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Iron in PDB 5bwe: Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate

Enzymatic activity of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate

All present enzymatic activity of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate:
4.1.99.11;

Protein crystallography data

The structure of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate, PDB code: 5bwe was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.27 / 3.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.534, 115.360, 121.701, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 23.7

Iron Binding Sites:

The binding sites of Iron atom in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate (pdb code 5bwe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate, PDB code: 5bwe:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5bwe

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Iron binding site 1 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:0.2
occ:1.00
 FE1 B:SF4101 0.0 0.2 1.0
S2 B:SF4101 2.3 0.3 1.0
S4 B:SF4101 2.3 0.3 1.0
S3 B:SF4101 2.3 0.6 1.0
SG B:CYS29 2.7 0.8 1.0
FE3 B:SF4101 2.7 0.2 1.0
FE2 B:SF4101 2.7 0.5 1.0
FE4 B:SF4101 2.7 0.6 1.0
CB B:CYS29 3.1 0.0 1.0
S1 B:SF4101 3.9 0.4 1.0
CB B:TRP31 4.2 0.9 1.0
CA B:HIS70 4.3 1.0 1.0
CD1 B:TRP31 4.3 0.4 1.0
CA B:CYS29 4.6 0.8 1.0
CD2 B:HIS70 4.6 0.4 1.0
CG B:TRP31 4.7 0.8 1.0
N B:HIS70 4.8 0.4 1.0
CA B:CYS26 4.8 0.4 1.0
CB B:HIS70 4.8 0.3 1.0
N B:GLN32 4.9 0.8 1.0
CG B:HIS70 5.0 0.6 1.0
N B:TRP31 5.0 0.3 1.0

Iron binding site 2 out of 8 in 5bwe

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Iron binding site 2 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:0.5
occ:1.00
 FE2 B:SF4101 0.0 0.5 1.0
S1 B:SF4101 2.3 0.4 1.0
S4 B:SF4101 2.3 0.3 1.0
S3 B:SF4101 2.3 0.6 1.0
FE3 B:SF4101 2.7 0.2 1.0
FE1 B:SF4101 2.7 0.2 1.0
FE4 B:SF4101 2.7 0.6 1.0
SG B:CYS44 2.7 0.6 1.0
CB B:CYS44 3.3 0.0 1.0
S2 B:SF4101 3.9 0.3 1.0
NH2 B:ARG69 4.2 0.3 1.0
CA B:CYS44 4.2 0.7 1.0
CB B:ALA46 4.5 0.3 1.0
CB B:TRP31 4.6 0.9 1.0
SG B:CYS67 4.8 0.3 1.0
CD1 B:LEU59 5.0 0.9 1.0

Iron binding site 3 out of 8 in 5bwe

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Iron binding site 3 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:0.2
occ:1.00
 FE3 B:SF4101 0.0 0.2 1.0
S4 B:SF4101 2.3 0.3 1.0
S1 B:SF4101 2.3 0.4 1.0
S2 B:SF4101 2.3 0.3 1.0
SG B:CYS26 2.7 0.1 1.0
FE4 B:SF4101 2.7 0.6 1.0
FE2 B:SF4101 2.7 0.5 1.0
FE1 B:SF4101 2.7 0.2 1.0
CB B:CYS26 3.4 0.7 1.0
CA B:CYS26 3.6 0.4 1.0
S3 B:SF4101 3.9 0.6 1.0
N B:CYS26 4.3 0.7 1.0
CD1 B:LEU59 4.4 0.9 1.0
CA B:THR66 4.5 0.8 1.0
C B:THR66 4.7 0.7 1.0
CD2 B:LEU59 4.7 0.9 1.0
C B:CYS26 4.8 0.8 1.0
N B:CYS67 4.8 0.7 1.0
CB B:CYS29 4.8 0.0 1.0
O B:THR65 4.8 0.8 1.0
N B:THR66 4.9 0.2 1.0
O B:CYS26 4.9 0.9 1.0

Iron binding site 4 out of 8 in 5bwe

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Iron binding site 4 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:0.6
occ:1.00
 FE4 B:SF4101 0.0 0.6 1.0
S1 B:SF4101 2.3 0.4 1.0
S2 B:SF4101 2.3 0.3 1.0
S3 B:SF4101 2.3 0.6 1.0
SG B:CYS67 2.7 0.3 1.0
FE3 B:SF4101 2.7 0.2 1.0
FE1 B:SF4101 2.7 0.2 1.0
FE2 B:SF4101 2.7 0.5 1.0
CB B:CYS67 3.5 0.1 1.0
N B:CYS67 3.5 0.7 1.0
S4 B:SF4101 3.9 0.3 1.0
CA B:CYS67 3.9 0.7 1.0
C B:THR66 4.1 0.7 1.0
NH2 B:ARG69 4.2 0.3 1.0
C B:CYS67 4.4 0.9 1.0
N B:HIS70 4.4 0.4 1.0
O B:CYS67 4.5 0.4 1.0
CA B:THR66 4.7 0.8 1.0
CA B:HIS70 4.7 1.0 1.0
NE B:ARG69 4.7 1.0 1.0
O B:THR66 4.8 0.7 1.0
C B:ARG69 4.9 0.1 1.0
CZ B:ARG69 4.9 0.4 1.0
CB B:HIS70 4.9 0.3 1.0
CB B:ARG69 5.0 1.0 1.0
N B:ARG69 5.0 0.6 1.0

Iron binding site 5 out of 8 in 5bwe

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Iron binding site 5 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:0.0
occ:1.00
 FE1 F:SF4101 0.0 0.0 1.0
S4 F:SF4101 2.3 0.2 1.0
S2 F:SF4101 2.3 0.2 1.0
S3 F:SF4101 2.3 0.5 1.0
SG F:CYS29 2.7 1.0 1.0
FE2 F:SF4101 2.7 0.3 1.0
FE3 F:SF4101 2.7 0.1 1.0
FE4 F:SF4101 2.7 0.4 1.0
CB F:CYS29 3.1 0.2 1.0
S1 F:SF4101 3.9 0.2 1.0
CB F:TRP31 4.1 0.5 1.0
CA F:HIS70 4.3 0.4 1.0
CD1 F:TRP31 4.5 0.0 1.0
CA F:CYS29 4.6 0.1 1.0
CD2 F:HIS70 4.7 0.6 1.0
CG F:TRP31 4.7 0.4 1.0
N F:HIS70 4.8 0.8 1.0
CA F:CYS26 4.8 1.0 1.0
N F:GLN32 4.8 0.9 1.0
CB F:HIS70 4.8 0.6 1.0
N F:TRP31 4.9 0.2 1.0
CA F:TRP31 5.0 0.3 1.0

Iron binding site 6 out of 8 in 5bwe

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Iron binding site 6 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:0.3
occ:1.00
 FE2 F:SF4101 0.0 0.3 1.0
S1 F:SF4101 2.3 0.2 1.0
S3 F:SF4101 2.3 0.5 1.0
S4 F:SF4101 2.3 0.2 1.0
SG F:CYS44 2.7 0.7 1.0
FE1 F:SF4101 2.7 0.0 1.0
FE3 F:SF4101 2.7 0.1 1.0
FE4 F:SF4101 2.7 0.4 1.0
CB F:CYS44 3.4 0.1 1.0
S2 F:SF4101 3.9 0.2 1.0
NH2 F:ARG69 4.1 0.3 1.0
CA F:CYS44 4.2 0.7 1.0
CB F:ALA46 4.5 0.5 1.0
CB F:TRP31 4.6 0.5 1.0
SG F:CYS67 4.8 0.1 1.0
CZ F:ARG69 5.0 0.3 1.0
C F:CYS44 5.0 0.2 1.0
CD1 F:LEU59 5.0 0.6 1.0

Iron binding site 7 out of 8 in 5bwe

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Iron binding site 7 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:0.1
occ:1.00
 FE3 F:SF4101 0.0 0.1 1.0
S4 F:SF4101 2.3 0.2 1.0
S1 F:SF4101 2.3 0.2 1.0
S2 F:SF4101 2.3 0.2 1.0
SG F:CYS26 2.7 0.8 1.0
FE4 F:SF4101 2.7 0.4 1.0
FE1 F:SF4101 2.7 0.0 1.0
FE2 F:SF4101 2.7 0.3 1.0
CB F:CYS26 3.4 0.5 1.0
CA F:CYS26 3.6 1.0 1.0
S3 F:SF4101 3.9 0.5 1.0
N F:CYS26 4.3 0.3 1.0
CD1 F:LEU59 4.4 0.6 1.0
CA F:THR66 4.6 0.1 1.0
C F:CYS26 4.7 0.4 1.0
CD2 F:LEU59 4.7 0.6 1.0
CB F:CYS29 4.8 0.2 1.0
C F:THR66 4.8 1.0 1.0
N F:CYS67 4.8 0.1 1.0
O F:CYS26 4.9 0.4 1.0
O F:THR65 4.9 0.2 1.0
N F:THR66 5.0 0.5 1.0

Iron binding site 8 out of 8 in 5bwe

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Iron binding site 8 out of 8 in the Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Benzylsuccinate Synthase Alpha-Beta-Gamma Complex with Bound Toluene and Fumarate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:0.4
occ:1.00
 FE4 F:SF4101 0.0 0.4 1.0
S1 F:SF4101 2.3 0.2 1.0
S3 F:SF4101 2.3 0.5 1.0
S2 F:SF4101 2.3 0.2 1.0
FE3 F:SF4101 2.7 0.1 1.0
FE1 F:SF4101 2.7 0.0 1.0
SG F:CYS67 2.7 0.1 1.0
FE2 F:SF4101 2.7 0.3 1.0
CB F:CYS67 3.5 0.9 1.0
N F:CYS67 3.6 0.1 1.0
S4 F:SF4101 3.9 0.2 1.0
CA F:CYS67 4.0 0.1 1.0
NH2 F:ARG69 4.2 0.3 1.0
C F:THR66 4.2 1.0 1.0
N F:HIS70 4.4 0.8 1.0
C F:CYS67 4.4 0.3 1.0
O F:CYS67 4.5 0.8 1.0
CA F:HIS70 4.7 0.4 1.0
NE F:ARG69 4.7 1.0 1.0
CA F:THR66 4.7 0.1 1.0
C F:ARG69 4.8 0.8 1.0
O F:THR66 4.8 0.0 1.0
CZ F:ARG69 4.9 0.3 1.0
CB F:HIS70 4.9 0.6 1.0
CB F:ARG69 4.9 0.9 1.0
N F:ARG69 5.0 0.4 1.0

Reference:

M.A.Funk, E.N.Marsh, C.L.Drennan. Substrate-Bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation. J.Biol.Chem. V. 290 22398 2015.
ISSN: ESSN 1083-351X
PubMed: 26224635
DOI: 10.1074/JBC.M115.670737
Page generated: Mon Aug 5 20:09:10 2024

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