 22.1 1.0
N A:SER217 4.9 21.1 1.0
SG A:CYS346 4.9 18.8 1.0
NE2 A:GLN134 5.0 16.3 1.0

Iron binding site 5 out of 8 in 6uqm

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Iron binding site 5 out of 8 in the Crystal Structure of R173A 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 R173A 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
 FE1 B:SF4601 0.0 17.0 1.0
S4 B:SF4601 2.3 15.6 1.0
S3 B:SF4601 2.3 16.8 1.0
S2 B:SF4601 2.3 15.8 1.0
SG B:CYS346 2.3 16.9 1.0
FE4 B:SF4601 2.7 16.3 1.0
FE2 B:SF4601 2.7 15.7 1.0
FE3 B:SF4601 2.8 16.4 1.0
CB B:CYS346 3.2 13.7 1.0
S1 B:SF4601 3.9 17.2 1.0
CB B:ALA348 4.0 11.7 1.0
N B:ALA348 4.2 16.0 1.0
OG B:SER217 4.4 17.8 1.0
CA B:CYS346 4.6 17.2 1.0
N B:SER347 4.6 14.9 1.0
CA B:ALA348 4.7 17.2 1.0
O2 B:LMR602 4.7 16.2 1.0
SG B:CYS252 4.7 17.4 1.0
N B:SER217 4.7 12.7 1.0
O B:ALA251 4.7 20.5 1.0
C B:CYS346 4.8 18.5 1.0
O1B B:LMR602 4.8 15.0 1.0
CB B:CYS252 4.8 13.6 1.0
CA B:GLY214 4.9 13.2 1.0
SG B:CYS133 4.9 15.6 1.0

Iron binding site 6 out of 8 in 6uqm

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Iron binding site 6 out of 8 in the Crystal Structure of R173A 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 R173A 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
SG B:CYS133 2.3 15.6 1.0
S3 B:SF4601 2.3 16.8 1.0
S4 B:SF4601 2.3 15.6 1.0
S1 B:SF4601 2.3 17.2 1.0
FE1 B:SF4601 2.7 17.0 1.0
FE3 B:SF4601 2.8 16.4 1.0
FE4 B:SF4601 2.8 16.3 1.0
CB B:CYS133 3.5 15.0 1.0
S2 B:SF4601 3.9 15.8 1.0
CB B:ALA348 4.0 11.7 1.0
O B:HOH796 4.3 17.0 1.0
NE2 B:GLN134 4.4 13.0 1.0
CB B:ASP135 4.4 15.2 1.0
O2 B:LMR602 4.4 16.2 1.0
O B:HOH907 4.8 23.0 1.0
SG B:CYS346 4.8 16.9 1.0
O1B B:LMR602 4.8 15.0 1.0
CA B:GLY515 4.8 18.8 1.0
CA B:CYS133 4.8 19.4 1.0
O B:ASP135 4.8 13.6 1.0
SG B:CYS252 4.9 17.4 1.0
N B:ASP135 5.0 18.2 1.0

Iron binding site 7 out of 8 in 6uqm

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Iron binding site 7 out of 8 in the Crystal Structure of R173A 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 R173A 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:16.4
occ:1.00
 FE3 B:SF4601 0.0 16.4 1.0
S1 B:SF4601 2.3 17.2 1.0
O2 B:LMR602 2.3 16.2 1.0
S2 B:SF4601 2.3 15.8 1.0
O1B B:LMR602 2.3 15.0 1.0
S4 B:SF4601 2.3 15.6 1.0
FE4 B:SF4601 2.7 16.3 1.0
FE2 B:SF4601 2.8 15.7 1.0
FE1 B:SF4601 2.8 17.0 1.0
C1 B:LMR602 3.1 13.8 1.0
C2 B:LMR602 3.2 16.2 1.0
N B:GLY216 3.9 13.2 1.0
CA B:GLY216 3.9 15.0 1.0
S3 B:SF4601 3.9 16.8 1.0
NZ B:LYS491 4.1 15.4 1.0
OD2 B:ASP135 4.1 14.6 1.0
O4B B:LMR602 4.1 22.6 1.0
C3 B:LMR602 4.3 17.3 1.0
C4 B:LMR602 4.3 19.8 1.0
O1A B:LMR602 4.3 14.3 1.0
CB B:ASP135 4.5 15.2 1.0
SG B:CYS133 4.6 15.6 1.0
CE B:LYS491 4.7 16.8 1.0
CG B:ASP135 4.7 15.9 1.0
SG B:CYS252 4.8 17.4 1.0
C B:GLY216 4.8 14.7 1.0
N B:SER217 4.9 12.7 1.0
SG B:CYS346 4.9 16.9 1.0
NE2 B:GLN134 4.9 13.0 1.0

Iron binding site 8 out of 8 in 6uqm

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Iron binding site 8 out of 8 in the Crystal Structure of R173A 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 R173A 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:16.3
occ:1.00
 FE4 B:SF4601 0.0 16.3 1.0
S1 B:SF4601 2.3 17.2 1.0
S2 B:SF4601 2.3 15.8 1.0
S3 B:SF4601 2.3 16.8 1.0
SG B:CYS252 2.3 17.4 1.0
FE1 B:SF4601 2.7 17.0 1.0
FE3 B:SF4601 2.7 16.4 1.0
FE2 B:SF4601 2.8 15.7 1.0
CB B:CYS252 3.2 13.6 1.0
NZ B:LYS491 3.6 15.4 1.0
S4 B:SF4601 3.9 15.6 1.0
O1B B:LMR602 3.9 15.0 1.0
CE B:LYS491 4.0 16.8 1.0
N B:GLY515 4.4 18.4 1.0
CA B:CYS252 4.5 21.4 1.0
N B:CYS252 4.5 19.9 1.0
C B:ALA251 4.5 18.0 1.0
CA B:GLY515 4.5 18.8 1.0
O B:HOH907 4.6 23.0 1.0
O B:ALA251 4.6 20.5 1.0
SG B:CYS346 4.7 16.9 1.0
CB B:CYS346 4.7 13.7 1.0
SG B:CYS133 4.7 15.6 1.0
C B:GLY514 4.9 16.4 1.0
CD B:LYS491 4.9 16.7 1.0
O2 B:LMR602 5.0 16.2 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 12:37:22 2024

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