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Iron in PDB 6uoj: Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Succinate

Enzymatic activity of Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Succinate

All present enzymatic activity of Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Succinate:
4.2.1.2;

Protein crystallography data

The structure of Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Succinate, PDB code: 6uoj 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) 49.06 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.610, 84.838, 240.542, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 20.2

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6uoj

Go back to Iron Binding Sites List in 6uoj
Iron binding site 1 out of 8 in the Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:26.4
occ:1.00
 FE1 A:SF4601 0.0 26.4 1.0
S4 A:SF4601 2.3 23.8 1.0
SG A:CYS133 2.3 27.2 1.0
S3 A:SF4601 2.3 28.3 1.0
S2 A:SF4601 2.3 26.9 1.0
FE3 A:SF4601 2.7 26.8 1.0
FE2 A:SF4601 2.7 22.7 1.0
FE4 A:SF4601 2.8 61.1 1.0
CB A:CYS133 3.4 21.6 1.0
S1 A:SF4601 3.9 25.8 1.0
CB A:ALA348 4.0 19.2 1.0
O A:HOH708 4.2 42.0 1.0
O A:HOH808 4.4 18.0 1.0
O A:HOH838 4.6 32.4 1.0
CB A:ASP135 4.6 22.6 1.0
NE2 A:GLN134 4.7 19.6 1.0
CA A:CYS133 4.8 23.4 1.0
SG A:CYS252 4.8 22.9 1.0
O A:ASP135 4.8 25.6 1.0
SG A:CYS346 4.9 25.1 1.0
CA A:GLY515 4.9 30.2 1.0
N A:ASP135 5.0 21.2 1.0

Iron binding site 2 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.7
occ:1.00
 FE2 A:SF4601 0.0 22.7 1.0
SG A:CYS346 2.3 25.1 1.0
S3 A:SF4601 2.3 28.3 1.0
S1 A:SF4601 2.3 25.8 1.0
S4 A:SF4601 2.3 23.8 1.0
FE3 A:SF4601 2.7 26.8 1.0
FE1 A:SF4601 2.7 26.4 1.0
FE4 A:SF4601 2.8 61.1 1.0
CB A:CYS346 3.2 22.8 1.0
CB A:ALA348 3.8 19.2 1.0
S2 A:SF4601 3.9 26.9 1.0
N A:ALA348 4.0 24.0 1.0
O A:HOH708 4.4 42.0 1.0
OG A:SER217 4.4 31.6 1.0
CA A:ALA348 4.4 30.1 1.0
O A:HOH783 4.5 26.3 1.0
N A:SER347 4.5 26.6 1.0
CA A:CYS346 4.6 23.0 1.0
SG A:CYS252 4.7 22.9 1.0
CB A:SER217 4.8 27.8 1.0
C A:CYS346 4.8 24.4 1.0
O A:ALA251 4.8 32.1 1.0
CB A:CYS252 4.9 26.1 1.0
SG A:CYS133 4.9 27.2 1.0
O A:ALA348 4.9 24.0 1.0
N A:SER217 5.0 28.7 1.0
CA A:GLY214 5.0 21.3 1.0

Iron binding site 3 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:26.8
occ:1.00
 FE3 A:SF4601 0.0 26.8 1.0
S2 A:SF4601 2.3 26.9 1.0
SG A:CYS252 2.3 22.9 1.0
S1 A:SF4601 2.3 25.8 1.0
S4 A:SF4601 2.3 23.8 1.0
FE2 A:SF4601 2.7 22.7 1.0
FE1 A:SF4601 2.7 26.4 1.0
FE4 A:SF4601 2.7 61.1 1.0
CB A:CYS252 3.2 26.1 1.0
NZ A:LYS491 3.7 23.0 1.0
S3 A:SF4601 3.9 28.3 1.0
O A:HOH838 4.1 32.4 1.0
CE A:LYS491 4.2 28.1 1.0
N A:CYS252 4.4 28.8 1.0
CA A:CYS252 4.5 29.9 1.0
C A:ALA251 4.5 27.6 1.0
N A:GLY515 4.5 33.6 1.0
O2 A:SIN602 4.5 30.8 1.0
O A:ALA251 4.6 32.1 1.0
O A:HOH708 4.6 42.0 1.0
CA A:GLY515 4.7 30.2 1.0
SG A:CYS346 4.7 25.1 1.0
SG A:CYS133 4.7 27.2 1.0
CB A:CYS346 4.7 22.8 1.0
C A:GLY514 4.9 28.3 1.0

Iron binding site 4 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:61.1
occ:1.00
 FE4 A:SF4601 0.0 61.1 1.0
O A:HOH708 1.9 42.0 1.0
S1 A:SF4601 2.3 25.8 1.0
S2 A:SF4601 2.3 26.9 1.0
S3 A:SF4601 2.3 28.3 1.0
FE3 A:SF4601 2.7 26.8 1.0
FE2 A:SF4601 2.8 22.7 1.0
FE1 A:SF4601 2.8 26.4 1.0
O2 A:SIN602 3.1 30.8 1.0
OD2 A:ASP135 3.9 23.4 1.0
S4 A:SF4601 3.9 23.8 1.0
N A:GLY216 4.0 20.6 1.0
C1 A:SIN602 4.0 37.4 1.0
C3 A:SIN602 4.0 32.6 1.0
NZ A:LYS491 4.2 23.0 1.0
C2 A:SIN602 4.2 36.0 1.0
CA A:GLY216 4.2 23.2 1.0
N A:SER217 4.5 28.7 1.0
CB A:ASP135 4.6 22.6 1.0
CG A:ASP135 4.7 32.0 1.0
SG A:CYS133 4.7 27.2 1.0
CA A:GLY214 4.7 21.3 1.0
SG A:CYS346 4.8 25.1 1.0
SG A:CYS252 4.8 22.9 1.0
N A:GLY215 4.8 19.1 1.0
C A:GLY216 4.8 29.3 1.0
C A:GLY214 4.9 25.7 1.0
CE A:LYS491 5.0 28.1 1.0

Iron binding site 5 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:24.3
occ:1.00
 FE1 B:SF4601 0.0 24.3 1.0
S4 B:SF4601 2.2 25.7 1.0
S3 B:SF4601 2.2 25.6 1.0
SG B:CYS133 2.3 22.4 1.0
S2 B:SF4601 2.3 24.9 1.0
FE2 B:SF4601 2.7 24.1 1.0
FE3 B:SF4601 2.8 25.8 1.0
FE4 B:SF4601 3.0 62.1 1.0
CB B:CYS133 3.5 17.8 1.0
S1 B:SF4601 3.9 24.9 1.0
CB B:ALA348 4.0 25.0 1.0
CB B:ASP135 4.3 15.8 1.0
O B:HOH781 4.3 32.2 1.0
NE2 B:GLN134 4.5 18.3 1.0
O B:HOH826 4.5 23.8 1.0
O B:ASP135 4.7 26.6 1.0
SG B:CYS252 4.8 27.2 1.0
CA B:CYS133 4.8 23.4 1.0
SG B:CYS346 4.8 25.4 1.0
N B:ASP135 4.9 16.8 1.0
CA B:GLY515 4.9 21.8 1.0
N B:ALA348 5.0 23.2 1.0

Iron binding site 6 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:24.1
occ:1.00
 FE2 B:SF4601 0.0 24.1 1.0
S3 B:SF4601 2.3 25.6 1.0
S4 B:SF4601 2.3 25.7 1.0
SG B:CYS346 2.3 25.4 1.0
S1 B:SF4601 2.3 24.9 1.0
FE1 B:SF4601 2.7 24.3 1.0
FE3 B:SF4601 2.8 25.8 1.0
FE4 B:SF4601 3.0 62.1 1.0
CB B:CYS346 3.2 24.4 1.0
CB B:ALA348 3.8 25.0 1.0
S2 B:SF4601 3.9 24.9 1.0
N B:ALA348 4.0 23.2 1.0
OG B:SER217 4.4 27.5 1.0
O B:HOH798 4.4 22.9 1.0
CA B:ALA348 4.4 22.3 1.0
N B:SER347 4.5 18.8 1.0
CA B:CYS346 4.5 21.9 1.0
CB B:SER217 4.7 25.7 1.0
SG B:CYS252 4.7 27.2 1.0
C B:CYS346 4.8 28.5 1.0
O B:ALA251 4.8 26.9 1.0
N B:SER217 4.9 26.5 1.0
CB B:CYS252 4.9 26.8 1.0
CA B:GLY214 4.9 20.0 1.0
SG B:CYS133 4.9 22.4 1.0

Iron binding site 7 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:25.8
occ:1.00
 FE3 B:SF4601 0.0 25.8 1.0
S2 B:SF4601 2.2 24.9 1.0
S1 B:SF4601 2.3 24.9 1.0
SG B:CYS252 2.3 27.2 1.0
S4 B:SF4601 2.3 25.7 1.0
FE2 B:SF4601 2.8 24.1 1.0
FE1 B:SF4601 2.8 24.3 1.0
FE4 B:SF4601 2.9 62.1 1.0
CB B:CYS252 3.3 26.8 1.0
NZ B:LYS491 3.5 15.1 1.0
S3 B:SF4601 3.9 25.6 1.0
CE B:LYS491 4.1 20.2 1.0
O B:HOH826 4.1 23.8 1.0
O2 B:SIN602 4.4 22.0 1.0
N B:CYS252 4.4 23.8 1.0
C B:ALA251 4.4 24.6 1.0
CA B:CYS252 4.5 31.2 1.0
N B:GLY515 4.5 25.9 1.0
O B:ALA251 4.6 26.9 1.0
SG B:CYS346 4.7 25.4 1.0
CB B:CYS346 4.7 24.4 1.0
CA B:GLY515 4.7 21.8 1.0
SG B:CYS133 4.8 22.4 1.0
C B:GLY514 4.9 24.3 1.0
CA B:ALA251 5.0 25.0 1.0

Iron binding site 8 out of 8 in 6uoj

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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 Succinate


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 Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:62.1
occ:1.00
 FE4 B:SF4601 0.0 62.1 1.0
S1 B:SF4601 2.4 24.9 1.0
S2 B:SF4601 2.4 24.9 1.0
S3 B:SF4601 2.5 25.6 1.0
O2 B:SIN602 2.9 22.0 1.0
FE3 B:SF4601 2.9 25.8 1.0
FE2 B:SF4601 3.0 24.1 1.0
FE1 B:SF4601 3.0 24.3 1.0
C2 B:SIN602 3.3 27.8 1.0
C1 B:SIN602 3.5 29.0 1.0
C3 B:SIN602 3.7 21.1 1.0
N B:GLY216 3.7 21.1 1.0
OD1 B:ASP135 3.7 18.8 1.0
CA B:GLY216 3.9 25.0 1.0
NZ B:LYS491 4.1 15.1 1.0
S4 B:SF4601 4.1 25.7 1.0
CB B:ASP135 4.3 15.8 1.0
N B:SER217 4.4 26.5 1.0
CG B:ASP135 4.5 24.1 1.0
CA B:GLY214 4.6 20.0 1.0
C B:GLY216 4.6 28.1 1.0
N B:GLY215 4.7 17.8 1.0
O1 B:SIN602 4.7 32.4 1.0
C B:GLY214 4.8 19.9 1.0
C4 B:SIN602 4.9 28.9 1.0
SG B:CYS133 4.9 22.4 1.0
CE B:LYS491 4.9 20.2 1.0
C B:GLY215 4.9 26.8 1.0
SG B:CYS346 5.0 25.4 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 12:23:46 2024

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