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Iron in PDB 4eht: Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp

Protein crystallography data

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp, PDB code: 4eht was solved by S.H.Knauer, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.154, 161.005, 63.576, 90.00, 110.75, 90.00
R / Rfree (%) 17.6 / 20.5

Other elements in 4eht:

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp (pdb code 4eht). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp, PDB code: 4eht:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4eht

Go back to Iron Binding Sites List in 4eht
Iron binding site 1 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:23.6
occ:1.00
FE1 A:SF4301 0.0 23.6 1.0
S2 A:SF4301 2.2 26.5 1.0
S3 A:SF4301 2.2 24.2 1.0
S4 A:SF4301 2.2 23.8 1.0
SG B:CYS125 2.3 24.0 1.0
FE3 A:SF4301 2.8 20.5 1.0
FE4 A:SF4301 2.8 25.0 1.0
FE2 A:SF4301 2.9 21.5 1.0
HB2 B:CYS125 3.2 26.4 1.0
CB B:CYS125 3.3 22.1 1.0
HA B:CYS125 3.4 27.9 1.0
H B:ALA127 3.5 26.3 1.0
H B:ALA126 3.6 26.4 1.0
CA B:CYS125 3.8 23.3 1.0
S1 A:SF4301 3.9 26.6 1.0
HA B:CYS164 3.9 27.6 1.0
N B:ALA126 4.1 22.1 1.0
HB3 B:CYS125 4.1 26.4 1.0
H B:THR165 4.2 25.2 1.0
HB3 B:ALA127 4.2 26.0 1.0
HB2 B:ALA127 4.2 26.0 1.0
O A:HOH569 4.2 35.8 0.5
C B:CYS125 4.3 26.0 1.0
N B:ALA127 4.4 22.0 1.0
SG A:CYS164 4.5 26.0 1.0
HG1 B:THR165 4.5 26.7 1.0
CB B:ALA127 4.6 21.8 1.0
HB2 A:CYS164 4.7 22.9 1.0
CA B:CYS164 4.8 23.1 1.0
O A:HOH569 4.9 41.8 0.5
HB2 A:CYS125 4.9 28.4 1.0
HB3 B:ALA126 4.9 27.2 1.0
O B:HOH438 4.9 36.1 1.0
SG B:CYS164 4.9 24.0 1.0
N B:THR165 5.0 21.1 1.0
SG A:CYS125 5.0 24.2 1.0

Iron binding site 2 out of 4 in 4eht

Go back to Iron Binding Sites List in 4eht
Iron binding site 2 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:21.5
occ:1.00
FE2 A:SF4301 0.0 21.5 1.0
S4 A:SF4301 2.2 23.8 1.0
S1 A:SF4301 2.2 26.6 1.0
S3 A:SF4301 2.3 24.2 1.0
SG A:CYS125 2.3 24.2 1.0
FE4 A:SF4301 2.7 25.0 1.0
FE3 A:SF4301 2.8 20.5 1.0
FE1 A:SF4301 2.9 23.6 1.0
HB2 A:CYS125 3.2 28.4 1.0
CB A:CYS125 3.3 23.8 1.0
HA A:CYS125 3.5 34.7 1.0
H A:ALA127 3.6 30.7 1.0
H A:ALA126 3.7 29.1 1.0
S2 A:SF4301 3.8 26.5 1.0
HA A:CYS164 3.8 28.4 1.0
CA A:CYS125 3.9 29.0 1.0
O A:HOH569 4.1 41.8 0.5
N A:ALA126 4.1 24.3 1.0
HB3 A:CYS125 4.1 28.4 1.0
H A:THR165 4.1 34.8 1.0
HB3 A:ALA127 4.1 25.0 1.0
HB2 A:ALA127 4.1 25.0 1.0
C A:CYS125 4.3 30.8 1.0
N A:ALA127 4.4 25.7 1.0
SG B:CYS164 4.4 24.0 1.0
HG1 A:THR165 4.4 24.1 1.0
CB A:ALA127 4.6 20.9 1.0
O A:HOH569 4.7 35.8 0.5
CA A:CYS164 4.8 23.7 1.0
SG A:CYS164 4.9 26.0 1.0
HB2 B:CYS164 4.9 20.7 1.0
HB2 A:CYS164 4.9 22.9 1.0
N A:THR165 4.9 29.0 1.0
HB2 B:CYS125 5.0 26.4 1.0
SG B:CYS125 5.0 24.0 1.0

Iron binding site 3 out of 4 in 4eht

Go back to Iron Binding Sites List in 4eht
Iron binding site 3 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:20.5
occ:1.00
FE3 A:SF4301 0.0 20.5 1.0
S4 A:SF4301 2.2 23.8 1.0
S1 A:SF4301 2.2 26.6 1.0
S2 A:SF4301 2.2 26.5 1.0
SG A:CYS164 2.2 26.0 1.0
FE4 A:SF4301 2.8 25.0 1.0
FE1 A:SF4301 2.8 23.6 1.0
FE2 A:SF4301 2.8 21.5 1.0
HA A:CYS164 3.0 28.4 1.0
H A:THR165 3.1 34.8 1.0
CB A:CYS164 3.2 19.1 1.0
HB2 A:CYS164 3.3 22.9 1.0
H B:ALA126 3.3 26.4 1.0
CA A:CYS164 3.5 23.7 1.0
H A:VAL166 3.5 26.0 1.0
N A:THR165 3.6 29.0 1.0
HA B:CYS125 3.7 27.9 1.0
S3 A:SF4301 3.8 24.2 1.0
HG23 A:VAL166 3.9 38.4 1.0
C A:CYS164 3.9 28.3 1.0
HB3 A:CYS164 4.1 22.9 1.0
HB3 B:ALA126 4.1 27.2 1.0
N B:ALA126 4.1 22.1 1.0
HB A:THR165 4.2 22.7 1.0
HG1 A:THR165 4.3 24.1 1.0
N A:VAL166 4.4 21.7 1.0
HB A:VAL166 4.5 34.3 1.0
HG23 B:VAL166 4.5 33.8 1.0
CA B:CYS125 4.6 23.3 1.0
SG B:CYS125 4.6 24.0 1.0
HB2 B:ALA126 4.6 27.2 1.0
CA A:THR165 4.7 27.9 1.0
CG2 A:VAL166 4.7 32.1 1.0
H B:ALA127 4.7 26.3 1.0
H B:THR165 4.7 25.2 1.0
HB B:THR165 4.7 34.5 1.0
CB B:ALA126 4.7 22.8 1.0
CB A:THR165 4.8 19.0 1.0
HG21 A:VAL166 4.9 38.4 1.0
SG B:CYS164 4.9 24.0 1.0
C B:CYS125 4.9 26.0 1.0
N A:CYS164 4.9 25.9 1.0
HB2 B:CYS125 4.9 26.4 1.0
SG A:CYS125 4.9 24.2 1.0
HG1 B:THR165 4.9 26.7 1.0
CB B:CYS125 5.0 22.1 1.0
OG1 A:THR165 5.0 20.2 1.0
O A:CYS164 5.0 27.0 1.0
H A:PHE167 5.0 32.7 1.0

Iron binding site 4 out of 4 in 4eht

Go back to Iron Binding Sites List in 4eht
Iron binding site 4 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:25.0
occ:1.00
FE4 A:SF4301 0.0 25.0 1.0
S3 A:SF4301 2.2 24.2 1.0
S2 A:SF4301 2.2 26.5 1.0
S1 A:SF4301 2.3 26.6 1.0
SG B:CYS164 2.3 24.0 1.0
FE2 A:SF4301 2.7 21.5 1.0
FE3 A:SF4301 2.8 20.5 1.0
FE1 A:SF4301 2.8 23.6 1.0
HA B:CYS164 3.0 27.6 1.0
H B:THR165 3.1 25.2 1.0
CB B:CYS164 3.3 17.3 1.0
H A:ALA126 3.3 29.1 1.0
HB2 B:CYS164 3.4 20.7 1.0
CA B:CYS164 3.5 23.1 1.0
H B:VAL166 3.5 28.3 1.0
N B:THR165 3.6 21.1 1.0
S4 A:SF4301 3.7 23.8 1.0
HA A:CYS125 3.7 34.7 1.0
HG23 B:VAL166 3.8 33.8 1.0
C B:CYS164 4.0 25.3 1.0
HB3 B:CYS164 4.2 20.7 1.0
N A:ALA126 4.2 24.3 1.0
HB B:THR165 4.2 34.5 1.0
HB3 A:ALA126 4.3 25.3 1.0
HB B:VAL166 4.4 30.7 1.0
N B:VAL166 4.4 23.7 1.0
HG1 B:THR165 4.5 26.7 1.0
SG A:CYS125 4.5 24.2 1.0
CA A:CYS125 4.5 29.0 1.0
CG2 B:VAL166 4.6 28.2 1.0
HG23 A:VAL166 4.7 38.4 1.0
CA B:THR165 4.7 25.8 1.0
HG21 B:VAL166 4.7 33.8 1.0
H A:ALA127 4.7 30.7 1.0
H A:THR165 4.7 34.8 1.0
HB2 A:CYS125 4.7 28.4 1.0
HB A:THR165 4.8 22.7 1.0
CB B:THR165 4.8 28.8 1.0
HB2 A:ALA126 4.8 25.3 1.0
CB A:CYS125 4.8 23.8 1.0
SG A:CYS164 4.9 26.0 1.0
HG1 A:THR165 4.9 24.1 1.0
C A:CYS125 4.9 30.8 1.0
N B:CYS164 4.9 25.9 1.0
CB A:ALA126 4.9 21.2 1.0
SG B:CYS125 5.0 24.0 1.0
CB B:VAL166 5.0 25.7 1.0

Reference:

S.H.Knauer, W.Buckel, H.Dobbek. On the Atp-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-Coa Dehydratase. Biochemistry V. 51 6609 2012.
ISSN: ISSN 0006-2960
PubMed: 22827463
DOI: 10.1021/BI300571Z
Page generated: Sun Dec 13 15:32:43 2020

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