Iron in PDB 8vcw: X-Ray Crystal Structure of the Biotin Synthase From B. Obeum

Enzymatic activity of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum

All present enzymatic activity of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum:
2.8.1.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum, PDB code: 8vcw was solved by J.C.Lachowicz, T.L.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.209, 50.776, 161.878, 90, 90, 90
R / Rfree (%) 15 / 17.3

Other elements in 8vcw:

The structure of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum (pdb code 8vcw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum, PDB code: 8vcw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 8vcw

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Iron binding site 1 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:9.4
occ:1.00
 FE1 A:Q46403 0.0 9.4 1.0
S4 A:Q46403 2.2 9.6 1.0
S3 A:Q46403 2.2 8.7 1.0
S2 A:Q46403 2.2 9.1 1.0
SG A:CYS198 2.3 8.7 1.0
FE3 A:Q46403 2.7 8.8 1.0
FE4 A:Q46403 2.7 9.1 1.0
FE2 A:Q46403 2.7 9.1 1.0
CB A:CYS198 3.3 9.0 1.0
S1 A:Q46403 3.8 9.2 1.0
OG A:SER226 4.1 10.4 1.0
O A:HOH720 4.2 16.7 1.0
CD2 A:HIS161 4.2 10.7 1.0
NE A:ARG268 4.3 10.8 1.0
CD A:ARG268 4.4 9.6 1.0
S5 A:Q46403 4.6 10.0 1.0
CA A:CYS198 4.7 7.3 1.0
CB A:HIS161 4.7 8.9 1.0
CG A:HIS161 4.7 9.4 1.0
SG A:CYS52 4.8 8.7 1.0
SG A:CYS138 4.9 10.0 1.0
CZ A:ARG268 4.9 9.2 1.0
CB A:SER226 5.0 11.8 1.0
CG A:PRO228 5.0 10.5 1.0

Iron binding site 2 out of 9 in 8vcw

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Iron binding site 2 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:8.8
occ:1.00
 FE3 A:Q46403 0.0 8.8 1.0
S5 A:Q46403 2.2 10.0 1.0
S1 A:Q46403 2.2 9.2 1.0
S4 A:Q46403 2.3 9.6 1.0
S2 A:Q46403 2.3 9.1 1.0
FE1 A:Q46403 2.7 9.4 1.0
FE4 A:Q46403 2.7 9.1 1.0
FE2 A:Q46403 2.7 9.1 1.0
S3 A:Q46403 3.8 8.7 1.0
CB A:SER106 4.1 9.0 1.0
CB A:HIS161 4.1 8.9 1.0
OG A:SER106 4.2 9.7 1.0
CD2 A:HIS161 4.2 10.7 1.0
CG A:HIS161 4.2 9.4 1.0
CB A:CYS138 4.4 8.1 1.0
CG2 A:ILE54 4.5 10.2 1.0
N1 A:DTB405 4.6 10.1 1.0
SG A:CYS198 4.6 8.7 1.0
SG A:CYS138 4.6 10.0 1.0
SG A:CYS52 4.8 8.7 1.0
NE2 A:HIS161 4.9 12.1 1.0

Iron binding site 3 out of 9 in 8vcw

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Iron binding site 3 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:9.1
occ:1.00
 FE2 A:Q46403 0.0 9.1 1.0
S4 A:Q46403 2.2 9.6 1.0
S3 A:Q46403 2.2 8.7 1.0
S1 A:Q46403 2.3 9.2 1.0
SG A:CYS138 2.3 10.0 1.0
FE3 A:Q46403 2.7 8.8 1.0
FE4 A:Q46403 2.7 9.1 1.0
FE1 A:Q46403 2.7 9.4 1.0
CB A:CYS138 3.1 8.1 1.0
S2 A:Q46403 3.9 9.1 1.0
CD A:ARG104 4.0 9.4 1.0
CG A:ARG104 4.2 9.2 1.0
O A:HOH720 4.3 16.7 1.0
CB A:CYS52 4.4 7.7 1.0
CB A:SER159 4.5 9.9 1.0
SG A:CYS52 4.6 8.7 1.0
CA A:CYS138 4.6 7.0 1.0
CB A:SER106 4.7 9.0 1.0
S5 A:Q46403 4.7 10.0 1.0
SG A:CYS198 4.9 8.7 1.0
OG A:SER159 4.9 11.6 1.0

Iron binding site 4 out of 9 in 8vcw

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Iron binding site 4 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:9.1
occ:1.00
 FE4 A:Q46403 0.0 9.1 1.0
S2 A:Q46403 2.2 9.1 1.0
S1 A:Q46403 2.2 9.2 1.0
SG A:CYS52 2.3 8.7 1.0
S3 A:Q46403 2.3 8.7 1.0
FE1 A:Q46403 2.7 9.4 1.0
FE3 A:Q46403 2.7 8.8 1.0
FE2 A:Q46403 2.7 9.1 1.0
CB A:CYS52 3.1 7.7 1.0
S4 A:Q46403 3.8 9.6 1.0
CD A:ARG268 3.9 9.6 1.0
NE A:ARG268 4.2 10.8 1.0
NH1 A:ARG268 4.2 10.1 1.0
CZ A:ARG268 4.4 9.2 1.0
CG1 A:ILE292 4.4 9.5 1.0
CA A:CYS52 4.5 7.2 1.0
S5 A:Q46403 4.7 10.0 1.0
SG A:CYS198 4.8 8.7 1.0
CD1 A:ILE292 4.8 13.6 1.0
SG A:CYS138 4.9 10.0 1.0
C A:CYS52 4.9 7.7 1.0
CG A:ARG104 5.0 9.2 1.0

Iron binding site 5 out of 9 in 8vcw

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Iron binding site 5 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:10.3
occ:1.00
 FE1 A:SF4404 0.0 10.3 1.0
S2 A:SF4404 2.3 11.2 1.0
SG A:CYS62 2.3 10.1 1.0
S4 A:SF4404 2.3 10.8 1.0
S3 A:SF4404 2.3 11.0 1.0
FE3 A:SF4404 2.7 10.8 1.0
FE4 A:SF4404 2.7 11.0 1.0
FE2 A:SF4404 2.8 12.9 1.0
CB A:CYS62 3.2 9.3 1.0
S1 A:SF4404 3.9 11.5 1.0
CB A:GLU64 3.9 8.8 1.0
N A:GLY111 4.2 10.1 1.0
N A:SAM401 4.2 16.9 1.0
CG A:GLU64 4.3 12.5 1.0
O A:GLY111 4.4 12.0 1.0
C A:GLY111 4.6 11.5 1.0
CA A:CYS62 4.6 8.1 1.0
SG A:CYS66 4.7 11.2 1.0
CA A:GLY111 4.7 12.3 1.0
N A:GLU64 4.8 8.9 1.0
SG A:CYS69 4.8 11.3 1.0
O A:SAM401 4.8 14.3 1.0
CA A:GLU64 4.8 9.9 1.0
O A:GLU64 4.9 9.9 1.0

Iron binding site 6 out of 9 in 8vcw

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Iron binding site 6 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:12.9
occ:1.00
 FE2 A:SF4404 0.0 12.9 1.0
O A:SAM401 2.3 14.3 1.0
S3 A:SF4404 2.4 11.0 1.0
S1 A:SF4404 2.4 11.5 1.0
N A:SAM401 2.4 16.9 1.0
S4 A:SF4404 2.4 10.8 1.0
FE1 A:SF4404 2.8 10.3 1.0
FE4 A:SF4404 2.8 11.0 1.0
FE3 A:SF4404 2.9 10.8 1.0
C A:SAM401 3.1 14.9 1.0
CA A:SAM401 3.2 13.8 1.0
CG A:SAM401 3.9 23.6 1.0
SD A:SAM401 3.9 48.1 1.0
S2 A:SF4404 4.1 11.2 1.0
CB A:SAM401 4.1 18.4 1.0
O A:HOH762 4.2 17.9 1.0
O A:HOH512 4.2 17.7 1.0
O A:HOH808 4.3 30.4 1.0
OXT A:SAM401 4.3 16.7 1.0
O A:GLY111 4.4 12.0 1.0
SG A:CYS62 4.8 10.1 1.0
N A:GLY111 4.9 10.1 1.0
SG A:CYS69 5.0 11.3 1.0
C5' A:SAM401 5.0 23.9 1.0

Iron binding site 7 out of 9 in 8vcw

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Iron binding site 7 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:10.8
occ:1.00
 FE3 A:SF4404 0.0 10.8 1.0
S4 A:SF4404 2.3 10.8 1.0
SG A:CYS66 2.3 11.2 1.0
S1 A:SF4404 2.3 11.5 1.0
S2 A:SF4404 2.3 11.2 1.0
FE1 A:SF4404 2.7 10.3 1.0
FE4 A:SF4404 2.7 11.0 1.0
FE2 A:SF4404 2.9 12.9 1.0
CB A:CYS66 3.3 9.6 1.0
S3 A:SF4404 3.9 11.0 1.0
OH A:TYR68 4.1 12.4 1.0
CB A:GLU64 4.2 8.8 1.0
O A:SAM401 4.2 14.3 1.0
O A:HOH512 4.2 17.7 1.0
O A:HOH619 4.3 15.4 1.0
CE1 A:HIS178 4.4 14.5 1.0
N A:CYS66 4.5 9.2 1.0
CA A:CYS66 4.5 9.1 1.0
CB A:CYS69 4.5 9.7 1.0
SG A:CYS69 4.6 11.3 1.0
CZ A:TYR68 4.7 10.8 1.0
SG A:CYS62 4.7 10.1 1.0
CE1 A:TYR68 4.9 10.3 1.0
CG A:GLU64 4.9 12.5 1.0

Iron binding site 8 out of 9 in 8vcw

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Iron binding site 8 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:11.0
occ:1.00
 FE4 A:SF4404 0.0 11.0 1.0
S3 A:SF4404 2.3 11.0 1.0
S2 A:SF4404 2.3 11.2 1.0
S1 A:SF4404 2.3 11.5 1.0
SG A:CYS69 2.3 11.3 1.0
FE1 A:SF4404 2.7 10.3 1.0
FE3 A:SF4404 2.7 10.8 1.0
FE2 A:SF4404 2.8 12.9 1.0
CB A:CYS69 3.2 9.7 1.0
S4 A:SF4404 3.9 10.8 1.0
O A:HOH832 3.9 27.6 1.0
O A:HOH808 4.5 30.4 1.0
CA A:CYS69 4.6 9.2 1.0
SG A:CYS66 4.7 11.2 1.0
CB A:CYS66 4.7 9.6 1.0
CB A:GLN71 4.7 10.8 1.0
N A:SER72 4.7 9.5 1.0
SG A:CYS62 4.7 10.1 1.0
CB A:CYS62 4.9 9.3 1.0
O A:SAM401 4.9 14.3 1.0
N A:SAM401 4.9 16.9 1.0
CE1 A:TYR68 4.9 10.3 1.0
C A:GLN71 4.9 9.5 1.0

Iron binding site 9 out of 9 in 8vcw

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Iron binding site 9 out of 9 in the X-Ray Crystal Structure of the Biotin Synthase From B. Obeum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of X-Ray Crystal Structure of the Biotin Synthase From B. Obeum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe406

b:17.3
occ:1.00
 O3 A:BTB402 2.0 18.8 1.0
ND1 A:HIS74 2.1 11.8 1.0
O6 A:BTB402 2.1 23.6 1.0
O8 A:BTB402 2.2 20.2 1.0
O4 A:BTB402 2.2 26.4 1.0
N A:BTB402 2.3 29.3 1.0
C2 A:BTB402 2.8 27.3 1.0
C3 A:BTB402 2.9 23.2 1.0
C6 A:BTB402 2.9 28.1 1.0
CE1 A:HIS74 3.0 12.5 1.0
C7 A:BTB402 3.0 20.6 1.0
C4 A:BTB402 3.0 26.8 1.0
C5 A:BTB402 3.0 25.4 1.0
C8 A:BTB402 3.1 25.8 1.0
CG A:HIS74 3.2 10.2 1.0
CB A:HIS74 3.6 11.0 1.0
NE2 A:HIS74 4.1 11.7 1.0
O A:HOH529 4.2 25.4 1.0
CD2 A:HIS74 4.2 11.9 1.0
C1 A:BTB402 4.3 36.0 1.0
CA A:HIS74 4.4 9.4 1.0
O A:HOH522 4.5 33.2 1.0
O A:HIS74 4.8 14.9 1.0
O1 A:BTB402 5.0 38.1 1.0

Reference:

J.C.Lachowicz, T.L.Grove. X-Ray Crystal Structure of the Biotin Synthase From B. Obeum To Be Published.
Page generated: Sat Aug 10 18:38:46 2024

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