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

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

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

Protein crystallography data

The structure of Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Malonate, PDB code: 6uoi 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) 49.07 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.578, 85.102, 240.231, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.6

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:18.1
occ:1.00
 FE1 A:F3S605 0.0 18.1 1.0
S1 A:F3S605 2.2 20.0 1.0
SG A:CYS346 2.3 19.6 1.0
S3 A:F3S605 2.3 18.9 1.0
S2 A:F3S605 2.3 20.5 1.0
FE4 A:F3S605 2.7 20.1 1.0
FE3 A:F3S605 2.7 19.3 1.0
CB A:CYS346 3.2 18.4 1.0
CB A:ALA348 3.8 19.7 1.0
S4 A:F3S605 3.9 21.6 1.0
N A:ALA348 4.0 16.2 1.0
O A:HOH763 4.1 17.2 1.0
OG A:SER217 4.5 25.1 1.0
O A:HOH861 4.5 28.6 1.0
CA A:ALA348 4.5 22.8 1.0
N A:SER347 4.5 17.0 1.0
CA A:CYS346 4.6 21.8 1.0
SG A:CYS252 4.6 21.5 1.0
CB A:SER217 4.7 18.3 1.0
CB A:CYS252 4.8 26.6 1.0
O A:ALA251 4.8 20.7 1.0
C A:CYS346 4.8 22.3 1.0
O A:ALA348 4.9 23.4 1.0
CA A:GLY214 4.9 15.5 1.0
SG A:CYS133 4.9 21.0 1.0
N A:SER217 5.0 19.1 1.0

Iron binding site 2 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:19.3
occ:1.00
 FE3 A:F3S605 0.0 19.3 1.0
S1 A:F3S605 2.3 20.0 1.0
S3 A:F3S605 2.3 18.9 1.0
SG A:CYS133 2.3 21.0 1.0
S4 A:F3S605 2.3 21.6 1.0
FE4 A:F3S605 2.7 20.1 1.0
FE1 A:F3S605 2.7 18.1 1.0
CB A:CYS133 3.4 19.8 1.0
S2 A:F3S605 4.0 20.5 1.0
CB A:ALA348 4.0 19.7 1.0
O A:HOH763 4.1 17.2 1.0
O A:HOH833 4.3 20.6 1.0
CB A:ASP135 4.3 16.5 1.0
O A:HOH940 4.6 23.4 1.0
O A:HOH862 4.6 36.2 1.0
NE2 A:GLN134 4.6 19.4 1.0
O A:ASP135 4.7 19.5 1.0
SG A:CYS252 4.7 21.5 1.0
CA A:CYS133 4.8 21.4 1.0
SG A:CYS346 4.8 19.6 1.0
CA A:GLY515 4.9 22.7 1.0
N A:ASP135 4.9 18.8 1.0

Iron binding site 3 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:20.1
occ:1.00
 FE4 A:F3S605 0.0 20.1 1.0
S4 A:F3S605 2.2 21.6 1.0
SG A:CYS252 2.3 21.5 1.0
S2 A:F3S605 2.3 20.5 1.0
S3 A:F3S605 2.3 18.9 1.0
FE1 A:F3S605 2.7 18.1 1.0
FE3 A:F3S605 2.7 19.3 1.0
CB A:CYS252 3.2 26.6 1.0
NZ A:LYS491 3.5 27.0 0.2
NZ A:LYS491 3.5 26.4 0.8
S1 A:F3S605 3.9 20.0 1.0
O A:HOH940 4.1 23.4 1.0
CE A:LYS491 4.1 27.7 0.8
O A:HOH705 4.1 21.4 1.0
CE A:LYS491 4.2 27.9 0.2
O A:HOH763 4.2 17.2 1.0
N A:CYS252 4.5 19.8 1.0
C A:ALA251 4.5 21.6 1.0
CA A:CYS252 4.5 23.6 1.0
O A:ALA251 4.6 20.7 1.0
N A:GLY515 4.6 29.4 1.0
SG A:CYS346 4.7 19.6 1.0
SG A:CYS133 4.7 21.0 1.0
CB A:CYS346 4.8 18.4 1.0
CA A:GLY515 4.8 22.7 1.0
CD A:LYS491 4.9 28.9 0.8
CA A:ALA251 5.0 19.1 1.0

Iron binding site 4 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:27.1
occ:0.50
 O A:HOH815 2.9 29.6 1.0
O A:HOH1033 3.0 47.0 1.0
ND2 A:ASN219 3.1 16.5 1.0
NH1 A:ARG471 3.1 23.3 1.0
OG1 A:THR468 3.3 23.9 1.0
CB A:THR468 3.4 23.0 1.0
CG2 A:THR468 3.5 23.2 1.0
CD A:ARG471 3.7 23.9 1.0
CG A:ARG471 3.8 24.3 1.0
CG A:ASN219 4.1 18.3 1.0
CB A:ASN219 4.1 14.1 1.0
CA A:GLY216 4.1 23.7 1.0
CZ A:ARG471 4.2 21.6 1.0
O B:HOH1096 4.3 50.7 1.0
NE A:ARG471 4.4 22.5 1.0
O B:ALA336 4.4 22.3 1.0
O A:GLY216 4.6 19.0 1.0
NZ A:LYS220 4.7 33.8 1.0
O1B A:MLA601 4.8 22.1 1.0
CA A:THR468 4.9 21.4 1.0
C A:GLY216 4.9 21.2 1.0
O A:HOH705 4.9 21.4 1.0
O A:ALA250 5.0 32.3 1.0

Iron binding site 5 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:18.8
occ:1.00
 FE1 B:F3S604 0.0 18.8 1.0
S1 B:F3S604 2.2 18.7 1.0
SG B:CYS133 2.3 18.9 1.0
S2 B:F3S604 2.3 18.2 1.0
S3 B:F3S604 2.3 20.7 1.0
FE3 B:F3S604 2.7 19.1 1.0
FE4 B:F3S604 2.8 18.6 1.0
CB B:CYS133 3.4 15.7 1.0
S4 B:F3S604 4.0 20.0 1.0
CB B:ALA348 4.0 16.5 1.0
O B:HOH771 4.1 19.8 1.0
CB B:ASP135 4.2 16.9 1.0
O B:HOH864 4.4 23.7 1.0
NE2 B:GLN134 4.5 15.0 1.0
O B:HOH923 4.5 21.4 1.0
O B:ASP135 4.7 16.2 1.0
O B:HOH932 4.7 33.3 1.0
SG B:CYS252 4.8 19.3 1.0
CA B:CYS133 4.8 19.2 1.0
SG B:CYS346 4.9 19.1 1.0
N B:ASP135 4.9 16.7 1.0
CA B:GLY515 5.0 19.6 1.0

Iron binding site 6 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:19.1
occ:1.00
 FE3 B:F3S604 0.0 19.1 1.0
S1 B:F3S604 2.2 18.7 1.0
S4 B:F3S604 2.3 20.0 1.0
SG B:CYS346 2.3 19.1 1.0
S3 B:F3S604 2.3 20.7 1.0
FE4 B:F3S604 2.7 18.6 1.0
FE1 B:F3S604 2.7 18.8 1.0
CB B:CYS346 3.2 15.7 1.0
CB B:ALA348 3.8 16.5 1.0
S2 B:F3S604 3.9 18.2 1.0
O B:HOH771 4.0 19.8 1.0
N B:ALA348 4.0 18.4 1.0
OG B:SER217 4.4 27.5 1.0
O B:HOH893 4.4 25.2 1.0
CA B:ALA348 4.5 19.2 1.0
N B:SER347 4.5 19.6 1.0
CA B:CYS346 4.6 17.7 1.0
SG B:CYS252 4.7 19.3 1.0
CB B:SER217 4.7 20.4 1.0
O B:ALA251 4.7 22.5 1.0
CB B:CYS252 4.8 19.6 1.0
C B:CYS346 4.8 20.6 1.0
O B:ALA348 4.9 19.3 1.0
SG B:CYS133 4.9 18.9 1.0
CA B:GLY214 5.0 18.9 1.0
N B:SER217 5.0 18.6 1.0

Iron binding site 7 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe604

b:18.6
occ:1.00
 FE4 B:F3S604 0.0 18.6 1.0
S2 B:F3S604 2.3 18.2 1.0
S4 B:F3S604 2.3 20.0 1.0
SG B:CYS252 2.3 19.3 1.0
S3 B:F3S604 2.3 20.7 1.0
FE3 B:F3S604 2.7 19.1 1.0
FE1 B:F3S604 2.8 18.8 1.0
CB B:CYS252 3.2 19.6 1.0
NZ B:LYS491 3.5 19.0 1.0
S1 B:F3S604 3.9 18.7 1.0
O B:HOH923 4.1 21.4 1.0
O B:HOH726 4.1 19.6 1.0
CE B:LYS491 4.2 16.3 1.0
O B:HOH771 4.3 19.8 1.0
C B:ALA251 4.4 18.8 1.0
N B:CYS252 4.4 21.1 1.0
CA B:CYS252 4.5 22.7 1.0
O B:ALA251 4.5 22.5 1.0
N B:GLY515 4.6 20.6 1.0
SG B:CYS346 4.6 19.1 1.0
SG B:CYS133 4.7 18.9 1.0
CB B:CYS346 4.7 15.7 1.0
CA B:GLY515 4.7 19.6 1.0
CA B:ALA251 5.0 18.3 1.0
C B:GLY514 5.0 21.0 1.0
CD B:LYS491 5.0 19.9 1.0

Iron binding site 8 out of 8 in 6uoi

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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 Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe605

b:27.9
occ:0.60
 O B:HOH811 2.8 27.2 1.0
O B:HOH1062 2.9 47.1 1.0
ND2 B:ASN219 3.0 14.9 1.0
NH1 B:ARG471 3.2 16.1 1.0
OG1 B:THR468 3.4 20.2 1.0
CB B:THR468 3.5 17.9 1.0
CG2 B:THR468 3.5 19.9 1.0
CG B:ARG471 3.8 16.2 1.0
CD B:ARG471 3.8 15.5 1.0
CG B:ASN219 4.0 17.2 1.0
CB B:ASN219 4.0 17.0 1.0
CA B:GLY216 4.2 21.4 1.0
O A:HOH1086 4.2 44.1 1.0
CZ B:ARG471 4.3 16.2 1.0
O B:GLY216 4.5 19.0 1.0
NE B:ARG471 4.5 15.2 1.0
NZ B:LYS220 4.5 30.2 0.6
O A:ALA336 4.6 14.6 1.0
C B:GLY216 4.9 24.0 1.0
O1A B:MLA601 4.9 18.4 1.0
O B:ALA250 4.9 29.3 1.0
CA B:THR468 5.0 18.6 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 12:23:44 2024

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