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Iron in PDB 3o3n: (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa

Protein crystallography data

The structure of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa, PDB code: 3o3n was solved by S.H.Knauer, W.Buckel, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.648, 126.683, 177.699, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.3

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa (pdb code 3o3n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa, PDB code: 3o3n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 3o3n

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Iron binding site 1 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe409

b:34.1
occ:1.00
 FE1 A:SF4409 0.0 34.1 1.0
S2 A:SF4409 2.2 31.0 1.0
S4 A:SF4409 2.3 28.4 1.0
S3 A:SF4409 2.4 29.9 1.0
SG A:CYS346 2.4 31.5 1.0
FE3 A:SF4409 2.9 34.6 1.0
CB A:CYS346 3.0 26.5 1.0
FE4 A:SF4409 3.1 32.0 1.0
FE2 A:SF4409 3.1 27.3 1.0
CA A:CYS346 3.6 25.8 1.0
S1 A:SF4409 3.6 32.1 1.0
O B:HOH425 4.2 24.6 1.0
N A:CYS346 4.4 28.8 1.0
C A:CYS346 4.6 26.3 1.0
CI2 A:IRC410 4.7 41.0 0.7
OI2 A:IRC410 4.8 41.5 0.7
CB A:CYS117 4.8 20.3 1.0
OI1 A:IRC410 4.9 37.2 0.7
SG A:CYS117 5.0 26.0 1.0

Iron binding site 2 out of 16 in 3o3n

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Iron binding site 2 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe409

b:27.3
occ:1.00
 FE2 A:SF4409 0.0 27.3 1.0
S4 A:SF4409 2.2 28.4 1.0
S1 A:SF4409 2.3 32.1 1.0
S3 A:SF4409 2.3 29.9 1.0
SG A:CYS84 2.3 22.2 1.0
CB A:CYS84 3.0 18.3 1.0
FE1 A:SF4409 3.1 34.1 1.0
FE3 A:SF4409 3.3 34.6 1.0
FE4 A:SF4409 3.4 32.0 1.0
S2 A:SF4409 4.2 31.0 1.0
CD2 A:TYR86 4.3 23.2 1.0
CA A:CYS84 4.4 19.1 1.0
NE2 A:GLN375 4.6 36.7 1.0
CB A:TYR86 4.7 22.2 1.0
O A:SER345 4.8 26.4 1.0
CG A:TYR86 4.8 22.9 1.0
CB A:SER345 4.9 26.0 1.0
C A:SER345 4.9 26.7 1.0
CA A:CYS346 4.9 25.8 1.0
C A:CYS84 5.0 17.5 1.0

Iron binding site 3 out of 16 in 3o3n

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Iron binding site 3 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe409

b:34.6
occ:1.00
 FE3 A:SF4409 0.0 34.6 1.0
OI1 A:IRC410 2.2 37.2 0.7
S4 A:SF4409 2.3 28.4 1.0
S1 A:SF4409 2.3 32.1 1.0
S2 A:SF4409 2.3 31.0 1.0
FE1 A:SF4409 2.9 34.1 1.0
CI1 A:IRC410 3.0 42.0 0.7
FE4 A:SF4409 3.2 32.0 1.0
CI2 A:IRC410 3.2 41.0 0.7
FE2 A:SF4409 3.3 27.3 1.0
S3 A:SF4409 3.9 29.9 1.0
OI2 A:IRC410 4.0 41.5 0.7
OE1 A:GLU55 4.1 21.8 1.0
CD2 A:TYR86 4.1 23.2 1.0
CE2 A:TYR86 4.3 19.8 1.0
CI3 A:IRC410 4.3 40.9 0.7
CD1 A:ILE265 4.6 45.3 1.0
S1P A:IRC410 4.7 45.5 0.7
CD1 A:ILE116 4.7 22.7 1.0
CD A:GLU55 4.7 24.3 1.0
SG A:CYS346 5.0 31.5 1.0

Iron binding site 4 out of 16 in 3o3n

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Iron binding site 4 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe409

b:32.0
occ:1.00
 FE4 A:SF4409 0.0 32.0 1.0
S3 A:SF4409 2.2 29.9 1.0
SG A:CYS117 2.2 26.0 1.0
S1 A:SF4409 2.3 32.1 1.0
S2 A:SF4409 2.3 31.0 1.0
CB A:CYS117 3.0 20.3 1.0
FE1 A:SF4409 3.1 34.1 1.0
FE3 A:SF4409 3.2 34.6 1.0
FE2 A:SF4409 3.4 27.3 1.0
S4 A:SF4409 4.1 28.4 1.0
CG1 A:VAL120 4.3 18.1 1.0
CA A:CYS117 4.3 21.2 1.0
CD1 A:ILE116 4.4 22.7 1.0
O B:HOH425 4.5 24.6 1.0
CG1 A:ILE116 4.5 26.0 1.0
CB A:GLN119 4.6 19.4 1.0
N A:CYS117 4.6 22.6 1.0
O A:ILE116 4.6 22.1 1.0
C A:ILE116 4.7 24.0 1.0
C A:CYS117 4.9 19.1 1.0
N A:VAL120 5.0 18.2 1.0

Iron binding site 5 out of 16 in 3o3n

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Iron binding site 5 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe386

b:25.4
occ:1.00
 FE1 B:SF4386 0.0 25.4 1.0
S2 B:SF4386 2.2 26.0 1.0
S B:H2S387 2.3 28.9 1.0
S4 B:SF4386 2.3 25.9 1.0
S3 B:SF4386 2.4 28.1 1.0
FE3 B:SF4386 2.6 20.9 1.0
FE4 B:SF4386 2.9 24.2 1.0
FE2 B:SF4386 3.0 27.1 1.0
S1 B:SF4386 4.1 22.6 1.0
CD1 B:ILE237 4.3 20.4 1.0
CG2 B:ILE74 4.4 27.7 1.0
SG B:CYS72 4.6 24.8 1.0
CG1 B:ILE237 4.7 23.7 1.0
CG2 B:ILE237 4.9 23.2 1.0
CD1 B:LEU102 4.9 17.1 1.0
SG B:CYS99 4.9 21.2 1.0
SG B:CYS325 4.9 21.5 1.0
CG B:LEU102 4.9 19.0 1.0
CG B:MET75 5.0 28.4 1.0
CB B:PRO35 5.0 40.3 1.0

Iron binding site 6 out of 16 in 3o3n

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Iron binding site 6 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe386

b:27.1
occ:1.00
 FE2 B:SF4386 0.0 27.1 1.0
S4 B:SF4386 2.2 25.9 1.0
S3 B:SF4386 2.2 28.1 1.0
S1 B:SF4386 2.3 22.6 1.0
SG B:CYS325 2.4 21.5 1.0
FE3 B:SF4386 2.5 20.9 1.0
FE4 B:SF4386 2.9 24.2 1.0
FE1 B:SF4386 3.0 25.4 1.0
CB B:CYS325 3.2 20.1 1.0
CA B:CYS325 3.6 20.2 1.0
CD B:PRO327 3.9 17.1 1.0
S2 B:SF4386 4.0 26.0 1.0
C B:CYS325 4.2 19.4 1.0
CG B:PRO327 4.4 15.4 1.0
CD1 B:ILE237 4.5 20.4 1.0
N B:ASP326 4.6 18.5 1.0
SG B:CYS72 4.6 24.8 1.0
CG1 B:ILE237 4.6 23.7 1.0
CB B:CYS72 4.8 25.1 1.0
CB B:PRO327 4.9 16.8 1.0
N B:PRO327 4.9 18.6 1.0
N B:CYS325 4.9 21.6 1.0
O B:CYS325 4.9 18.8 1.0
S B:H2S387 5.0 28.9 1.0

Iron binding site 7 out of 16 in 3o3n

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Iron binding site 7 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe386

b:20.9
occ:1.00
 FE3 B:SF4386 0.0 20.9 1.0
S4 B:SF4386 2.2 25.9 1.0
S2 B:SF4386 2.3 26.0 1.0
S1 B:SF4386 2.3 22.6 1.0
SG B:CYS72 2.4 24.8 1.0
FE2 B:SF4386 2.5 27.1 1.0
FE1 B:SF4386 2.6 25.4 1.0
FE4 B:SF4386 2.6 24.2 1.0
CB B:CYS72 3.4 25.1 1.0
S3 B:SF4386 3.5 28.1 1.0
CG B:MET75 4.1 28.4 1.0
CG2 B:ILE74 4.2 27.7 1.0
O B:HOH445 4.4 7.8 1.0
CB B:THR101 4.5 18.4 1.0
CG2 B:THR101 4.5 16.2 1.0
S B:H2S387 4.6 28.9 1.0
SG B:CYS325 4.7 21.5 1.0
CB B:CYS325 4.8 20.1 1.0
SG B:CYS99 4.8 21.2 1.0
OG1 B:THR101 4.8 16.4 1.0
CA B:CYS72 4.8 23.9 1.0
CA B:CYS325 4.8 20.2 1.0
CB B:MET75 4.9 28.5 1.0

Iron binding site 8 out of 16 in 3o3n

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Iron binding site 8 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe386

b:24.2
occ:1.00
 FE4 B:SF4386 0.0 24.2 1.0
S1 B:SF4386 2.3 22.6 1.0
S3 B:SF4386 2.3 28.1 1.0
S2 B:SF4386 2.3 26.0 1.0
SG B:CYS99 2.4 21.2 1.0
FE3 B:SF4386 2.6 20.9 1.0
FE2 B:SF4386 2.9 27.1 1.0
FE1 B:SF4386 2.9 25.4 1.0
CB B:CYS99 3.5 21.0 1.0
S4 B:SF4386 4.0 25.9 1.0
O B:HOH389 4.0 14.5 1.0
CB B:THR101 4.3 18.4 1.0
CG B:LEU102 4.4 19.0 1.0
CG B:PRO327 4.5 15.4 1.0
CD B:PRO327 4.6 17.1 1.0
CD1 B:LEU102 4.6 17.1 1.0
N B:LEU102 4.7 21.9 1.0
OG1 B:THR101 4.7 16.4 1.0
SG B:CYS72 4.7 24.8 1.0
CA B:CYS99 4.9 20.0 1.0
S B:H2S387 5.0 28.9 1.0

Iron binding site 9 out of 16 in 3o3n

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Iron binding site 9 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe409

b:33.0
occ:1.00
 FE1 C:SF4409 0.0 33.0 1.0
S2 C:SF4409 2.2 28.9 1.0
S4 C:SF4409 2.3 29.4 1.0
SG C:CYS346 2.4 34.2 1.0
S3 C:SF4409 2.4 29.8 1.0
CB C:CYS346 2.9 28.4 1.0
FE3 C:SF4409 2.9 36.8 1.0
FE4 C:SF4409 3.1 30.4 1.0
FE2 C:SF4409 3.2 23.4 1.0
CA C:CYS346 3.5 26.9 1.0
S1 C:SF4409 3.7 29.3 1.0
O C:HOH917 4.0 31.4 0.7
N C:CYS346 4.4 26.6 1.0
O D:HOH397 4.5 26.0 1.0
C C:CYS346 4.6 26.4 1.0
CI2 C:IRC410 4.8 42.6 0.7
OI1 C:IRC410 4.8 36.5 0.7
CB C:CYS117 4.8 17.4 1.0
OI2 C:IRC410 4.9 43.6 0.7
SG C:CYS117 4.9 21.6 1.0

Iron binding site 10 out of 16 in 3o3n

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Iron binding site 10 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with Its Substrate (R)-2-Hydroxyisocaproyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe409

b:23.4
occ:1.00
 FE2 C:SF4409 0.0 23.4 1.0
S4 C:SF4409 2.2 29.4 1.0
S1 C:SF4409 2.3 29.3 1.0
S3 C:SF4409 2.3 29.8 1.0
SG C:CYS84 2.3 20.5 1.0
CB C:CYS84 3.1 17.3 1.0
FE1 C:SF4409 3.2 33.0 1.0
FE3 C:SF4409 3.2 36.8 1.0
FE4 C:SF4409 3.4 30.4 1.0
CD2 C:TYR86 4.0 21.0 1.0
S2 C:SF4409 4.2 28.9 1.0
NE2 C:GLN375 4.3 36.3 1.0
CB C:TYR86 4.4 20.2 1.0
CA C:CYS84 4.4 17.3 1.0
CG C:TYR86 4.6 22.3 1.0
CB C:SER345 4.9 24.7 1.0
O C:SER345 4.9 25.2 1.0
CE2 C:TYR86 4.9 20.1 1.0
CA C:CYS346 4.9 26.9 1.0
C C:SER345 5.0 25.3 1.0

Reference:

S.H.Knauer, W.Buckel, H.Dobbek. Structural Basis For Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-Coa Dehydratase. J.Am.Chem.Soc. V. 133 4342 2011.
ISSN: ISSN 0002-7863
PubMed: 21366233
DOI: 10.1021/JA1076537
Page generated: Sun Aug 4 16:57:32 2024

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