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Iron in PDB 6uo0: Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate

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

All present enzymatic activity of Crystal Structure 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 Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6uo0 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) 48.91 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.613, 84.681, 239.658, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate (pdb code 6uo0). 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 Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate, PDB code: 6uo0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6uo0

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Iron binding site 1 out of 8 in the Crystal Structure 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 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:21.5
occ:1.00
 FE1 A:SF4601 0.0 21.5 1.0
S4 A:SF4601 2.3 21.2 1.0
SG A:CYS133 2.3 21.8 1.0
S3 A:SF4601 2.3 20.5 1.0
S2 A:SF4601 2.3 21.8 1.0
FE3 A:SF4601 2.7 19.6 1.0
FE2 A:SF4601 2.8 20.4 1.0
FE4 A:SF4601 2.8 22.8 1.0
CB A:CYS133 3.5 23.7 1.0
S1 A:SF4601 3.9 20.5 1.0
CB A:ALA348 4.0 24.0 1.0
CB A:ASP135 4.3 19.4 1.0
O A:HOH810 4.4 21.9 1.0
O2 A:LMR602 4.4 20.6 1.0
NE2 A:GLN134 4.4 17.9 1.0
O A:HOH770 4.7 22.0 1.0
O A:ASP135 4.8 16.3 1.0
SG A:CYS252 4.8 21.7 1.0
CA A:CYS133 4.8 21.8 1.0
SG A:CYS346 4.8 19.3 1.0
CA A:GLY515 4.9 21.5 1.0
N A:ASP135 5.0 23.9 1.0

Iron binding site 2 out of 8 in 6uo0

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Iron binding site 2 out of 8 in the Crystal Structure 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 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:20.4
occ:1.00
 FE2 A:SF4601 0.0 20.4 1.0
S3 A:SF4601 2.3 20.5 1.0
SG A:CYS346 2.3 19.3 1.0
S4 A:SF4601 2.3 21.2 1.0
S1 A:SF4601 2.3 20.5 1.0
FE3 A:SF4601 2.7 19.6 1.0
FE4 A:SF4601 2.7 22.8 1.0
FE1 A:SF4601 2.8 21.5 1.0
CB A:CYS346 3.3 19.5 1.0
S2 A:SF4601 3.9 21.8 1.0
CB A:ALA348 3.9 24.0 1.0
N A:ALA348 4.2 18.7 1.0
OG A:SER217 4.5 20.7 1.0
CA A:CYS346 4.6 22.8 1.0
CA A:ALA348 4.6 20.8 1.0
N A:SER347 4.7 17.1 1.0
SG A:CYS252 4.7 21.7 1.0
N A:SER217 4.7 21.5 1.0
O2 A:LMR602 4.7 20.6 1.0
CB A:CYS252 4.8 29.1 1.0
O A:ALA251 4.8 18.2 1.0
O A:HOH800 4.8 23.3 1.0
C A:CYS346 4.9 19.8 1.0
CA A:GLY214 4.9 21.5 1.0
CB A:SER217 4.9 18.4 1.0
SG A:CYS133 4.9 21.8 1.0
O1B A:LMR602 5.0 22.3 1.0

Iron binding site 3 out of 8 in 6uo0

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Iron binding site 3 out of 8 in the Crystal Structure 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 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:19.6
occ:1.00
 FE3 A:SF4601 0.0 19.6 1.0
S2 A:SF4601 2.2 21.8 1.0
SG A:CYS252 2.3 21.7 1.0
S4 A:SF4601 2.3 21.2 1.0
S1 A:SF4601 2.3 20.5 1.0
FE4 A:SF4601 2.7 22.8 1.0
FE2 A:SF4601 2.7 20.4 1.0
FE1 A:SF4601 2.7 21.5 1.0
NZ A:LYS491 3.1 21.8 0.3
CB A:CYS252 3.2 29.1 1.0
NZ A:LYS491 3.7 21.8 0.7
S3 A:SF4601 3.9 20.5 1.0
CE A:LYS491 4.0 24.1 0.3
CE A:LYS491 4.0 20.3 0.7
O1B A:LMR602 4.0 22.3 1.0
O A:HOH770 4.3 22.0 1.0
N A:CYS252 4.4 22.1 1.0
CA A:CYS252 4.4 25.3 1.0
C A:ALA251 4.5 20.8 1.0
N A:GLY515 4.5 22.0 1.0
CA A:GLY515 4.6 21.5 1.0
O A:ALA251 4.6 18.2 1.0
CD A:LYS491 4.6 24.8 0.3
SG A:CYS346 4.7 19.3 1.0
SG A:CYS133 4.7 21.8 1.0
CB A:CYS346 4.8 19.5 1.0
C A:GLY514 4.9 20.8 1.0
O2 A:LMR602 4.9 20.6 1.0
CD A:LYS491 5.0 25.9 0.7
CA A:ALA251 5.0 21.1 1.0

Iron binding site 4 out of 8 in 6uo0

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Iron binding site 4 out of 8 in the Crystal Structure 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 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:22.8
occ:1.00
 FE4 A:SF4601 0.0 22.8 1.0
S1 A:SF4601 2.3 20.5 1.0
O2 A:LMR602 2.3 20.6 1.0
S2 A:SF4601 2.3 21.8 1.0
S3 A:SF4601 2.3 20.5 1.0
O1B A:LMR602 2.6 22.3 1.0
FE3 A:SF4601 2.7 19.6 1.0
FE2 A:SF4601 2.7 20.4 1.0
FE1 A:SF4601 2.8 21.5 1.0
C2 A:LMR602 3.2 26.6 1.0
C1 A:LMR602 3.3 23.4 1.0
C3 A:LMR602 3.7 25.9 1.0
NZ A:LYS491 3.8 21.8 0.3
N A:GLY216 3.8 20.7 1.0
S4 A:SF4601 3.9 21.2 1.0
CA A:GLY216 4.0 18.4 1.0
NZ A:LYS491 4.0 21.8 0.7
OD2 A:ASP135 4.1 18.7 1.0
CB A:ASP135 4.5 19.4 1.0
O1A A:LMR602 4.5 25.4 1.0
CE A:LYS491 4.6 20.3 0.7
SG A:CYS133 4.7 21.8 1.0
CE A:LYS491 4.7 24.1 0.3
N A:SER217 4.7 21.5 1.0
CG A:ASP135 4.7 22.5 1.0
SG A:CYS252 4.8 21.7 1.0
C A:GLY216 4.8 23.9 1.0
SG A:CYS346 4.8 19.3 1.0
C4 A:LMR602 4.9 24.8 1.0
N A:GLY215 4.9 18.3 1.0
CA A:GLY214 5.0 21.5 1.0

Iron binding site 5 out of 8 in 6uo0

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Iron binding site 5 out of 8 in the Crystal Structure 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 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:18.2
occ:1.00
 FE1 B:SF4601 0.0 18.2 1.0
S3 B:SF4601 2.3 18.4 1.0
SG B:CYS133 2.3 18.8 1.0
S4 B:SF4601 2.3 19.6 1.0
S2 B:SF4601 2.3 18.2 1.0
FE2 B:SF4601 2.8 17.8 1.0
FE3 B:SF4601 2.8 18.6 1.0
FE4 B:SF4601 2.8 19.2 1.0
CB B:CYS133 3.5 14.6 1.0
S1 B:SF4601 3.9 18.6 1.0
CB B:ALA348 4.0 17.2 1.0
O B:HOH933 4.3 20.9 1.0
CB B:ASP135 4.3 14.6 1.0
O2 B:LMR602 4.4 17.4 1.0
NE2 B:GLN134 4.5 16.1 1.0
O B:HOH826 4.6 23.0 1.0
O B:ASP135 4.7 15.8 1.0
CA B:CYS133 4.8 22.0 1.0
SG B:CYS346 4.8 19.2 1.0
CA B:GLY515 4.8 23.0 1.0
SG B:CYS252 4.8 17.9 1.0
C3 B:LMR602 4.9 14.7 1.0
O1B B:LMR602 5.0 19.6 1.0
N B:ASP135 5.0 18.2 1.0
N B:ALA348 5.0 16.5 1.0
NZ B:LYS491 5.0 19.4 0.1

Iron binding site 6 out of 8 in 6uo0

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Iron binding site 6 out of 8 in the Crystal Structure 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 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:17.8
occ:1.00
 FE2 B:SF4601 0.0 17.8 1.0
S4 B:SF4601 2.3 19.6 1.0
S1 B:SF4601 2.3 18.6 1.0
SG B:CYS346 2.3 19.2 1.0
S3 B:SF4601 2.3 18.4 1.0
FE3 B:SF4601 2.7 18.6 1.0
FE1 B:SF4601 2.8 18.2 1.0
FE4 B:SF4601 2.8 19.2 1.0
CB B:CYS346 3.2 14.8 1.0
CB B:ALA348 3.9 17.2 1.0
S2 B:SF4601 3.9 18.2 1.0
N B:ALA348 4.1 16.5 1.0
OG B:SER217 4.4 20.1 1.0
N B:SER347 4.5 18.1 1.0
CA B:ALA348 4.5 19.1 1.0
CA B:CYS346 4.5 18.6 1.0
SG B:CYS252 4.7 17.9 1.0
O B:ALA251 4.7 21.8 1.0
O2 B:LMR602 4.7 17.4 1.0
C B:CYS346 4.8 22.4 1.0
CB B:CYS252 4.8 17.8 1.0
N B:SER217 4.8 19.4 1.0
O B:HOH807 4.8 26.1 1.0
O1B B:LMR602 4.9 19.6 1.0
CB B:SER217 4.9 17.0 1.0
CA B:GLY214 4.9 22.4 1.0
SG B:CYS133 5.0 18.8 1.0
O B:ALA348 5.0 18.5 1.0

Iron binding site 7 out of 8 in 6uo0

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Iron binding site 7 out of 8 in the Crystal Structure 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 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:18.6
occ:1.00
 FE3 B:SF4601 0.0 18.6 1.0
S2 B:SF4601 2.3 18.2 1.0
SG B:CYS252 2.3 17.9 1.0
S1 B:SF4601 2.3 18.6 1.0
S4 B:SF4601 2.3 19.6 1.0
FE4 B:SF4601 2.7 19.2 1.0
FE2 B:SF4601 2.7 17.8 1.0
FE1 B:SF4601 2.8 18.2 1.0
NZ B:LYS491 3.0 19.4 0.1
CB B:CYS252 3.2 17.8 1.0
NZ B:LYS491 3.7 18.2 0.9
S3 B:SF4601 3.9 18.4 1.0
O1B B:LMR602 4.0 19.6 1.0
CE B:LYS491 4.0 18.2 0.1
CE B:LYS491 4.1 16.4 0.9
O B:HOH826 4.3 23.0 1.0
CA B:CYS252 4.4 18.7 1.0
N B:CYS252 4.4 16.8 1.0
C B:ALA251 4.4 20.7 1.0
N B:GLY515 4.5 24.3 1.0
CA B:GLY515 4.5 23.0 1.0
O B:ALA251 4.5 21.8 1.0
CD B:LYS491 4.7 20.6 0.1
SG B:CYS346 4.7 19.2 1.0
SG B:CYS133 4.7 18.8 1.0
CB B:CYS346 4.7 14.8 1.0
C B:GLY514 4.8 17.0 1.0
O2 B:LMR602 4.9 17.4 1.0
CD B:LYS491 4.9 22.5 0.9
C1 B:LMR602 5.0 24.8 1.0
CA B:ALA251 5.0 14.6 1.0

Iron binding site 8 out of 8 in 6uo0

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Iron binding site 8 out of 8 in the Crystal Structure 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 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:19.2
occ:1.00
 FE4 B:SF4601 0.0 19.2 1.0
S2 B:SF4601 2.3 18.2 1.0
S1 B:SF4601 2.3 18.6 1.0
O2 B:LMR602 2.3 17.4 1.0
S3 B:SF4601 2.3 18.4 1.0
O1B B:LMR602 2.4 19.6 1.0
FE3 B:SF4601 2.7 18.6 1.0
FE2 B:SF4601 2.8 17.8 1.0
FE1 B:SF4601 2.8 18.2 1.0
C2 B:LMR602 3.1 19.8 1.0
C1 B:LMR602 3.1 24.8 1.0
NZ B:LYS491 3.5 19.4 0.1
C3 B:LMR602 3.6 14.7 1.0
S4 B:SF4601 3.9 19.6 1.0
N B:GLY216 3.9 14.9 1.0
CA B:GLY216 4.1 16.9 1.0
NZ B:LYS491 4.1 18.2 0.9
OD2 B:ASP135 4.1 16.3 1.0
O1A B:LMR602 4.4 21.7 1.0
CB B:ASP135 4.5 14.6 1.0
CE B:LYS491 4.6 18.2 0.1
SG B:CYS133 4.7 18.8 1.0
CE B:LYS491 4.7 16.4 0.9
SG B:CYS252 4.7 17.9 1.0
CG B:ASP135 4.7 15.0 1.0
N B:SER217 4.8 19.4 1.0
SG B:CYS346 4.8 19.2 1.0
N B:GLY215 4.9 17.4 1.0
CA B:GLY214 4.9 22.4 1.0
C B:GLY216 4.9 22.7 1.0
C4 B:LMR602 4.9 18.1 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 12:23:40 2024

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