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Iron in PDB 6msn: Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate

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

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

Protein crystallography data

The structure of Crystal Structure of Cytosolic Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate, PDB code: 6msn was solved by P.R.Feliciano, C.L.Drennan, M.C.Nonato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.96 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.727, 84.680, 239.988, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.1
occ:1.00
 FE1 A:SF4601 0.0 12.1 1.0
SG A:CYS133 2.3 12.5 1.0
S4 A:SF4601 2.3 11.9 1.0
S3 A:SF4601 2.3 12.2 1.0
S2 A:SF4601 2.3 11.9 1.0
FE2 A:SF4601 2.7 12.6 1.0
FE3 A:SF4601 2.7 12.3 1.0
FE4 A:SF4601 2.7 13.4 1.0
CB A:CYS133 3.4 12.4 1.0
S1 A:SF4601 3.9 12.4 1.0
CB A:ALA348 3.9 14.6 1.0
O A:HOH863 4.2 14.8 1.0
S06 A:JYD602 4.4 14.5 0.5
CB A:ASP135 4.4 11.4 0.6
NE2 A:GLN134 4.5 11.8 1.0
O A:HOH861 4.6 21.6 1.0
CA A:GLY515 4.7 10.5 1.0
CA A:CYS133 4.8 11.0 1.0
CB A:ASP135 4.8 14.2 0.4
O A:ASP135 4.8 12.3 0.4
SG A:CYS346 4.8 12.1 1.0
S06 A:JYD602 4.8 11.9 0.5
SG A:CYS252 4.8 12.2 1.0
O A:ASP135 4.9 13.8 0.6
C01 A:JYD602 4.9 13.1 0.5
N A:ALA348 5.0 12.3 1.0

Iron binding site 2 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.6
occ:1.00
 FE2 A:SF4601 0.0 12.6 1.0
S4 A:SF4601 2.3 11.9 1.0
S3 A:SF4601 2.3 12.2 1.0
S1 A:SF4601 2.3 12.4 1.0
SG A:CYS346 2.3 12.1 1.0
FE3 A:SF4601 2.7 12.3 1.0
FE1 A:SF4601 2.7 12.1 1.0
FE4 A:SF4601 2.8 13.4 1.0
CB A:CYS346 3.2 11.3 1.0
CB A:ALA348 3.8 14.6 1.0
S2 A:SF4601 3.9 11.9 1.0
N A:ALA348 4.0 12.3 1.0
OG A:SER217 4.5 16.7 1.0
CA A:ALA348 4.5 11.8 1.0
N A:SER347 4.5 11.0 1.0
CA A:CYS346 4.6 11.5 1.0
CB A:CYS252 4.7 11.1 1.0
SG A:CYS252 4.7 12.2 1.0
O A:ALA251 4.7 11.2 1.0
CB A:SER217 4.7 17.1 1.0
S06 A:JYD602 4.7 14.5 0.5
S06 A:JYD602 4.8 11.9 0.5
C A:CYS346 4.8 10.1 1.0
O A:HOH837 4.9 18.1 1.0
CA A:GLY214 4.9 11.8 1.0
SG A:CYS133 4.9 12.5 1.0

Iron binding site 3 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.3
occ:1.00
 FE3 A:SF4601 0.0 12.3 1.0
S2 A:SF4601 2.3 11.9 1.0
S4 A:SF4601 2.3 11.9 1.0
SG A:CYS252 2.3 12.2 1.0
S1 A:SF4601 2.3 12.4 1.0
FE2 A:SF4601 2.7 12.6 1.0
FE4 A:SF4601 2.7 13.4 1.0
FE1 A:SF4601 2.7 12.1 1.0
CB A:CYS252 3.1 11.1 1.0
NZ A:LYS491 3.6 11.2 1.0
S3 A:SF4601 3.9 12.2 1.0
CE A:LYS491 4.1 13.1 1.0
O04 A:JYD602 4.1 17.1 0.5
O A:HOH861 4.2 21.6 1.0
S06 A:JYD602 4.3 11.9 0.5
CA A:CYS252 4.4 12.3 1.0
N A:GLY515 4.4 12.9 1.0
C A:ALA251 4.5 9.9 1.0
N A:CYS252 4.5 11.6 1.0
CA A:GLY515 4.5 10.5 1.0
O A:ALA251 4.6 11.2 1.0
SG A:CYS346 4.7 12.1 1.0
SG A:CYS133 4.7 12.5 1.0
CB A:CYS346 4.7 11.3 1.0
C A:GLY514 4.8 13.8 1.0
CD A:LYS491 5.0 12.7 1.0
S06 A:JYD602 5.0 14.5 0.5

Iron binding site 4 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:13.4
occ:1.00
 FE4 A:SF4601 0.0 13.4 1.0
S06 A:JYD602 2.2 11.9 0.5
S2 A:SF4601 2.3 11.9 1.0
S1 A:SF4601 2.3 12.4 1.0
S3 A:SF4601 2.3 12.2 1.0
S06 A:JYD602 2.3 14.5 0.5
O04 A:JYD602 2.7 17.1 0.5
FE3 A:SF4601 2.7 12.3 1.0
FE1 A:SF4601 2.7 12.1 1.0
FE2 A:SF4601 2.8 12.6 1.0
C02 A:JYD602 3.4 11.7 0.5
C03 A:JYD602 3.4 13.5 0.5
C02 A:JYD602 3.5 11.0 0.5
C01 A:JYD602 3.5 13.1 0.5
C01 A:JYD602 3.9 12.4 0.5
S4 A:SF4601 3.9 11.9 1.0
OD2 A:ASP135 4.0 16.4 0.6
NZ A:LYS491 4.1 11.2 1.0
N A:GLY216 4.2 13.7 1.0
CB A:ASP135 4.4 11.4 0.6
OD2 A:ASP135 4.5 16.4 0.4
CA A:GLY216 4.6 13.7 1.0
SG A:CYS133 4.6 12.5 1.0
CG A:ASP135 4.6 15.8 0.6
O05 A:JYD602 4.7 18.8 0.5
CB A:ASP135 4.7 14.2 0.4
CE A:LYS491 4.7 13.1 1.0
C03 A:JYD602 4.7 18.6 0.5
SG A:CYS252 4.8 12.2 1.0
N A:SER217 4.8 13.1 1.0
CA A:GLY214 4.8 11.8 1.0
C07 A:JYD602 4.8 14.2 0.5
SG A:CYS346 4.8 12.1 1.0
N A:GLY215 4.9 12.1 1.0

Iron binding site 5 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.1
occ:1.00
 FE1 B:SF4601 0.0 12.1 1.0
S4 B:SF4601 2.3 11.8 1.0
S3 B:SF4601 2.3 12.0 1.0
S2 B:SF4601 2.3 12.1 1.0
SG B:CYS346 2.3 11.7 1.0
FE4 B:SF4601 2.7 12.3 1.0
FE2 B:SF4601 2.7 11.8 1.0
FE3 B:SF4601 2.8 12.1 1.0
CB B:CYS346 3.2 10.4 1.0
CB B:ALA348 3.8 11.2 1.0
S1 B:SF4601 3.9 11.5 1.0
N B:ALA348 4.0 11.3 1.0
OG B:SER217 4.4 13.1 0.8
CA B:ALA348 4.5 12.0 1.0
N B:SER347 4.5 11.0 1.0
CA B:CYS346 4.5 10.2 1.0
CB B:SER217 4.7 12.8 0.2
SG B:CYS252 4.7 11.9 1.0
O B:ALA251 4.7 12.0 1.0
CB B:CYS252 4.7 11.2 1.0
S06 B:JYD602 4.7 11.8 0.5
CB B:SER217 4.7 13.1 0.8
C B:CYS346 4.8 10.9 1.0
S06 B:JYD602 4.8 11.6 0.5
O B:HOH794 4.9 16.8 1.0
CA B:GLY214 4.9 10.2 1.0
SG B:CYS133 5.0 12.5 1.0

Iron binding site 6 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:11.8
occ:1.00
 FE2 B:SF4601 0.0 11.8 1.0
S3 B:SF4601 2.3 12.0 1.0
SG B:CYS133 2.3 12.5 1.0
S4 B:SF4601 2.3 11.8 1.0
S1 B:SF4601 2.3 11.5 1.0
FE1 B:SF4601 2.7 12.1 1.0
FE3 B:SF4601 2.8 12.1 1.0
FE4 B:SF4601 2.8 12.3 1.0
CB B:CYS133 3.4 11.4 1.0
S2 B:SF4601 3.9 12.1 1.0
CB B:ALA348 3.9 11.2 1.0
O B:HOH836 4.2 15.8 1.0
S06 B:JYD602 4.4 11.8 0.5
CB B:ASP135 4.4 10.6 0.7
NE2 B:GLN134 4.5 10.8 1.0
O B:HOH874 4.6 18.7 1.0
CA B:GLY515 4.7 14.5 1.0
CB B:ASP135 4.8 11.9 0.3
CA B:CYS133 4.8 12.6 1.0
O B:ASP135 4.8 14.1 0.3
SG B:CYS346 4.8 11.7 1.0
SG B:CYS252 4.8 11.9 1.0
S06 B:JYD602 4.9 11.6 0.5
O B:ASP135 4.9 13.7 0.7
C01 B:JYD602 5.0 11.3 0.5
N B:ALA348 5.0 11.3 1.0

Iron binding site 7 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.1
occ:1.00
 FE3 B:SF4601 0.0 12.1 1.0
S06 B:JYD602 2.3 11.6 0.5
S2 B:SF4601 2.3 12.1 1.0
S1 B:SF4601 2.3 11.5 1.0
S4 B:SF4601 2.3 11.8 1.0
S06 B:JYD602 2.3 11.8 0.5
O04 B:JYD602 2.7 13.3 0.5
FE4 B:SF4601 2.7 12.3 1.0
FE2 B:SF4601 2.8 11.8 1.0
FE1 B:SF4601 2.8 12.1 1.0
C02 B:JYD602 3.3 9.3 0.5
C03 B:JYD602 3.3 11.5 0.5
C02 B:JYD602 3.5 10.3 0.5
C01 B:JYD602 3.5 11.3 0.5
C01 B:JYD602 3.8 9.8 0.5
S3 B:SF4601 3.9 12.0 1.0
OD2 B:ASP135 4.0 13.8 0.7
NZ B:LYS491 4.0 11.9 1.0
N B:GLY216 4.3 12.4 1.0
CB B:ASP135 4.4 10.6 0.7
OD2 B:ASP135 4.5 13.8 0.3
O05 B:JYD602 4.6 15.0 0.5
SG B:CYS133 4.6 12.5 1.0
CA B:GLY216 4.6 15.9 1.0
CG B:ASP135 4.6 14.0 0.7
CE B:LYS491 4.7 12.6 1.0
CB B:ASP135 4.7 11.9 0.3
SG B:CYS252 4.7 11.9 1.0
C03 B:JYD602 4.8 11.7 0.5
N B:SER217 4.8 11.9 0.2
N B:SER217 4.8 12.4 0.8
CA B:GLY214 4.8 10.2 1.0
SG B:CYS346 4.9 11.7 1.0
C07 B:JYD602 4.9 11.3 0.5
N B:GLY215 4.9 13.2 1.0
C07 B:JYD602 4.9 11.1 0.5

Iron binding site 8 out of 8 in 6msn

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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 Inhibitor Thiomalate


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

b:12.3
occ:1.00
 FE4 B:SF4601 0.0 12.3 1.0
SG B:CYS252 2.3 11.9 1.0
S1 B:SF4601 2.3 11.5 1.0
S3 B:SF4601 2.3 12.0 1.0
S2 B:SF4601 2.3 12.1 1.0
FE1 B:SF4601 2.7 12.1 1.0
FE3 B:SF4601 2.7 12.1 1.0
FE2 B:SF4601 2.8 11.8 1.0
CB B:CYS252 3.1 11.2 1.0
NZ B:LYS491 3.6 11.9 1.0
S4 B:SF4601 3.9 11.8 1.0
CE B:LYS491 4.0 12.6 1.0
O04 B:JYD602 4.1 13.3 0.5
O B:HOH874 4.3 18.7 1.0
S06 B:JYD602 4.3 11.6 0.5
CA B:CYS252 4.4 12.1 1.0
N B:GLY515 4.4 13.7 1.0
C B:ALA251 4.5 12.8 1.0
N B:CYS252 4.5 11.8 1.0
CA B:GLY515 4.5 14.5 1.0
O B:ALA251 4.5 12.0 1.0
SG B:CYS346 4.7 11.7 1.0
CB B:CYS346 4.7 10.4 1.0
SG B:CYS133 4.7 12.5 1.0
C B:GLY514 4.8 12.4 1.0
CD B:LYS491 4.9 15.1 1.0
S06 B:JYD602 5.0 11.8 0.5

Reference:

P.R.Feliciano, C.L.Drennan, M.C.Nonato. Crystal Structures of Fumarate Hydratases From Leishmania Major in A Complex with Inhibitor 2-Thiomalate. Acs Chem. Biol. V. 14 266 2019.
ISSN: ESSN 1554-8937
PubMed: 30645090
DOI: 10.1021/ACSCHEMBIO.8B00972
Page generated: Wed Aug 7 02:25:55 2024

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