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

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

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

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate, PDB code: 6mso 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) 48.88 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.741, 138.443, 138.073, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.5

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate (pdb code 6mso). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Mitochondrial Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate, PDB code: 6mso:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6mso

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Iron binding site 1 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:22.3
occ:1.00
 FE1 A:SF4601 0.0 22.3 1.0
S06 A:JYD608 2.2 17.6 0.3
S4 A:SF4601 2.3 22.6 1.0
S3 A:SF4601 2.3 15.1 1.0
S2 A:SF4601 2.3 19.6 1.0
S06 A:JYD608 2.3 21.7 0.7
O05 A:JYD608 2.6 17.7 0.7
FE2 A:SF4601 2.7 20.8 1.0
FE3 A:SF4601 2.8 19.9 1.0
FE4 A:SF4601 2.8 18.7 1.0
C03 A:JYD608 3.4 17.1 0.7
C02 A:JYD608 3.4 17.5 0.7
C02 A:JYD608 3.7 17.8 0.3
C01 A:JYD608 3.8 18.0 0.3
C01 A:JYD608 3.8 18.0 0.7
S1 A:SF4601 3.9 15.8 1.0
NZ A:LYS474 4.0 14.9 1.0
N A:GLY197 4.3 16.0 1.0
OD2 A:ASP116 4.5 20.6 1.0
SG A:CYS114 4.5 15.1 1.0
O05 A:JYD608 4.5 17.3 0.3
CA A:GLY197 4.6 15.9 1.0
C03 A:JYD608 4.6 17.2 0.3
O04 A:JYD608 4.6 17.3 0.7
CB A:ASP116 4.7 13.2 1.0
CE A:LYS474 4.7 14.9 1.0
SG A:CYS233 4.8 17.8 1.0
N A:SER198 4.8 16.3 1.0
CA A:GLY195 4.8 17.1 1.0
SG A:CYS328 4.9 15.3 1.0
C07 A:JYD608 4.9 17.9 0.7
N A:GLY196 5.0 12.3 1.0

Iron binding site 2 out of 16 in 6mso

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Iron binding site 2 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:20.8
occ:1.00
 FE2 A:SF4601 0.0 20.8 1.0
SG A:CYS233 2.2 17.8 1.0
S3 A:SF4601 2.3 15.1 1.0
S1 A:SF4601 2.3 15.8 1.0
S4 A:SF4601 2.3 22.6 1.0
FE4 A:SF4601 2.7 18.7 1.0
FE3 A:SF4601 2.7 19.9 1.0
FE1 A:SF4601 2.7 22.3 1.0
CB A:CYS233 3.2 16.6 1.0
NZ A:LYS474 3.6 14.9 1.0
S2 A:SF4601 3.9 19.6 1.0
CE A:LYS474 4.1 14.9 1.0
O05 A:JYD608 4.2 17.7 0.7
N A:GLY498 4.4 16.5 1.0
O A:HOH863 4.5 28.7 1.0
CA A:CYS233 4.5 15.0 1.0
N A:CYS233 4.5 13.5 1.0
C A:ALA232 4.6 13.3 1.0
S06 A:JYD608 4.6 17.6 0.3
CA A:GLY498 4.6 16.8 1.0
O A:ALA232 4.7 15.6 1.0
SG A:CYS114 4.7 15.1 1.0
C A:GLY497 4.7 16.6 1.0
CB A:CYS328 4.7 13.8 1.0
SG A:CYS328 4.7 15.3 1.0
CD A:LYS474 4.8 15.2 1.0

Iron binding site 3 out of 16 in 6mso

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Iron binding site 3 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:19.9
occ:1.00
 FE3 A:SF4601 0.0 19.9 1.0
S2 A:SF4601 2.3 19.6 1.0
S4 A:SF4601 2.3 22.6 1.0
S1 A:SF4601 2.3 15.8 1.0
SG A:CYS328 2.3 15.3 1.0
FE2 A:SF4601 2.7 20.8 1.0
FE4 A:SF4601 2.7 18.7 1.0
FE1 A:SF4601 2.8 22.3 1.0
CB A:CYS328 3.2 13.8 1.0
CB A:ALA330 3.8 14.1 1.0
S3 A:SF4601 3.9 15.1 1.0
N A:ALA330 4.2 14.3 1.0
OG A:SER198 4.3 16.5 1.0
CA A:CYS328 4.6 16.8 1.0
CA A:ALA330 4.6 14.3 1.0
CB A:SER198 4.6 14.0 1.0
SG A:CYS233 4.7 17.8 1.0
N A:SER329 4.7 14.3 1.0
S06 A:JYD608 4.7 21.7 0.7
CB A:CYS233 4.8 16.6 1.0
O A:ALA232 4.8 15.6 1.0
S06 A:JYD608 4.8 17.6 0.3
C A:CYS328 4.9 15.9 1.0
SG A:CYS114 4.9 15.1 1.0
CA A:GLY195 4.9 17.1 1.0
O A:HOH775 4.9 5.7 1.0
N A:SER198 4.9 16.3 1.0
O05 A:JYD608 5.0 17.7 0.7

Iron binding site 4 out of 16 in 6mso

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Iron binding site 4 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:18.7
occ:1.00
 FE4 A:SF4601 0.0 18.7 1.0
SG A:CYS114 2.2 15.1 1.0
S1 A:SF4601 2.3 15.8 1.0
S3 A:SF4601 2.3 15.1 1.0
S2 A:SF4601 2.3 19.6 1.0
FE2 A:SF4601 2.7 20.8 1.0
FE3 A:SF4601 2.7 19.9 1.0
FE1 A:SF4601 2.8 22.3 1.0
CB A:CYS114 3.4 13.9 1.0
S4 A:SF4601 3.9 22.6 1.0
CB A:ALA330 4.1 14.1 1.0
O A:HOH807 4.1 15.4 1.0
S06 A:JYD608 4.5 21.7 0.7
NE2 A:GLN115 4.5 13.9 1.0
O A:HOH863 4.6 28.7 1.0
SG A:CYS233 4.8 17.8 1.0
CA A:GLY498 4.8 16.8 1.0
CA A:CYS114 4.8 19.2 1.0
CB A:ASP116 4.8 13.2 1.0
S06 A:JYD608 4.8 17.6 0.3
SG A:CYS328 4.8 15.3 1.0
O A:ASP116 4.9 14.0 1.0

Iron binding site 5 out of 16 in 6mso

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Iron binding site 5 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:23.4
occ:1.00
 FE1 B:SF4601 0.0 23.4 1.0
S2 B:SF4601 2.3 14.7 1.0
S3 B:SF4601 2.3 15.8 1.0
S4 B:SF4601 2.3 17.2 1.0
SG B:CYS328 2.3 14.4 1.0
FE2 B:SF4601 2.7 24.1 1.0
FE4 B:SF4601 2.7 22.1 1.0
FE3 B:SF4601 2.8 21.4 1.0
CB B:CYS328 3.1 14.2 1.0
S1 B:SF4601 3.9 24.0 1.0
CB B:ALA330 3.9 13.3 1.0
N B:ALA330 4.1 13.1 1.0
OG B:SER198 4.4 20.8 1.0
CA B:CYS328 4.5 15.8 1.0
N B:SER329 4.5 16.8 1.0
CA B:ALA330 4.6 13.1 1.0
O B:ALA232 4.7 18.5 1.0
SG B:CYS233 4.7 17.7 1.0
CB B:SER198 4.7 12.3 1.0
C B:CYS328 4.7 16.6 1.0
CB B:CYS233 4.8 14.6 1.0
S06 B:JYD604 4.8 16.0 0.6
S06 B:JYD604 4.8 14.9 0.4
N B:SER198 4.8 15.9 1.0
CA B:GLY195 4.9 12.5 1.0
SG B:CYS114 5.0 17.8 1.0

Iron binding site 6 out of 16 in 6mso

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Iron binding site 6 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:24.1
occ:1.00
 FE2 B:SF4601 0.0 24.1 1.0
S4 B:SF4601 2.3 17.2 1.0
S1 B:SF4601 2.3 24.0 1.0
SG B:CYS233 2.3 17.7 1.0
S3 B:SF4601 2.3 15.8 1.0
FE1 B:SF4601 2.7 23.4 1.0
FE3 B:SF4601 2.7 21.4 1.0
FE4 B:SF4601 2.7 22.1 1.0
CB B:CYS233 3.2 14.6 1.0
NZ B:LYS474 3.6 22.9 1.0
S2 B:SF4601 3.9 14.7 1.0
CE B:LYS474 4.1 14.1 1.0
O04 B:JYD604 4.3 13.5 0.6
N B:GLY498 4.3 14.7 1.0
CA B:CYS233 4.5 15.2 1.0
CA B:GLY498 4.5 14.7 1.0
N B:CYS233 4.6 16.6 1.0
C B:ALA232 4.6 16.3 1.0
O B:ALA232 4.6 18.5 1.0
SG B:CYS114 4.7 17.8 1.0
S06 B:JYD604 4.7 14.9 0.4
C B:GLY497 4.7 17.9 1.0
CB B:CYS328 4.7 14.2 1.0
SG B:CYS328 4.8 14.4 1.0
CD B:LYS474 5.0 14.4 1.0

Iron binding site 7 out of 16 in 6mso

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Iron binding site 7 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:21.4
occ:1.00
 FE3 B:SF4601 0.0 21.4 1.0
SG B:CYS114 2.3 17.8 1.0
S4 B:SF4601 2.3 17.2 1.0
S1 B:SF4601 2.3 24.0 1.0
S2 B:SF4601 2.3 14.7 1.0
FE2 B:SF4601 2.7 24.1 1.0
FE4 B:SF4601 2.8 22.1 1.0
FE1 B:SF4601 2.8 23.4 1.0
CB B:CYS114 3.4 13.4 1.0
S3 B:SF4601 3.9 15.8 1.0
CB B:ALA330 4.1 13.3 1.0
O B:HOH751 4.1 4.7 1.0
NE2 B:GLN115 4.5 13.9 1.0
S06 B:JYD604 4.5 16.0 0.6
CB B:ASP116 4.7 13.2 1.0
CA B:CYS114 4.7 16.4 1.0
CA B:GLY498 4.8 14.7 1.0
S06 B:JYD604 4.8 14.9 0.4
O B:ASP116 4.8 14.2 1.0
SG B:CYS328 4.8 14.4 1.0
SG B:CYS233 4.8 17.7 1.0
N B:ALA330 5.0 13.1 1.0

Iron binding site 8 out of 16 in 6mso

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Iron binding site 8 out of 16 in the Crystal Structure of Mitochondrial 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 Mitochondrial 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:22.1
occ:1.00
 FE4 B:SF4601 0.0 22.1 1.0
S06 B:JYD604 2.3 14.9 0.4
S3 B:SF4601 2.3 15.8 1.0
S2 B:SF4601 2.3 14.7 1.0
S1 B:SF4601 2.3 24.0 1.0
S06 B:JYD604 2.4 16.0 0.6
FE1 B:SF4601 2.7 23.4 1.0
FE2 B:SF4601 2.7 24.1 1.0
FE3 B:SF4601 2.8 21.4 1.0
O04 B:JYD604 2.8 13.5 0.6
C02 B:JYD604 3.5 11.0 0.6
C03 B:JYD604 3.6 12.1 0.6
C02 B:JYD604 3.7 11.5 0.4
C01 B:JYD604 3.8 10.9 0.4
S4 B:SF4601 3.9 17.2 1.0
C01 B:JYD604 4.0 10.6 0.6
NZ B:LYS474 4.1 22.9 1.0
N B:GLY197 4.2 20.8 1.0
OD1 B:ASP116 4.4 20.0 1.0
O05 B:JYD604 4.4 12.3 0.4
CA B:GLY197 4.4 12.7 1.0
SG B:CYS114 4.5 17.8 1.0
C03 B:JYD604 4.5 11.6 0.4
CB B:ASP116 4.6 13.2 1.0
N B:SER198 4.7 15.9 1.0
O05 B:JYD604 4.8 12.4 0.6
CA B:GLY195 4.8 12.5 1.0
SG B:CYS233 4.8 17.7 1.0
SG B:CYS328 4.9 14.4 1.0
CE B:LYS474 4.9 14.1 1.0
N B:GLY196 4.9 12.6 1.0
CG B:ASP116 5.0 18.9 1.0

Iron binding site 9 out of 16 in 6mso

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Iron binding site 9 out of 16 in the Crystal Structure of Mitochondrial 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 9 of Crystal Structure of Mitochondrial Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:28.7
occ:1.00
 FE1 C:SF4601 0.0 28.7 1.0
S4 C:SF4601 2.3 24.9 1.0
S3 C:SF4601 2.3 31.1 1.0
S2 C:SF4601 2.3 27.9 1.0
SG C:CYS233 2.3 28.5 1.0
FE4 C:SF4601 2.7 32.0 1.0
FE2 C:SF4601 2.7 30.2 1.0
FE3 C:SF4601 2.7 30.0 1.0
CB C:CYS233 3.0 27.0 1.0
NZ C:LYS474 3.7 25.6 1.0
S1 C:SF4601 3.9 30.6 1.0
O04 C:JYD604 4.1 43.0 1.0
CE C:LYS474 4.3 25.8 1.0
CA C:CYS233 4.3 28.1 1.0
N C:CYS233 4.4 28.8 1.0
N C:GLY498 4.4 32.4 1.0
O C:HOH750 4.4 26.9 1.0
C C:ALA232 4.4 30.2 1.0
O C:ALA232 4.6 33.7 1.0
CB C:CYS328 4.7 21.1 1.0
SG C:CYS328 4.7 22.0 1.0
SG C:CYS114 4.7 27.6 1.0
CA C:GLY498 4.7 36.7 1.0
C C:GLY497 4.8 33.5 1.0
CD C:LYS474 4.9 25.1 1.0
S06 C:JYD604 4.9 40.5 1.0

Iron binding site 10 out of 16 in 6mso

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Iron binding site 10 out of 16 in the Crystal Structure of Mitochondrial 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 10 of Crystal Structure of Mitochondrial Fumarate Hydratase From Leishmania Major in A Complex with Inhibitor Thiomalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:30.2
occ:1.00
 FE2 C:SF4601 0.0 30.2 1.0
S06 C:JYD604 2.2 40.5 1.0
S3 C:SF4601 2.3 31.1 1.0
S4 C:SF4601 2.3 24.9 1.0
S1 C:SF4601 2.3 30.6 1.0
O04 C:JYD604 2.7 43.0 1.0
FE1 C:SF4601 2.7 28.7 1.0
FE3 C:SF4601 2.8 30.0 1.0
FE4 C:SF4601 2.8 32.0 1.0
C02 C:JYD604 3.3 37.5 1.0
C03 C:JYD604 3.4 42.1 1.0
C01 C:JYD604 3.7 35.5 1.0
S2 C:SF4601 3.9 27.9 1.0
N C:GLY197 4.1 24.6 1.0
NZ C:LYS474 4.2 25.6 1.0
CA C:GLY197 4.3 27.3 1.0
SG C:CYS114 4.5 27.6 1.0
OD2 C:ASP116 4.6 32.5 1.0
N C:SER198 4.6 30.9 1.0
O05 C:JYD604 4.7 45.5 1.0
CB C:ASP116 4.8 26.5 1.0
SG C:CYS233 4.8 28.5 1.0
SG C:CYS328 4.8 22.0 1.0
CE C:LYS474 4.9 25.8 1.0
C C:GLY197 4.9 30.7 1.0
CA C:GLY195 4.9 23.8 1.0
C07 C:JYD604 4.9 32.7 1.0

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 02:26:43 2024

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