Iron in PDB 8vdw: X-Ray Crystal Structure of the Biotin Synthase From V. Parvula

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

The structure of X-Ray Crystal Structure of the Biotin Synthase From V. Parvula, PDB code: 8vdw 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)	29.60 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.465, 70.218, 195.85, 90, 90, 90
R / Rfree (%)	17.9 / 22.7

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

Sodium

(Na)

1 atom

Pages:

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

Binding sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula (pdb code 8vdw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula, PDB code: 8vdw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.9 occ:1.00 FE1 A:Q46401 0.0 17.9 1.0 S2 A:Q46401 2.2 18.3 1.0 S3 A:Q46401 2.2 19.3 1.0 S4 A:Q46401 2.2 20.0 1.0 SG A:CYS216 2.3 19.9 1.0 FE3 A:Q46401 2.7 18.2 1.0 FE4 A:Q46401 2.8 17.1 1.0 FE2 A:Q46401 2.8 17.7 1.0 CB A:CYS216 3.3 18.5 1.0 S1 A:Q46401 3.7 20.4 1.0 NE A:ARG286 4.2 14.9 1.0 OG A:SER244 4.3 21.8 1.0 CD2 A:HIS179 4.4 18.9 1.0 CD A:ARG286 4.6 16.5 1.0 S5 A:Q46401 4.7 19.4 1.0 CA A:CYS216 4.7 17.4 1.0 CG A:PRO246 4.8 17.6 1.0 CD A:ARG177 4.8 25.0 1.0 O A:HOH613 4.9 25.8 1.0 SG A:CYS156 4.9 21.6 1.0 CZ A:ARG286 5.0 18.0 1.0

Iron binding site 2 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.2 occ:1.00 FE3 A:Q46401 0.0 18.2 1.0 S1 A:Q46401 2.1 20.4 1.0 S4 A:Q46401 2.2 20.0 1.0 S2 A:Q46401 2.2 18.3 1.0 S5 A:Q46401 2.2 19.4 1.0 FE1 A:Q46401 2.7 17.9 1.0 FE2 A:Q46401 2.7 17.7 1.0 FE4 A:Q46401 2.7 17.1 1.0 S3 A:Q46401 3.6 19.3 1.0 CB A:SER123 4.0 20.9 1.0 CD2 A:HIS179 4.2 18.9 1.0 OG A:SER123 4.2 21.6 1.0 CE A:MET311 4.3 17.3 1.0 CG A:HIS179 4.3 20.0 1.0 CB A:HIS179 4.4 18.6 1.0 N1 A:DTB404 4.4 19.6 1.0 CB A:CYS156 4.5 20.1 1.0 CG2 A:ILE71 4.6 19.4 1.0 SG A:CYS216 4.6 19.9 1.0 SG A:CYS156 4.7 21.6 1.0 SG A:CYS69 4.8 18.1 1.0 NE2 A:HIS179 4.9 20.9 1.0 CS A:DTB404 5.0 21.0 1.0

Iron binding site 3 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.7 occ:1.00 FE2 A:Q46401 0.0 17.7 1.0 S4 A:Q46401 2.1 20.0 1.0 S1 A:Q46401 2.2 20.4 1.0 S3 A:Q46401 2.2 19.3 1.0 SG A:CYS156 2.3 21.6 1.0 FE3 A:Q46401 2.7 18.2 1.0 FE4 A:Q46401 2.8 17.1 1.0 FE1 A:Q46401 2.8 17.9 1.0 CB A:CYS156 3.1 20.1 1.0 S2 A:Q46401 3.7 18.3 1.0 CD A:ARG121 4.2 19.4 1.0 CG A:ARG121 4.4 20.4 1.0 CB A:ARG177 4.4 21.2 1.0 CD A:ARG177 4.4 25.0 1.0 CB A:CYS69 4.5 17.2 1.0 CA A:CYS156 4.6 20.9 1.0 S5 A:Q46401 4.6 19.4 1.0 CB A:SER123 4.7 20.9 1.0 SG A:CYS69 4.7 18.1 1.0 SG A:CYS216 4.9 19.9 1.0

Iron binding site 4 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.1 occ:1.00 FE4 A:Q46401 0.0 17.1 1.0 S3 A:Q46401 2.1 19.3 1.0 S1 A:Q46401 2.2 20.4 1.0 S2 A:Q46401 2.2 18.3 1.0 SG A:CYS69 2.3 18.1 1.0 FE3 A:Q46401 2.7 18.2 1.0 FE1 A:Q46401 2.8 17.9 1.0 FE2 A:Q46401 2.8 17.7 1.0 CB A:CYS69 3.1 17.2 1.0 NE A:ARG286 3.7 14.9 1.0 S4 A:Q46401 3.7 20.0 1.0 CD A:ARG286 3.8 16.5 1.0 CE A:MET311 3.8 17.3 1.0 CZ A:ARG286 4.1 18.0 1.0 NH2 A:ARG286 4.3 17.3 1.0 CA A:CYS69 4.6 16.4 1.0 S5 A:Q46401 4.7 19.4 1.0 SG A:CYS216 4.9 19.9 1.0 NH1 A:ARG286 4.9 19.5 1.0 SG A:CYS156 4.9 21.6 1.0

Iron binding site 5 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:33.6 occ:1.00 FE1 A:SF4403 0.0 33.6 1.0 S4 A:SF4403 2.3 30.8 1.0 S2 A:SF4403 2.3 30.0 1.0 S3 A:SF4403 2.3 31.6 1.0 SG A:CYS86 2.3 31.5 1.0 FE4 A:SF4403 2.7 30.1 1.0 FE3 A:SF4403 2.7 30.2 1.0 FE2 A:SF4403 2.8 33.1 1.0 CB A:CYS86 3.1 32.9 1.0 S1 A:SF4403 3.8 23.6 1.0 CA A:CYS86 4.5 30.5 1.0 CB A:GLN88 4.6 29.8 1.0 SG A:CYS83 4.6 33.1 1.0 N A:SAM402 4.7 36.9 1.0 CB A:CYS83 4.7 32.9 1.0 SG A:CYS79 4.8 36.6 1.0 N A:SER89 4.8 31.5 1.0 CE1 A:PHE85 4.9 23.7 1.0 OXT A:SAM402 4.9 34.1 1.0 C A:GLN88 5.0 33.2 1.0 N A:GLN88 5.0 36.3 1.0 CB A:CYS79 5.0 38.5 1.0

Iron binding site 6 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:33.1 occ:1.00 FE2 A:SF4403 0.0 33.1 1.0 S1 A:SF4403 2.3 23.6 1.0 N A:SAM402 2.3 36.9 1.0 S3 A:SF4403 2.3 31.6 1.0 S4 A:SF4403 2.4 30.8 1.0 OXT A:SAM402 2.4 34.1 1.0 FE3 A:SF4403 2.7 30.2 1.0 FE1 A:SF4403 2.8 33.6 1.0 FE4 A:SF4403 2.8 30.1 1.0 C A:SAM402 3.1 34.6 1.0 CA A:SAM402 3.2 35.4 1.0 CG A:SAM402 3.4 43.3 1.0 CB A:SAM402 3.9 37.6 1.0 S2 A:SF4403 3.9 30.0 1.0 O A:HOH515 4.3 33.7 1.0 O A:SAM402 4.4 37.5 1.0 O A:GLY128 4.4 32.2 1.0 CE A:SAM402 4.6 49.8 1.0 C5' A:SAM402 4.6 34.5 1.0 SD A:SAM402 4.6 48.8 1.0 SG A:CYS79 4.8 36.6 1.0 O A:HOH719 4.8 37.6 1.0 SG A:CYS83 4.9 33.1 1.0 SG A:CYS86 4.9 31.5 1.0 N A:GLY128 5.0 32.1 1.0

Iron binding site 7 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:30.2 occ:1.00 FE3 A:SF4403 0.0 30.2 1.0 S1 A:SF4403 2.3 23.6 1.0 S2 A:SF4403 2.3 30.0 1.0 SG A:CYS79 2.3 36.6 1.0 S4 A:SF4403 2.3 30.8 1.0 FE1 A:SF4403 2.7 33.6 1.0 FE4 A:SF4403 2.7 30.1 1.0 FE2 A:SF4403 2.7 33.1 1.0 CB A:CYS79 3.3 38.5 1.0 CB A:GLU81 3.7 36.4 1.0 S3 A:SF4403 3.9 31.6 1.0 N A:SAM402 4.0 36.9 1.0 CG A:GLU81 4.1 36.9 1.0 N A:GLY128 4.2 32.1 1.0 O A:GLY128 4.3 32.2 1.0 C A:GLY128 4.4 35.2 1.0 SG A:CYS83 4.6 33.1 1.0 CA A:GLU81 4.7 37.5 1.0 CA A:GLY128 4.7 32.4 1.0 CA A:CYS79 4.7 39.2 1.0 N A:GLU81 4.8 32.4 1.0 OXT A:SAM402 4.8 34.1 1.0 O A:GLU81 4.8 38.0 1.0 SG A:CYS86 4.9 31.5 1.0

Iron binding site 8 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:30.1 occ:1.00 FE4 A:SF4403 0.0 30.1 1.0 S2 A:SF4403 2.2 30.0 1.0 SG A:CYS83 2.2 33.1 1.0 S1 A:SF4403 2.2 23.6 1.0 S3 A:SF4403 2.4 31.6 1.0 FE1 A:SF4403 2.7 33.6 1.0 FE3 A:SF4403 2.7 30.2 1.0 FE2 A:SF4403 2.8 33.1 1.0 CB A:CYS83 3.2 32.9 1.0 S4 A:SF4403 3.9 30.8 1.0 CB A:GLU81 4.1 36.4 1.0 OXT A:SAM402 4.1 34.1 1.0 O A:HOH515 4.3 33.7 1.0 CB A:CYS86 4.4 32.9 1.0 CA A:CYS83 4.5 33.1 1.0 CE1 A:HIS196 4.5 40.7 1.0 N A:CYS83 4.5 33.7 1.0 O A:HOH668 4.5 29.6 1.0 CZ A:PHE85 4.6 24.4 1.0 SG A:CYS86 4.7 31.5 1.0 CE1 A:PHE85 4.7 23.7 1.0 CG A:GLU81 4.8 36.9 1.0 SG A:CYS79 4.9 36.6 1.0 N A:SAM402 5.0 36.9 1.0

Iron binding site 9 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


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 V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.8 occ:1.00 FE1 B:Q46401 0.0 22.8 1.0 S3 B:Q46401 2.0 23.7 1.0 S4 B:Q46401 2.1 26.9 1.0 S2 B:Q46401 2.2 23.6 1.0 SG B:CYS216 2.3 25.6 1.0 FE3 B:Q46401 2.8 22.8 1.0 FE4 B:Q46401 2.8 21.3 1.0 FE2 B:Q46401 2.8 22.8 1.0 CB B:CYS216 3.3 25.5 1.0 S1 B:Q46401 3.7 24.1 1.0 CD2 B:HIS179 4.3 23.5 1.0 NE B:ARG286 4.3 18.1 1.0 OG B:SER244 4.5 25.7 1.0 CD B:ARG286 4.5 19.1 1.0 O B:HOH580 4.6 38.7 1.0 CA B:CYS216 4.7 24.5 1.0 S5 B:Q46401 4.7 22.5 1.0 CG B:PRO246 4.8 27.0 1.0 O B:HOH503 4.8 34.8 1.0 CB B:PRO246 4.9 26.6 1.0 SG B:CYS156 4.9 24.2 1.0 CB B:ARG177 5.0 28.6 1.0 CG B:HIS179 5.0 25.7 1.0 SG B:CYS69 5.0 22.4 1.0

Iron binding site 10 out of 16 in the X-Ray Crystal Structure of the Biotin Synthase From V. Parvula


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of X-Ray Crystal Structure of the Biotin Synthase From V. Parvula within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:22.8 occ:1.00 FE3 B:Q46401 0.0 22.8 1.0 S1 B:Q46401 2.0 24.1 1.0 S4 B:Q46401 2.2 26.9 1.0 S2 B:Q46401 2.2 23.6 1.0 S5 B:Q46401 2.2 22.5 1.0 FE4 B:Q46401 2.7 21.3 1.0 FE1 B:Q46401 2.8 22.8 1.0 FE2 B:Q46401 2.8 22.8 1.0 S3 B:Q46401 3.5 23.7 1.0 CD2 B:HIS179 4.0 23.5 1.0 CB B:SER123 4.0 23.4 1.0 OG B:SER123 4.2 25.5 1.0 CE B:MET311 4.3 23.9 1.0 N1 B:DTB402 4.3 23.5 1.0 CG B:HIS179 4.3 25.7 1.0 CB B:HIS179 4.4 28.4 1.0 CG2 B:ILE71 4.5 25.1 1.0 CB B:CYS156 4.6 23.0 1.0 SG B:CYS216 4.6 25.6 1.0 SG B:CYS156 4.7 24.2 1.0 SG B:CYS69 4.8 22.4 1.0 CS B:DTB402 4.8 24.7 1.0 NE2 B:HIS179 4.9 26.6 1.0

J.C.Lachowicz, T.L.Grove. X-Ray Crystal Structure of the Biotin Synthase From V. Parvula To Be Published.