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Iron in PDB 6uqb: Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate

Enzymatic activity of Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate

All present enzymatic activity of Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate:
4.2.1.2;

Protein crystallography data

The structure of Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate, PDB code: 6uqb 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) 49.04 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.462, 84.943, 240.266, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate (pdb code 6uqb). 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate, PDB code: 6uqb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6uqb

Go back to Iron Binding Sites List in 6uqb
Iron binding site 1 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:20.4
occ:1.00
 FE1 A:SF4601 0.0 20.4 1.0
S4 A:SF4601 2.3 20.8 1.0
SG A:CYS133 2.3 20.2 1.0
S3 A:SF4601 2.3 19.3 1.0
S2 A:SF4601 2.3 22.5 1.0
FE2 A:SF4601 2.7 19.2 1.0
FE3 A:SF4601 2.8 19.7 1.0
FE4 A:SF4601 2.8 23.1 1.0
CB A:CYS133 3.5 19.2 1.0
S1 A:SF4601 3.9 20.9 1.0
CB A:ALA348 4.0 22.0 1.0
O A:HOH888 4.2 20.1 1.0
CB A:ASP135 4.4 22.3 1.0
O2 A:LMR602 4.4 20.7 1.0
NE2 A:GLN134 4.5 20.4 1.0
O A:HOH784 4.6 27.4 1.0
CA A:GLY515 4.8 19.8 1.0
O A:ASP135 4.8 18.2 1.0
CA A:CYS133 4.8 20.4 1.0
SG A:CYS252 4.8 22.4 1.0
SG A:CYS346 4.9 20.2 1.0
O1B A:LMR602 5.0 23.2 1.0
N A:ASP135 5.0 20.6 1.0

Iron binding site 2 out of 8 in 6uqb

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Iron binding site 2 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:19.2
occ:1.00
 FE2 A:SF4601 0.0 19.2 1.0
S3 A:SF4601 2.3 19.3 1.0
S4 A:SF4601 2.3 20.8 1.0
S1 A:SF4601 2.3 20.9 1.0
SG A:CYS346 2.3 20.2 1.0
FE3 A:SF4601 2.7 19.7 1.0
FE4 A:SF4601 2.7 23.1 1.0
FE1 A:SF4601 2.7 20.4 1.0
CB A:CYS346 3.2 18.3 1.0
CB A:ALA348 3.8 22.0 1.0
S2 A:SF4601 3.9 22.5 1.0
N A:ALA348 4.1 18.4 1.0
CA A:ALA348 4.5 23.1 1.0
CA A:CYS346 4.6 20.8 1.0
OG A:SER217 4.6 18.7 1.0
N A:SER347 4.7 18.3 1.0
SG A:CYS252 4.7 22.4 1.0
O2 A:LMR602 4.7 20.7 1.0
O A:ALA251 4.8 18.6 1.0
N A:SER217 4.8 16.6 1.0
CB A:CYS252 4.8 27.6 1.0
CA A:GLY214 4.8 16.7 1.0
C A:CYS346 4.8 19.4 1.0
O1B A:LMR602 4.8 23.2 1.0
O A:HOH860 4.9 23.2 1.0
SG A:CYS133 4.9 20.2 1.0
CB A:SER217 5.0 14.4 1.0

Iron binding site 3 out of 8 in 6uqb

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Iron binding site 3 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:19.7
occ:1.00
 FE3 A:SF4601 0.0 19.7 1.0
S2 A:SF4601 2.3 22.5 1.0
SG A:CYS252 2.3 22.4 1.0
S4 A:SF4601 2.3 20.8 1.0
S1 A:SF4601 2.3 20.9 1.0
FE4 A:SF4601 2.7 23.1 1.0
FE2 A:SF4601 2.7 19.2 1.0
FE1 A:SF4601 2.8 20.4 1.0
CB A:CYS252 3.2 27.6 1.0
NZ A:LYS491 3.6 21.9 1.0
S3 A:SF4601 3.9 19.3 1.0
O1B A:LMR602 4.0 23.2 1.0
CE A:LYS491 4.0 20.7 1.0
O A:HOH784 4.3 27.4 1.0
CA A:CYS252 4.5 22.9 1.0
N A:GLY515 4.5 20.9 1.0
N A:CYS252 4.5 19.1 1.0
C A:ALA251 4.5 20.1 1.0
CA A:GLY515 4.6 19.8 1.0
O A:ALA251 4.6 18.6 1.0
SG A:CYS346 4.7 20.2 1.0
CB A:CYS346 4.7 18.3 1.0
SG A:CYS133 4.7 20.2 1.0
C A:GLY514 4.8 19.6 1.0
O2 A:LMR602 4.9 20.7 1.0
CD A:LYS491 4.9 23.0 1.0

Iron binding site 4 out of 8 in 6uqb

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Iron binding site 4 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:23.1
occ:1.00
 FE4 A:SF4601 0.0 23.1 1.0
S1 A:SF4601 2.3 20.9 1.0
O2 A:LMR602 2.3 20.7 1.0
S2 A:SF4601 2.3 22.5 1.0
S3 A:SF4601 2.3 19.3 1.0
O1B A:LMR602 2.4 23.2 1.0
FE3 A:SF4601 2.7 19.7 1.0
FE2 A:SF4601 2.7 19.2 1.0
FE1 A:SF4601 2.8 20.4 1.0
C1 A:LMR602 3.2 23.7 1.0
C2 A:LMR602 3.2 25.7 1.0
C3 A:LMR602 3.8 21.1 1.0
N A:GLY216 3.8 21.1 1.0
S4 A:SF4601 3.9 20.8 1.0
CA A:GLY216 4.0 21.3 1.0
NZ A:LYS491 4.0 21.9 1.0
OD2 A:ASP135 4.1 19.7 1.0
O1A A:LMR602 4.4 24.8 1.0
CB A:ASP135 4.5 22.3 1.0
CE A:LYS491 4.6 20.7 1.0
SG A:CYS133 4.7 20.2 1.0
CG A:ASP135 4.7 23.9 1.0
SG A:CYS252 4.7 22.4 1.0
N A:SER217 4.8 16.6 1.0
SG A:CYS346 4.8 20.2 1.0
N A:GLY215 4.8 20.4 1.0
C A:GLY216 4.9 21.4 1.0
CA A:GLY214 4.9 16.7 1.0
C4 A:LMR602 4.9 23.4 1.0

Iron binding site 5 out of 8 in 6uqb

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Iron binding site 5 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:19.4
occ:1.00
 FE1 B:SF4601 0.0 19.4 1.0
S2 B:SF4601 2.3 21.6 1.0
S4 B:SF4601 2.3 18.9 1.0
S3 B:SF4601 2.3 22.0 1.0
SG B:CYS346 2.3 19.9 1.0
FE4 B:SF4601 2.7 19.6 1.0
FE2 B:SF4601 2.7 19.8 1.0
FE3 B:SF4601 2.8 20.1 1.0
CB B:CYS346 3.2 15.0 1.0
CB B:ALA348 3.9 15.5 1.0
S1 B:SF4601 3.9 20.1 1.0
N B:ALA348 4.1 16.2 1.0
OG B:SER217 4.5 20.9 1.0
CA B:ALA348 4.5 18.1 1.0
CA B:CYS346 4.6 18.9 1.0
N B:SER347 4.6 20.1 1.0
O2 B:LMR602 4.7 18.3 1.0
SG B:CYS252 4.7 19.6 1.0
O B:ALA251 4.7 22.9 1.0
O1B B:LMR602 4.8 21.4 1.0
CB B:CYS252 4.8 20.1 1.0
C B:CYS346 4.8 19.1 1.0
N B:SER217 4.8 16.8 1.0
CA B:GLY214 4.9 19.7 1.0
O B:HOH877 4.9 24.0 1.0
SG B:CYS133 4.9 20.4 1.0
CB B:SER217 4.9 16.5 1.0

Iron binding site 6 out of 8 in 6uqb

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Iron binding site 6 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:19.8
occ:1.00
 FE2 B:SF4601 0.0 19.8 1.0
S4 B:SF4601 2.3 18.9 1.0
S3 B:SF4601 2.3 22.0 1.0
SG B:CYS133 2.3 20.4 1.0
S1 B:SF4601 2.3 20.1 1.0
FE1 B:SF4601 2.7 19.4 1.0
FE4 B:SF4601 2.8 19.6 1.0
FE3 B:SF4601 2.8 20.1 1.0
CB B:CYS133 3.5 17.5 1.0
S2 B:SF4601 3.9 21.6 1.0
CB B:ALA348 4.0 15.5 1.0
O B:HOH934 4.3 21.9 1.0
O2 B:LMR602 4.4 18.3 1.0
CB B:ASP135 4.4 19.1 1.0
NE2 B:GLN134 4.5 15.4 1.0
O B:HOH915 4.5 25.2 1.0
CA B:GLY515 4.8 20.9 1.0
O B:ASP135 4.8 17.3 1.0
SG B:CYS346 4.8 19.9 1.0
SG B:CYS252 4.9 19.6 1.0
CA B:CYS133 4.9 24.1 1.0
O1B B:LMR602 4.9 21.4 1.0

Iron binding site 7 out of 8 in 6uqb

Go back to Iron Binding Sites List in 6uqb
Iron binding site 7 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:20.1
occ:1.00
 FE3 B:SF4601 0.0 20.1 1.0
S2 B:SF4601 2.3 21.6 1.0
S1 B:SF4601 2.3 20.1 1.0
O2 B:LMR602 2.3 18.3 1.0
S4 B:SF4601 2.3 18.9 1.0
O1B B:LMR602 2.3 21.4 1.0
FE4 B:SF4601 2.7 19.6 1.0
FE1 B:SF4601 2.8 19.4 1.0
FE2 B:SF4601 2.8 19.8 1.0
C1 B:LMR602 3.1 23.8 1.0
C2 B:LMR602 3.1 22.0 1.0
C3 B:LMR602 3.6 18.8 1.0
S3 B:SF4601 3.9 22.0 1.0
N B:GLY216 3.9 18.3 1.0
NZ B:LYS491 4.0 17.2 1.0
CA B:GLY216 4.0 20.2 1.0
OD1 B:ASP135 4.1 19.1 1.0
O1A B:LMR602 4.3 21.4 1.0
CB B:ASP135 4.5 19.1 1.0
CE B:LYS491 4.6 17.1 1.0
SG B:CYS133 4.7 20.4 1.0
SG B:CYS252 4.7 19.6 1.0
CG B:ASP135 4.7 19.3 1.0
N B:SER217 4.8 16.8 1.0
C4 B:LMR602 4.9 20.7 1.0
SG B:CYS346 4.9 19.9 1.0
N B:GLY215 4.9 20.1 1.0
CA B:GLY214 4.9 19.7 1.0
C B:GLY216 4.9 21.3 1.0

Iron binding site 8 out of 8 in 6uqb

Go back to Iron Binding Sites List in 6uqb
Iron binding site 8 out of 8 in the Crystal Structure of R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and 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 R471A Variant of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with S-Malate and Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:19.6
occ:1.00
 FE4 B:SF4601 0.0 19.6 1.0
S1 B:SF4601 2.3 20.1 1.0
S3 B:SF4601 2.3 22.0 1.0
S2 B:SF4601 2.3 21.6 1.0
SG B:CYS252 2.3 19.6 1.0
FE3 B:SF4601 2.7 20.1 1.0
FE1 B:SF4601 2.7 19.4 1.0
FE2 B:SF4601 2.8 19.8 1.0
CB B:CYS252 3.2 20.1 1.0
NZ B:LYS491 3.6 17.2 1.0
S4 B:SF4601 3.9 18.9 1.0
O1B B:LMR602 3.9 21.4 1.0
CE B:LYS491 4.0 17.1 1.0
O B:HOH915 4.3 25.2 1.0
N B:GLY515 4.5 23.2 1.0
CA B:CYS252 4.5 21.6 1.0
N B:CYS252 4.5 22.0 1.0
C B:ALA251 4.5 23.4 1.0
O B:ALA251 4.6 22.9 1.0
CA B:GLY515 4.6 20.9 1.0
SG B:CYS346 4.7 19.9 1.0
CB B:CYS346 4.7 15.0 1.0
SG B:CYS133 4.7 20.4 1.0
C B:GLY514 4.8 24.8 1.0
CD B:LYS491 4.9 20.4 1.0
O2 B:LMR602 5.0 18.3 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 12:36:44 2024

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