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Iron in PDB 1u8v: Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin

Enzymatic activity of Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin

All present enzymatic activity of Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin:
5.3.3.3;

Protein crystallography data

The structure of Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin, PDB code: 1u8v was solved by B.M.Martins, H.Dobbek, I.Cinkaya, W.Buckel, A.Messerschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.300, 130.200, 175.500, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.2

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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin (pdb code 1u8v). 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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin, PDB code: 1u8v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 1u8v

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Iron binding site 1 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe491

b:27.2
occ:1.00
 FE1 A:SF4491 0.0 27.2 1.0
S3 A:SF4491 2.3 25.0 1.0
S2 A:SF4491 2.4 27.2 1.0
S4 A:SF4491 2.4 25.1 1.0
NE2 A:HIS292 2.5 28.4 1.0
FE3 A:SF4491 2.7 23.5 1.0
FE2 A:SF4491 2.7 22.8 1.0
FE4 A:SF4491 2.7 23.5 1.0
CD2 A:HIS292 3.5 35.3 1.0
CE1 A:HIS292 3.5 27.3 1.0
CE1 A:TYR296 3.8 32.7 1.0
S1 A:SF4491 4.0 21.1 1.0
OE2 A:GLU455 4.4 28.4 1.0
CD1 A:TYR296 4.5 25.2 1.0
O A:HOH8628 4.6 49.6 1.0
ND1 A:HIS292 4.6 28.2 1.0
CG A:HIS292 4.6 29.9 1.0
CB A:CYS103 4.7 21.1 1.0
O A:HOH7164 4.7 30.3 1.0
CZ A:TYR296 4.7 30.1 1.0
SG A:CYS103 4.7 23.1 1.0
OH A:TYR296 4.7 31.8 1.0
SG A:CYS99 4.8 24.8 1.0
SG A:CYS299 4.8 23.7 1.0
CG1 A:VAL104 4.9 32.5 1.0

Iron binding site 2 out of 16 in 1u8v

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Iron binding site 2 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe491

b:22.8
occ:1.00
 FE2 A:SF4491 0.0 22.8 1.0
S4 A:SF4491 2.2 25.1 1.0
SG A:CYS299 2.3 23.7 1.0
S3 A:SF4491 2.3 25.0 1.0
S1 A:SF4491 2.4 21.1 1.0
FE4 A:SF4491 2.5 23.5 1.0
FE3 A:SF4491 2.6 23.5 1.0
FE1 A:SF4491 2.7 27.2 1.0
CB A:CYS299 3.2 21.0 1.0
S2 A:SF4491 3.9 27.2 1.0
O A:HOH6311 3.9 22.2 1.0
CD1 A:TYR296 4.2 25.2 1.0
CE1 A:TYR296 4.3 32.7 1.0
CE A:LYS300 4.6 25.3 1.0
SG A:CYS103 4.6 23.1 1.0
CA A:CYS299 4.7 13.4 1.0
NE2 A:HIS292 4.9 28.4 1.0
SG A:CYS99 4.9 24.8 1.0

Iron binding site 3 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 3 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe491

b:23.5
occ:1.00
 FE3 A:SF4491 0.0 23.5 1.0
S1 A:SF4491 2.3 21.1 1.0
S4 A:SF4491 2.3 25.1 1.0
S2 A:SF4491 2.3 27.2 1.0
SG A:CYS99 2.4 24.8 1.0
FE2 A:SF4491 2.6 22.8 1.0
FE4 A:SF4491 2.7 23.5 1.0
FE1 A:SF4491 2.7 27.2 1.0
CB A:CYS99 3.4 25.4 1.0
CA A:CYS99 3.8 24.7 1.0
S3 A:SF4491 3.9 25.0 1.0
N A:GLN101 4.1 18.3 1.0
O A:HOH7164 4.1 30.3 1.0
N A:PHE100 4.2 22.2 1.0
C A:CYS99 4.2 22.3 1.0
CA A:GLN101 4.5 20.7 1.0
O A:HOH6853 4.5 32.5 1.0
O A:HOH6311 4.6 22.2 1.0
SG A:CYS299 4.8 23.7 1.0
SG A:CYS103 4.9 23.1 1.0

Iron binding site 4 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 4 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe491

b:23.5
occ:1.00
 FE4 A:SF4491 0.0 23.5 1.0
S3 A:SF4491 2.2 25.0 1.0
S1 A:SF4491 2.3 21.1 1.0
SG A:CYS103 2.4 23.1 1.0
S2 A:SF4491 2.4 27.2 1.0
FE2 A:SF4491 2.5 22.8 1.0
FE3 A:SF4491 2.7 23.5 1.0
FE1 A:SF4491 2.7 27.2 1.0
CB A:CYS103 3.2 21.1 1.0
S4 A:SF4491 3.9 25.1 1.0
CE2 A:PHE100 4.3 15.3 1.0
N A:CYS103 4.3 18.9 1.0
CA A:CYS103 4.4 23.2 1.0
SG A:CYS299 4.4 23.7 1.0
CB A:CYS299 4.4 21.0 1.0
CZ A:PHE100 4.5 17.6 1.0
N A:GLN101 4.5 18.3 1.0
CD2 A:PHE100 4.7 17.8 1.0
NE2 A:GLN89 4.7 18.8 1.0
NE2 A:HIS292 4.8 28.4 1.0
SG A:CYS99 4.8 24.8 1.0
CA A:GLN101 4.9 20.7 1.0
C A:GLN101 4.9 27.1 1.0

Iron binding site 5 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 5 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe491

b:25.9
occ:1.00
 FE1 B:SF4491 0.0 25.9 1.0
S2 B:SF4491 2.3 22.4 1.0
S4 B:SF4491 2.4 24.2 1.0
S3 B:SF4491 2.4 22.4 1.0
NE2 B:HIS292 2.4 29.1 1.0
O B:HOH8832 2.4 43.5 1.0
FE2 B:SF4491 2.7 21.8 1.0
FE3 B:SF4491 2.7 21.4 1.0
FE4 B:SF4491 2.8 22.5 1.0
CE1 B:HIS292 3.3 27.9 1.0
CD2 B:HIS292 3.4 26.6 1.0
CE1 B:TYR296 3.9 27.4 1.0
S1 B:SF4491 4.1 18.8 1.0
O B:HOH7577 4.3 35.4 1.0
ND1 B:HIS292 4.4 29.3 1.0
O B:HOH6585 4.5 28.0 1.0
CD1 B:TYR296 4.5 23.6 1.0
OE2 B:GLU455 4.5 24.8 1.0
CG B:HIS292 4.6 19.8 1.0
SG B:CYS99 4.7 22.9 1.0
CZ B:TYR296 4.8 26.8 1.0
CG1 B:VAL104 4.8 40.0 1.0
CB B:CYS103 4.8 18.9 1.0
OH B:TYR296 4.8 29.1 1.0
SG B:CYS103 4.9 18.7 1.0
SG B:CYS299 4.9 21.2 1.0

Iron binding site 6 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 6 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe491

b:21.8
occ:1.00
 FE2 B:SF4491 0.0 21.8 1.0
S3 B:SF4491 2.3 22.4 1.0
S4 B:SF4491 2.3 24.2 1.0
SG B:CYS299 2.3 21.2 1.0
S1 B:SF4491 2.4 18.8 1.0
FE4 B:SF4491 2.6 22.5 1.0
FE3 B:SF4491 2.7 21.4 1.0
FE1 B:SF4491 2.7 25.9 1.0
CB B:CYS299 3.3 17.2 1.0
S2 B:SF4491 3.9 22.4 1.0
O B:HOH6022 3.9 23.6 1.0
CD1 B:TYR296 4.2 23.6 1.0
CE1 B:TYR296 4.4 27.4 1.0
SG B:CYS103 4.7 18.7 1.0
O B:HOH8832 4.7 43.5 1.0
CE B:LYS300 4.7 20.5 1.0
NE2 B:HIS292 4.8 29.1 1.0
CA B:CYS299 4.8 12.0 1.0
SG B:CYS99 4.9 22.9 1.0
O B:HOH7055 4.9 34.7 1.0

Iron binding site 7 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 7 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe491

b:21.4
occ:1.00
 FE3 B:SF4491 0.0 21.4 1.0
SG B:CYS99 2.3 22.9 1.0
S2 B:SF4491 2.3 22.4 1.0
S4 B:SF4491 2.3 24.2 1.0
S1 B:SF4491 2.3 18.8 1.0
FE4 B:SF4491 2.7 22.5 1.0
FE2 B:SF4491 2.7 21.8 1.0
FE1 B:SF4491 2.7 25.9 1.0
CB B:CYS99 3.3 27.0 1.0
O B:HOH8832 3.7 43.5 1.0
CA B:CYS99 3.8 19.0 1.0
O B:HOH6585 3.8 28.0 1.0
S3 B:SF4491 3.9 22.4 1.0
N B:GLN101 4.1 15.0 1.0
N B:PHE100 4.3 18.0 1.0
C B:CYS99 4.3 17.9 1.0
O B:HOH7055 4.3 34.7 1.0
CA B:GLN101 4.4 17.5 1.0
O B:HOH7577 4.6 35.4 1.0
O B:HOH6022 4.7 23.6 1.0
SG B:CYS299 4.9 21.2 1.0
SG B:CYS103 4.9 18.7 1.0

Iron binding site 8 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 8 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe491

b:22.5
occ:1.00
 FE4 B:SF4491 0.0 22.5 1.0
S3 B:SF4491 2.3 22.4 1.0
S1 B:SF4491 2.3 18.8 1.0
S2 B:SF4491 2.4 22.4 1.0
SG B:CYS103 2.4 18.7 1.0
FE2 B:SF4491 2.6 21.8 1.0
FE3 B:SF4491 2.7 21.4 1.0
FE1 B:SF4491 2.8 25.9 1.0
CB B:CYS103 3.2 18.9 1.0
S4 B:SF4491 3.9 24.2 1.0
N B:CYS103 4.4 15.3 1.0
CA B:CYS103 4.4 15.8 1.0
CE2 B:PHE100 4.4 21.1 1.0
SG B:CYS299 4.5 21.2 1.0
CB B:CYS299 4.6 17.2 1.0
N B:GLN101 4.6 15.0 1.0
NE2 B:HIS292 4.6 29.1 1.0
CZ B:PHE100 4.6 16.4 1.0
SG B:CYS99 4.7 22.9 1.0
CD2 B:PHE100 4.8 20.2 1.0
NE2 B:GLN89 4.8 21.6 1.0
CA B:GLN101 4.9 17.5 1.0
O B:HOH8832 4.9 43.5 1.0
C B:GLN101 4.9 21.4 1.0

Iron binding site 9 out of 16 in 1u8v

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Iron binding site 9 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe491

b:22.4
occ:1.00
 FE1 C:SF4491 0.0 22.4 1.0
S3 C:SF4491 2.2 21.2 1.0
S2 C:SF4491 2.3 20.3 1.0
S4 C:SF4491 2.4 21.0 1.0
NE2 C:HIS292 2.5 24.1 1.0
FE4 C:SF4491 2.7 19.7 1.0
FE2 C:SF4491 2.7 18.9 1.0
FE3 C:SF4491 2.7 18.8 1.0
CD2 C:HIS292 3.4 26.9 1.0
CE1 C:HIS292 3.4 27.7 1.0
CE1 C:TYR296 3.9 26.0 1.0
S1 C:SF4491 4.0 15.9 1.0
O C:HOH7597 4.3 30.5 1.0
CD1 C:TYR296 4.5 14.8 1.0
ND1 C:HIS292 4.6 20.3 1.0
OE2 C:GLU455 4.6 22.7 1.0
CB C:CYS103 4.6 16.9 1.0
CG C:HIS292 4.6 16.6 1.0
CG1 C:VAL104 4.7 27.3 1.0
CZ C:TYR296 4.7 24.3 1.0
O C:HOH6736 4.7 22.9 1.0
OH C:TYR296 4.7 22.6 1.0
SG C:CYS103 4.7 16.3 1.0
SG C:CYS99 4.8 17.9 1.0
SG C:CYS299 4.8 18.3 1.0

Iron binding site 10 out of 16 in 1u8v

Go back to Iron Binding Sites List in 1u8v
Iron binding site 10 out of 16 in the Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin


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 4-Hydroxybutyryl-Coa Dehydratase From Clostridium Aminobutyricum: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe491

b:18.9
occ:1.00
 FE2 C:SF4491 0.0 18.9 1.0
S4 C:SF4491 2.2 21.0 1.0
SG C:CYS299 2.3 18.3 1.0
S3 C:SF4491 2.3 21.2 1.0
S1 C:SF4491 2.4 15.9 1.0
FE4 C:SF4491 2.6 19.7 1.0
FE3 C:SF4491 2.7 18.8 1.0
FE1 C:SF4491 2.7 22.4 1.0
CB C:CYS299 3.2 18.1 1.0
O C:HOH6491 3.8 20.6 1.0
S2 C:SF4491 3.9 20.3 1.0
CD1 C:TYR296 4.2 14.8 1.0
CE1 C:TYR296 4.3 26.0 1.0
CE C:LYS300 4.6 20.4 1.0
SG C:CYS103 4.7 16.3 1.0
CA C:CYS299 4.7 12.5 1.0
O C:HOH7013 4.8 35.1 1.0
NE2 C:HIS292 4.9 24.1 1.0
SG C:CYS99 4.9 17.9 1.0

Reference:

B.M.Martins, H.Dobbek, I.Cinkaya, W.Buckel, A.Messerschmidt. Crystal Structure of 4-Hydroxybutyryl-Coa Dehydratase: Radical Catalysis Involving A [4FE-4S] Cluster and Flavin. Proc.Natl.Acad.Sci.Usa V. 101 15645 2004.
ISSN: ISSN 0027-8424
PubMed: 15496473
DOI: 10.1073/PNAS.0403952101
Page generated: Sun Dec 13 14:33:07 2020

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