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Iron in PDB 1r30: The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme

Enzymatic activity of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme

All present enzymatic activity of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme:
2.8.1.6;

Protein crystallography data

The structure of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme, PDB code: 1r30 was solved by F.Berkovitch, Y.Nicolet, J.T.Wan, J.T.Jarrett, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.45 / 3.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.690, 155.690, 90.880, 90.00, 90.00, 120.00
R / Rfree (%) 25.6 / 30

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme (pdb code 1r30). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme, PDB code: 1r30:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1r30

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Iron binding site 1 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.8
occ:1.00
 FE1 A:SF4401 0.0 50.8 1.0
S2 A:SF4401 2.3 50.8 1.0
S4 A:SF4401 2.3 50.8 1.0
S3 A:SF4401 2.3 50.8 1.0
SG A:CYS57 2.3 0.7 1.0
FE3 A:SF4401 3.0 50.8 1.0
FE4 A:SF4401 3.1 50.8 1.0
FE2 A:SF4401 3.3 50.8 1.0
CB A:CYS57 3.3 0.7 1.0
CB A:GLU55 3.9 0.9 1.0
N A:CYS57 4.1 73.2 1.0
NH1 A:ARG168 4.1 84.9 1.0
S1 A:SF4401 4.2 50.8 1.0
CA A:CYS57 4.3 73.2 1.0
CB A:CYS60 4.4 84.4 1.0
O A:SAM501 4.5 0.6 1.0
CG A:GLU55 4.6 0.9 1.0
SG A:CYS60 4.6 84.4 1.0
CZ A:ARG168 5.0 84.9 1.0
C A:GLU55 5.0 66.6 1.0
OH A:TYR59 5.0 67.8 1.0

Iron binding site 2 out of 12 in 1r30

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Iron binding site 2 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.8
occ:1.00
 FE2 A:SF4401 0.0 50.8 1.0
S3 A:SF4401 2.3 50.8 1.0
S1 A:SF4401 2.3 50.8 1.0
S4 A:SF4401 2.3 50.8 1.0
N A:SAM501 2.3 0.6 1.0
O A:SAM501 2.5 0.6 1.0
CB A:SAM501 2.6 0.6 1.0
CA A:SAM501 2.8 0.6 1.0
FE4 A:SF4401 3.0 50.8 1.0
C A:SAM501 3.0 0.6 1.0
FE3 A:SF4401 3.1 50.8 1.0
FE1 A:SF4401 3.3 50.8 1.0
CG A:SAM501 3.3 0.6 1.0
SD A:SAM501 4.0 0.6 1.0
S2 A:SF4401 4.1 50.8 1.0
OXT A:SAM501 4.3 0.6 1.0
O A:TRP102 4.7 98.8 1.0

Iron binding site 3 out of 12 in 1r30

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Iron binding site 3 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.8
occ:1.00
 FE3 A:SF4401 0.0 50.8 1.0
S2 A:SF4401 2.3 50.8 1.0
S4 A:SF4401 2.3 50.8 1.0
S1 A:SF4401 2.3 50.8 1.0
SG A:CYS60 2.3 84.4 1.0
FE4 A:SF4401 2.7 50.8 1.0
FE1 A:SF4401 3.0 50.8 1.0
FE2 A:SF4401 3.1 50.8 1.0
CB A:CYS60 3.3 84.4 1.0
S3 A:SF4401 3.7 50.8 1.0
CB A:GLN62 4.3 68.3 1.0
N A:SER63 4.6 90.2 1.0
SG A:CYS53 4.6 88.8 1.0
CA A:CYS60 4.8 59.1 1.0
CB A:CYS53 4.8 88.8 1.0
N A:GLN62 4.9 81.3 1.0
N A:SAM501 4.9 0.6 1.0
NE2 A:GLN62 4.9 68.3 1.0
CA A:GLN62 4.9 81.3 1.0
C A:GLN62 5.0 81.3 1.0
SG A:CYS57 5.0 0.7 1.0

Iron binding site 4 out of 12 in 1r30

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Iron binding site 4 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:50.8
occ:1.00
 FE4 A:SF4401 0.0 50.8 1.0
SG A:CYS53 2.2 88.8 1.0
S2 A:SF4401 2.3 50.8 1.0
S3 A:SF4401 2.3 50.8 1.0
S1 A:SF4401 2.3 50.8 1.0
FE3 A:SF4401 2.7 50.8 1.0
FE2 A:SF4401 3.0 50.8 1.0
FE1 A:SF4401 3.1 50.8 1.0
CB A:CYS53 3.3 88.8 1.0
S4 A:SF4401 3.7 50.8 1.0
N A:SAM501 4.1 0.6 1.0
CB A:GLU55 4.2 0.9 1.0
CG A:GLU55 4.4 0.9 1.0
O A:TRP102 4.4 98.8 1.0
O A:ALA101 4.6 58.9 1.0
C A:ALA101 4.6 58.9 1.0
CA A:CYS53 4.7 0.1 1.0
O A:SAM501 4.7 0.6 1.0
N A:GLU55 4.8 66.6 1.0
SG A:CYS60 4.8 84.4 1.0
CA A:ALA101 4.9 58.9 1.0
CA A:GLU55 5.0 66.6 1.0

Iron binding site 5 out of 12 in 1r30

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Iron binding site 5 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:35.8
occ:1.00
 FE1 A:FES402 0.0 35.8 1.0
S2 A:FES402 2.2 35.8 1.0
S1 A:FES402 2.2 35.8 1.0
SG A:CYS188 2.3 81.0 1.0
NH1 A:ARG260 2.4 50.1 1.0
CZ A:ARG260 3.0 50.1 1.0
NH2 A:ARG260 3.1 50.1 1.0
FE2 A:FES402 3.2 35.8 1.0
CB A:CYS188 3.5 81.0 1.0
NE A:ARG260 4.0 50.1 1.0
CB A:SER218 4.6 0.6 1.0
CZ A:PHE285 4.7 77.0 1.0
CD A:ARG260 4.7 50.1 1.0
SG A:CYS128 4.9 72.7 1.0
CA A:CYS188 4.9 73.9 1.0
CD A:PRO220 4.9 52.9 1.0
CG A:PRO220 4.9 52.9 1.0
ND2 A:ASN151 4.9 78.5 1.0
SG A:CYS97 4.9 72.0 1.0

Iron binding site 6 out of 12 in 1r30

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Iron binding site 6 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:35.8
occ:1.00
 FE2 A:FES402 0.0 35.8 1.0
S1 A:FES402 2.2 35.8 1.0
S2 A:FES402 2.2 35.8 1.0
SG A:CYS97 2.3 72.0 1.0
SG A:CYS128 2.3 72.7 1.0
FE1 A:FES402 3.2 35.8 1.0
CB A:CYS97 3.3 72.0 1.0
CB A:CYS128 3.4 72.7 1.0
NH1 A:ARG260 4.0 50.1 1.0
O A:CYS128 4.2 79.3 1.0
CA A:CYS97 4.3 94.6 1.0
CD A:ARG95 4.4 77.9 1.0
C A:CYS128 4.6 79.3 1.0
CA A:CYS128 4.6 79.3 1.0
NH2 A:ARG260 4.6 50.1 1.0
CZ A:ARG260 4.8 50.1 1.0
CG A:ARG95 4.9 77.9 1.0

Iron binding site 7 out of 12 in 1r30

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Iron binding site 7 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:71.3
occ:1.00
 FE1 B:SF4401 0.0 71.3 1.0
SG B:CYS57 2.3 84.5 1.0
S2 B:SF4401 2.3 71.3 1.0
S4 B:SF4401 2.3 71.3 1.0
S3 B:SF4401 2.3 71.3 1.0
FE3 B:SF4401 2.9 71.3 1.0
FE4 B:SF4401 3.1 71.3 1.0
FE2 B:SF4401 3.3 71.3 1.0
CB B:CYS57 3.3 84.5 1.0
S1 B:SF4401 4.0 71.3 1.0
NH1 B:ARG168 4.1 0.3 1.0
CB B:GLU55 4.1 0.9 1.0
N B:CYS57 4.2 92.0 1.0
CA B:CYS57 4.4 92.0 1.0
CB B:CYS60 4.4 0.2 1.0
SG B:CYS60 4.7 0.2 1.0
OH B:TYR59 4.7 84.5 1.0
CG B:GLU55 4.8 0.9 1.0
O B:SAM501 4.8 0.3 1.0
CZ B:ARG168 4.9 0.3 1.0
NH2 B:ARG168 4.9 0.3 1.0
CE2 B:TYR59 5.0 84.5 1.0

Iron binding site 8 out of 12 in 1r30

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Iron binding site 8 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:71.3
occ:1.00
 FE2 B:SF4401 0.0 71.3 1.0
S4 B:SF4401 2.3 71.3 1.0
S1 B:SF4401 2.3 71.3 1.0
S3 B:SF4401 2.3 71.3 1.0
N B:SAM501 2.5 0.3 1.0
CB B:SAM501 2.6 0.3 1.0
CA B:SAM501 3.0 0.3 1.0
CG B:SAM501 3.0 0.3 1.0
FE3 B:SF4401 3.1 71.3 1.0
O B:SAM501 3.2 0.3 1.0
FE4 B:SF4401 3.3 71.3 1.0
FE1 B:SF4401 3.3 71.3 1.0
C B:SAM501 3.6 0.3 1.0
SD B:SAM501 3.8 0.3 1.0
S2 B:SF4401 4.2 71.3 1.0
O3' B:SAM501 4.7 84.6 1.0
OXT B:SAM501 4.8 0.3 1.0
C5' B:SAM501 4.8 84.6 1.0
C3' B:SAM501 4.8 84.6 1.0
O B:TRP102 5.0 81.1 1.0

Iron binding site 9 out of 12 in 1r30

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Iron binding site 9 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:71.3
occ:1.00
 FE3 B:SF4401 0.0 71.3 1.0
SG B:CYS60 2.3 0.2 1.0
S1 B:SF4401 2.3 71.3 1.0
S2 B:SF4401 2.3 71.3 1.0
S4 B:SF4401 2.3 71.3 1.0
FE4 B:SF4401 2.8 71.3 1.0
FE1 B:SF4401 2.9 71.3 1.0
FE2 B:SF4401 3.1 71.3 1.0
CB B:CYS60 3.2 0.2 1.0
S3 B:SF4401 3.6 71.3 1.0
CB B:GLN62 4.4 0.3 1.0
N B:SER63 4.6 84.6 1.0
CA B:CYS60 4.6 69.3 1.0
SG B:CYS53 4.7 80.7 1.0
SG B:CYS57 4.8 84.5 1.0
N B:GLN62 4.9 0.5 1.0
CB B:CYS57 5.0 84.5 1.0
CB B:CYS53 5.0 80.7 1.0
CA B:GLN62 5.0 0.5 1.0

Iron binding site 10 out of 12 in 1r30

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Iron binding site 10 out of 12 in the The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Biotin Synthase, An S-Adenosylmethionine- Dependent Radical Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:71.3
occ:1.00
 FE4 B:SF4401 0.0 71.3 1.0
SG B:CYS53 2.3 80.7 1.0
S2 B:SF4401 2.3 71.3 1.0
S1 B:SF4401 2.3 71.3 1.0
S3 B:SF4401 2.3 71.3 1.0
FE3 B:SF4401 2.8 71.3 1.0
FE1 B:SF4401 3.1 71.3 1.0
FE2 B:SF4401 3.3 71.3 1.0
CB B:CYS53 3.4 80.7 1.0
S4 B:SF4401 3.9 71.3 1.0
CB B:GLU55 4.0 0.9 1.0
CG B:GLU55 4.2 0.9 1.0
N B:SAM501 4.4 0.3 1.0
O B:TRP102 4.5 81.1 1.0
N B:GLU55 4.6 85.8 1.0
CA B:CYS53 4.7 95.9 1.0
O B:ALA101 4.8 77.3 1.0
CA B:GLU55 4.8 85.8 1.0
C B:ALA101 4.9 77.3 1.0
SG B:CYS60 4.9 0.2 1.0
C B:CYS53 5.0 95.9 1.0

Reference:

F.Berkovitch, Y.Nicolet, J.T.Wan, J.T.Jarrett, C.L.Drennan. Crystal Structure of Biotin Synthase, An S-Adenosylmethionine-Dependent Radical Enzyme. Science V. 303 76 2004.
ISSN: ISSN 0036-8075
PubMed: 14704425
DOI: 10.1126/SCIENCE.1088493
Page generated: Sat Aug 3 13:59:30 2024

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