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

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

All present enzymatic activity of Crystal Structure of R173A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Fumarate and 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 Fumarate and S-Malate, PDB code: 6uqn 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) 49.20 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.148, 85.415, 240.724, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.3

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

Iron binding site 1 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:48.3
occ:1.00
 FE1 A:SF4601 0.0 48.3 1.0
S4 A:SF4601 2.3 50.7 1.0
S2 A:SF4601 2.3 54.5 1.0
SG A:CYS133 2.3 56.5 1.0
S3 A:SF4601 2.3 60.0 1.0
FE2 A:SF4601 2.7 67.0 1.0
FE3 A:SF4601 2.7 45.3 1.0
FE4 A:SF4601 2.7 49.8 1.0
CB A:CYS133 3.5 54.4 1.0
O2 A:LMR602 3.8 48.7 1.0
S1 A:SF4601 3.9 51.6 1.0
CB A:ASP135 4.3 59.2 1.0
CB A:ALA348 4.3 38.6 1.0
OE1 A:GLN134 4.8 58.4 1.0
O1B A:LMR602 4.8 47.9 1.0
SG A:CYS252 4.8 44.4 1.0
SG A:CYS346 4.8 74.3 1.0
NE2 A:GLN134 4.8 49.8 1.0
CA A:CYS133 4.9 50.5 1.0
N A:ASP135 4.9 62.7 1.0
O A:ASP135 4.9 55.7 1.0

Iron binding site 2 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:67.0
occ:1.00
 FE2 A:SF4601 0.0 67.0 1.0
SG A:CYS346 2.3 74.3 1.0
S1 A:SF4601 2.3 51.6 1.0
S4 A:SF4601 2.3 50.7 1.0
S3 A:SF4601 2.3 60.0 1.0
FE3 A:SF4601 2.7 45.3 1.0
FE1 A:SF4601 2.7 48.3 1.0
FE4 A:SF4601 2.7 49.8 1.0
CB A:CYS346 3.1 43.7 1.0
CB A:ALA348 3.8 38.6 1.0
S2 A:SF4601 3.9 54.5 1.0
N A:ALA348 4.1 36.7 1.0
CA A:CYS346 4.5 52.1 1.0
N A:SER347 4.5 49.1 1.0
CA A:ALA348 4.6 38.7 1.0
O A:ALA251 4.7 52.7 1.0
CB A:CYS252 4.7 45.4 1.0
SG A:CYS252 4.7 44.4 1.0
C A:CYS346 4.8 49.3 1.0
SG A:CYS133 4.8 56.5 1.0
OG A:SER217 4.9 57.6 1.0
N A:SER217 4.9 40.3 1.0
O1B A:LMR602 4.9 47.9 1.0
CB A:SER217 5.0 44.6 1.0

Iron binding site 3 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:45.3
occ:1.00
 FE3 A:SF4601 0.0 45.3 1.0
SG A:CYS252 2.3 44.4 1.0
S2 A:SF4601 2.3 54.5 1.0
S1 A:SF4601 2.3 51.6 1.0
S4 A:SF4601 2.3 50.7 1.0
FE2 A:SF4601 2.7 67.0 1.0
FE1 A:SF4601 2.7 48.3 1.0
FE4 A:SF4601 2.7 49.8 1.0
CB A:CYS252 3.2 45.4 1.0
O1B A:LMR602 3.8 47.9 1.0
S3 A:SF4601 3.9 60.0 1.0
NZ A:LYS491 4.2 46.6 1.0
CE A:LYS491 4.2 45.7 1.0
CA A:CYS252 4.4 48.5 1.0
O A:ALA251 4.5 52.7 1.0
N A:CYS252 4.5 52.6 1.0
C A:ALA251 4.5 50.8 1.0
O2 A:LMR602 4.5 48.7 1.0
N A:GLY515 4.7 43.4 1.0
SG A:CYS346 4.7 74.3 1.0
CA A:GLY515 4.7 62.6 1.0
CB A:CYS346 4.7 43.7 1.0
SG A:CYS133 4.8 56.5 1.0
C1 A:LMR602 4.9 47.2 1.0
C A:GLY514 4.9 49.9 1.0

Iron binding site 4 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:49.8
occ:1.00
 FE4 A:SF4601 0.0 49.8 1.0
S2 A:SF4601 2.3 54.5 1.0
S1 A:SF4601 2.3 51.6 1.0
S3 A:SF4601 2.3 60.0 1.0
O2 A:LMR602 2.5 48.7 1.0
O1B A:LMR602 2.5 47.9 1.0
FE2 A:SF4601 2.7 67.0 1.0
FE3 A:SF4601 2.7 45.3 1.0
FE1 A:SF4601 2.7 48.3 1.0
C2 A:LMR602 3.1 48.4 1.0
C1 A:LMR602 3.2 47.2 1.0
N A:GLY216 3.7 46.2 1.0
S4 A:SF4601 3.9 50.7 1.0
CA A:GLY216 3.9 36.5 1.0
OD2 A:ASP135 4.0 56.8 1.0
O1A A:LMR602 4.4 42.4 1.0
NZ A:LYS491 4.4 46.6 1.0
CB A:ASP135 4.5 59.2 1.0
N A:GLY215 4.6 51.6 1.0
C3 A:LMR602 4.6 59.6 1.0
N A:SER217 4.6 40.3 1.0
CG A:ASP135 4.7 64.6 1.0
SG A:CYS133 4.7 56.5 1.0
SG A:CYS346 4.8 74.3 1.0
C A:GLY216 4.8 36.5 1.0
O4B A:LMR602 4.8 74.2 1.0
SG A:CYS252 4.8 44.4 1.0
CA A:GLY214 4.8 43.9 1.0
C A:GLY215 4.8 44.4 1.0
C A:GLY214 4.9 46.5 1.0
CE A:LYS491 4.9 45.7 1.0

Iron binding site 5 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:46.8
occ:1.00
 FE1 B:SF4601 0.0 46.8 1.0
SG B:CYS346 2.3 49.6 1.0
S4 B:SF4601 2.3 54.3 1.0
S3 B:SF4601 2.3 43.8 1.0
S2 B:SF4601 2.3 43.3 1.0
FE2 B:SF4601 2.7 49.2 1.0
FE4 B:SF4601 2.7 45.2 1.0
FE3 B:SF4601 2.7 64.0 1.0
CB B:CYS346 3.1 44.9 1.0
S1 B:SF4601 3.9 63.7 1.0
CB B:ALA348 4.0 54.9 1.0
N B:ALA348 4.2 60.2 1.0
CA B:CYS346 4.5 44.4 1.0
N B:SER347 4.5 49.2 1.0
CB B:CYS252 4.7 47.1 1.0
SG B:CYS252 4.7 53.4 1.0
CA B:ALA348 4.7 49.8 1.0
O B:ALA251 4.7 48.1 1.0
C B:CYS346 4.8 50.8 1.0
SG B:CYS133 4.8 34.3 1.0
N B:SER217 4.9 40.5 1.0
O8 B:FUM602 4.9 45.1 1.0
CA B:GLY214 4.9 44.7 1.0

Iron binding site 6 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:49.2
occ:1.00
 FE2 B:SF4601 0.0 49.2 1.0
S3 B:SF4601 2.3 43.8 1.0
S4 B:SF4601 2.3 54.3 1.0
SG B:CYS133 2.3 34.3 1.0
S1 B:SF4601 2.3 63.7 1.0
FE1 B:SF4601 2.7 46.8 1.0
FE4 B:SF4601 2.7 45.2 1.0
FE3 B:SF4601 2.7 64.0 1.0
CB B:CYS133 3.5 45.5 1.0
S2 B:SF4601 3.9 43.3 1.0
CB B:ASP135 4.2 55.2 1.0
CB B:ALA348 4.3 54.9 1.0
NH2 B:ARG350 4.6 50.4 1.0
OE1 B:GLN134 4.7 45.2 1.0
NE2 B:GLN134 4.7 56.6 1.0
N B:ASP135 4.8 56.1 1.0
SG B:CYS346 4.8 49.6 1.0
SG B:CYS252 4.8 53.4 1.0
O8 B:FUM602 4.8 45.1 1.0
O B:ASP135 4.9 49.5 1.0
CA B:CYS133 4.9 55.7 1.0
CD B:GLN134 4.9 49.1 1.0
OD2 B:ASP135 5.0 40.6 1.0

Iron binding site 7 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:64.0
occ:1.00
 FE3 B:SF4601 0.0 64.0 1.0
S2 B:SF4601 2.3 43.3 1.0
S1 B:SF4601 2.3 63.7 1.0
S4 B:SF4601 2.3 54.3 1.0
O8 B:FUM602 2.3 45.1 1.0
FE4 B:SF4601 2.7 45.2 1.0
FE1 B:SF4601 2.7 46.8 1.0
FE2 B:SF4601 2.7 49.2 1.0
C6 B:FUM602 3.3 55.5 1.0
N B:GLY216 3.6 41.6 1.0
OD2 B:ASP135 3.9 40.6 1.0
S3 B:SF4601 3.9 43.8 1.0
CA B:GLY216 4.0 40.4 1.0
C5 B:FUM602 4.1 54.4 1.0
C4 B:FUM602 4.2 59.0 1.0
O7 B:FUM602 4.2 53.9 1.0
CB B:ASP135 4.4 55.2 1.0
N B:GLY215 4.5 46.8 1.0
NZ B:LYS491 4.5 48.8 1.0
CG B:ASP135 4.6 52.5 1.0
SG B:CYS133 4.7 34.3 1.0
SG B:CYS346 4.8 49.6 1.0
SG B:CYS252 4.8 53.4 1.0
C B:GLY215 4.8 43.2 1.0
CE B:LYS491 4.9 46.3 1.0
N B:SER217 4.9 40.5 1.0
CA B:GLY214 4.9 44.7 1.0
C B:GLY214 4.9 46.7 1.0

Iron binding site 8 out of 8 in 6uqn

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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 Fumarate and 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 Fumarate and S-Malate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:45.2
occ:1.00
 FE4 B:SF4601 0.0 45.2 1.0
S1 B:SF4601 2.3 63.7 1.0
SG B:CYS252 2.3 53.4 1.0
S2 B:SF4601 2.3 43.3 1.0
S3 B:SF4601 2.3 43.8 1.0
FE3 B:SF4601 2.7 64.0 1.0
FE2 B:SF4601 2.7 49.2 1.0
FE1 B:SF4601 2.7 46.8 1.0
CB B:CYS252 3.2 47.1 1.0
S4 B:SF4601 3.9 54.3 1.0
CE B:LYS491 4.1 46.3 1.0
NZ B:LYS491 4.2 48.8 1.0
CA B:CYS252 4.5 55.7 1.0
O8 B:FUM602 4.5 45.1 1.0
N B:GLY515 4.5 50.4 1.0
N B:CYS252 4.6 62.0 1.0
O B:ALA251 4.6 48.1 1.0
C B:ALA251 4.6 49.2 1.0
CA B:GLY515 4.7 49.3 1.0
SG B:CYS346 4.8 49.6 1.0
SG B:CYS133 4.8 34.3 1.0
CB B:CYS346 4.8 44.9 1.0
C B:GLY514 4.9 55.3 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 12:38:27 2024

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