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Iron in PDB 5l2r: Crystal Structure of Fumarate Hydratase From Leishmania Major

Enzymatic activity of Crystal Structure of Fumarate Hydratase From Leishmania Major

All present enzymatic activity of Crystal Structure of Fumarate Hydratase From Leishmania Major:
4.2.1.2;

Protein crystallography data

The structure of Crystal Structure of Fumarate Hydratase From Leishmania Major, PDB code: 5l2r 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) 120.74 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.675, 85.128, 241.476, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Fumarate Hydratase From Leishmania Major (pdb code 5l2r). 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 Fumarate Hydratase From Leishmania Major, PDB code: 5l2r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5l2r

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Iron binding site 1 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:20.0
occ:1.00
 FE1 A:SF4608 0.0 20.0 1.0
S4 A:SF4608 2.3 19.9 1.0
S3 A:SF4608 2.3 22.5 1.0
SG A:CYS133 2.3 21.7 1.0
S2 A:SF4608 2.3 24.5 1.0
FE2 A:SF4608 2.8 19.3 1.0
FE3 A:SF4608 2.8 20.4 1.0
FE4 A:SF4608 2.8 24.2 1.0
CB A:CYS133 3.4 20.2 1.0
S1 A:SF4608 4.0 21.1 1.0
CB A:ALA348 4.0 20.4 1.0
O2 A:LMR601 4.2 15.3 1.0
CB A:ASP135 4.3 19.3 1.0
O A:HOH888 4.3 18.3 1.0
NE2 A:GLN134 4.5 21.4 1.0
O A:HOH915 4.6 30.4 1.0
O A:ASP135 4.8 20.2 1.0
CA A:CYS133 4.8 23.5 1.0
SG A:CYS252 4.8 24.2 1.0
SG A:CYS346 4.9 22.1 1.0
CA A:GLY515 5.0 24.6 1.0
N A:ASP135 5.0 23.4 1.0

Iron binding site 2 out of 8 in 5l2r

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Iron binding site 2 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:19.3
occ:1.00
 FE2 A:SF4608 0.0 19.3 1.0
S3 A:SF4608 2.3 22.5 1.0
S4 A:SF4608 2.3 19.9 1.0
S1 A:SF4608 2.3 21.1 1.0
SG A:CYS346 2.4 22.1 1.0
FE3 A:SF4608 2.7 20.4 1.0
FE4 A:SF4608 2.7 24.2 1.0
FE1 A:SF4608 2.8 20.0 1.0
CB A:CYS346 3.3 19.7 1.0
CB A:ALA348 3.9 20.4 1.0
S2 A:SF4608 3.9 24.5 1.0
N A:ALA348 4.1 20.3 1.0
O2 A:LMR601 4.5 15.3 1.0
OG A:SER217 4.5 23.8 1.0
CA A:ALA348 4.6 25.1 1.0
N A:SER347 4.6 19.8 1.0
CA A:CYS346 4.6 19.6 1.0
SG A:CYS252 4.7 24.2 1.0
CB A:CYS252 4.8 28.5 1.0
N A:SER217 4.8 19.9 1.0
C A:CYS346 4.8 21.8 1.0
CA A:GLY214 4.9 17.8 1.0
O A:ALA251 4.9 18.9 1.0
CB A:SER217 4.9 18.6 1.0
O A:HOH808 4.9 18.6 1.0
O1B A:LMR601 4.9 20.1 1.0
SG A:CYS133 5.0 21.7 1.0

Iron binding site 3 out of 8 in 5l2r

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Iron binding site 3 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:20.4
occ:1.00
 FE3 A:SF4608 0.0 20.4 1.0
S2 A:SF4608 2.2 24.5 1.0
SG A:CYS252 2.3 24.2 1.0
S4 A:SF4608 2.3 19.9 1.0
S1 A:SF4608 2.3 21.1 1.0
FE4 A:SF4608 2.7 24.2 1.0
FE2 A:SF4608 2.7 19.3 1.0
FE1 A:SF4608 2.8 20.0 1.0
CB A:CYS252 3.2 28.5 1.0
NZ A:LYS491 3.6 26.6 1.0
S3 A:SF4608 3.9 22.5 1.0
O1B A:LMR601 4.0 20.1 1.0
CE A:LYS491 4.1 29.6 1.0
O A:HOH915 4.2 30.4 1.0
CA A:CYS252 4.4 25.2 1.0
N A:CYS252 4.5 20.4 1.0
C A:ALA251 4.5 19.8 1.0
N A:GLY515 4.5 28.7 1.0
O2 A:LMR601 4.5 15.3 1.0
O A:ALA251 4.6 18.9 1.0
CA A:GLY515 4.7 24.6 1.0
SG A:CYS133 4.7 21.7 1.0
SG A:CYS346 4.8 22.1 1.0
CB A:CYS346 4.8 19.7 1.0
C A:GLY514 4.9 23.1 1.0

Iron binding site 4 out of 8 in 5l2r

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Iron binding site 4 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe608

b:24.2
occ:1.00
 FE4 A:SF4608 0.0 24.2 1.0
O2 A:LMR601 2.0 15.3 1.0
S1 A:SF4608 2.3 21.1 1.0
S2 A:SF4608 2.3 24.5 1.0
S3 A:SF4608 2.3 22.5 1.0
O1B A:LMR601 2.5 20.1 1.0
FE3 A:SF4608 2.7 20.4 1.0
FE2 A:SF4608 2.7 19.3 1.0
FE1 A:SF4608 2.8 20.0 1.0
C2 A:LMR601 3.1 28.4 1.0
C1 A:LMR601 3.2 25.7 1.0
C3 A:LMR601 3.7 25.4 1.0
S4 A:SF4608 3.9 19.9 1.0
N A:GLY216 3.9 22.0 1.0
CA A:GLY216 4.0 21.9 1.0
OD2 A:ASP135 4.0 22.8 1.0
NZ A:LYS491 4.1 26.6 1.0
O1A A:LMR601 4.4 21.8 1.0
CB A:ASP135 4.5 19.3 1.0
CG A:ASP135 4.7 27.8 1.0
N A:SER217 4.7 19.9 1.0
SG A:CYS133 4.7 21.7 1.0
SG A:CYS252 4.7 24.2 1.0
CE A:LYS491 4.8 29.6 1.0
C A:GLY216 4.8 23.5 1.0
CA A:GLY214 4.9 17.8 1.0
SG A:CYS346 4.9 22.1 1.0
C4 A:LMR601 4.9 26.1 1.0
N A:GLY215 4.9 18.1 1.0

Iron binding site 5 out of 8 in 5l2r

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Iron binding site 5 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe611

b:16.8
occ:1.00
 FE1 B:SF4611 0.0 16.8 1.0
S3 B:SF4611 2.3 19.4 1.0
S2 B:SF4611 2.3 18.5 1.0
S4 B:SF4611 2.3 17.3 1.0
SG B:CYS346 2.3 18.6 1.0
FE4 B:SF4611 2.7 17.7 1.0
FE2 B:SF4611 2.7 18.0 1.0
FE3 B:SF4611 2.8 20.4 1.0
CB B:CYS346 3.2 16.1 1.0
CB B:ALA348 3.9 16.1 1.0
S1 B:SF4611 3.9 18.4 1.0
N B:ALA348 4.1 16.9 1.0
CA B:ALA348 4.5 17.0 1.0
OG B:SER217 4.6 19.4 1.0
CA B:CYS346 4.6 20.5 1.0
N B:SER347 4.6 20.6 1.0
O2 B:LMR601 4.7 18.6 1.0
O B:ALA251 4.7 18.9 1.0
CB B:CYS252 4.7 18.5 1.0
SG B:CYS252 4.7 19.4 1.0
O B:HOH803 4.8 21.4 1.0
C B:CYS346 4.9 23.2 1.0
N B:SER217 4.9 17.7 1.0
CB B:SER217 4.9 16.0 1.0
CA B:GLY214 4.9 17.1 1.0
SG B:CYS133 4.9 17.0 1.0
O1B B:LMR601 5.0 18.1 1.0
O B:ALA348 5.0 16.1 1.0

Iron binding site 6 out of 8 in 5l2r

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Iron binding site 6 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe611

b:18.0
occ:1.00
 FE2 B:SF4611 0.0 18.0 1.0
S4 B:SF4611 2.3 17.3 1.0
SG B:CYS133 2.3 17.0 1.0
S3 B:SF4611 2.3 19.4 1.0
S1 B:SF4611 2.3 18.4 1.0
FE1 B:SF4611 2.7 16.8 1.0
FE4 B:SF4611 2.8 17.7 1.0
FE3 B:SF4611 2.8 20.4 1.0
CB B:CYS133 3.5 17.1 1.0
S2 B:SF4611 3.9 18.5 1.0
CB B:ALA348 4.0 16.1 1.0
O2 B:LMR601 4.3 18.6 1.0
CB B:ASP135 4.3 15.8 1.0
O B:HOH911 4.4 21.8 1.0
NE2 B:GLN134 4.5 17.5 1.0
O B:HOH900 4.7 21.5 1.0
O B:ASP135 4.8 14.8 1.0
CA B:CYS133 4.8 23.7 1.0
SG B:CYS346 4.8 18.6 1.0
SG B:CYS252 4.9 19.4 1.0
CA B:GLY515 4.9 24.1 1.0
N B:ASP135 5.0 17.3 1.0

Iron binding site 7 out of 8 in 5l2r

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Iron binding site 7 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe611

b:20.4
occ:1.00
 FE3 B:SF4611 0.0 20.4 1.0
O2 B:LMR601 2.2 18.6 1.0
S2 B:SF4611 2.3 18.5 1.0
S1 B:SF4611 2.3 18.4 1.0
S4 B:SF4611 2.3 17.3 1.0
O1B B:LMR601 2.5 18.1 1.0
FE4 B:SF4611 2.7 17.7 1.0
FE1 B:SF4611 2.8 16.8 1.0
FE2 B:SF4611 2.8 18.0 1.0
C2 B:LMR601 3.2 21.4 1.0
C1 B:LMR601 3.2 22.4 1.0
C3 B:LMR601 3.7 18.0 1.0
S3 B:SF4611 3.9 19.4 1.0
N B:GLY216 3.9 18.3 1.0
CA B:GLY216 4.0 20.8 1.0
NZ B:LYS491 4.1 20.5 1.0
OD2 B:ASP135 4.1 14.5 1.0
O1A B:LMR601 4.5 20.4 1.0
CB B:ASP135 4.5 15.8 1.0
SG B:CYS133 4.7 17.0 1.0
CG B:ASP135 4.7 14.2 1.0
N B:SER217 4.7 17.7 1.0
SG B:CYS252 4.8 19.4 1.0
CA B:GLY214 4.8 17.1 1.0
C B:GLY216 4.9 22.8 1.0
CE B:LYS491 4.9 19.8 1.0
SG B:CYS346 4.9 18.6 1.0
N B:GLY215 4.9 15.5 1.0
C4 B:LMR601 4.9 19.4 1.0
C B:GLY214 5.0 14.8 1.0

Iron binding site 8 out of 8 in 5l2r

Go back to Iron Binding Sites List in 5l2r
Iron binding site 8 out of 8 in the Crystal Structure of Fumarate Hydratase From Leishmania Major


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 Fumarate Hydratase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe611

b:17.7
occ:1.00
 FE4 B:SF4611 0.0 17.7 1.0
S3 B:SF4611 2.3 19.4 1.0
S2 B:SF4611 2.3 18.5 1.0
S1 B:SF4611 2.3 18.4 1.0
SG B:CYS252 2.3 19.4 1.0
FE1 B:SF4611 2.7 16.8 1.0
FE3 B:SF4611 2.7 20.4 1.0
FE2 B:SF4611 2.8 18.0 1.0
CB B:CYS252 3.2 18.5 1.0
NZ B:LYS491 3.6 20.5 1.0
S4 B:SF4611 3.9 17.3 1.0
O1B B:LMR601 4.0 18.1 1.0
CE B:LYS491 4.1 19.8 1.0
O B:HOH900 4.3 21.5 1.0
CA B:CYS252 4.4 22.6 1.0
C B:ALA251 4.4 18.8 1.0
N B:CYS252 4.4 18.4 1.0
N B:GLY515 4.5 19.9 1.0
O B:ALA251 4.5 18.9 1.0
CA B:GLY515 4.7 24.1 1.0
SG B:CYS346 4.7 18.6 1.0
SG B:CYS133 4.7 17.0 1.0
CB B:CYS346 4.8 16.1 1.0
O2 B:LMR601 4.8 18.6 1.0
C B:GLY514 4.9 22.3 1.0
CD B:LYS491 5.0 20.5 1.0
CA B:ALA251 5.0 17.8 1.0

Reference:

P.R.Feliciano, C.L.Drennan, M.C.Nonato. Crystal Structure of An Fe-S Cluster-Containing Fumarate Hydratase Enzyme From Leishmania Major Reveals A Unique Protein Fold. Proc.Natl.Acad.Sci.Usa V. 113 9804 2016.
ISSN: ESSN 1091-6490
PubMed: 27528683
DOI: 10.1073/PNAS.1605031113
Page generated: Tue Aug 6 04:04:38 2024

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