Iron in PDB 3i04: Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster

All present enzymatic activity of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster:
1.2.7.4; 1.2.99.2; 2.3.1.169;

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04 was solved by Y.Kung, T.I.Doukov, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	99.830, 136.768, 141.611, 101.23, 109.18, 103.87
R / Rfree (%)	17.2 / 22.1

The structure of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster also contains other interesting chemical elements:

Nickel	(Ni)	8 atoms
Copper	(Cu)	4 atoms
Sodium	(Na)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Iron atom in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster (pdb code 3i04). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 56 binding sites of Iron where determined in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster, PDB code: 3i04:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:17.4 occ:1.00 FE1 A:SF4700 0.0 17.4 1.0 S2 A:SF4700 2.3 18.7 1.0 SG B:CYS67 2.3 18.1 1.0 S4 A:SF4700 2.3 16.6 1.0 S3 A:SF4700 2.3 16.3 1.0 FE3 A:SF4700 2.7 18.0 1.0 FE4 A:SF4700 2.8 20.6 1.0 FE2 A:SF4700 2.8 19.4 1.0 CB B:CYS67 3.1 14.4 1.0 O A:HOH787 3.9 21.8 1.0 S1 A:SF4700 3.9 17.6 1.0 NE B:ARG69 4.3 21.9 1.0 NE A:ARG69 4.4 19.5 1.0 CA B:CYS67 4.6 16.7 1.0 NH2 A:ARG69 4.6 18.4 1.0 SG A:CYS67 4.6 17.6 1.0 SG B:CYS59 4.7 20.5 1.0 SG A:CYS59 4.8 20.8 1.0 CD B:ARG69 4.8 19.8 1.0 CB A:CYS59 4.9 22.4 1.0 CZ A:ARG69 4.9 23.5 1.0 CG2 B:ILE61 5.0 22.0 1.0

Iron binding site 2 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:19.4 occ:1.00 FE2 A:SF4700 0.0 19.4 1.0 S1 A:SF4700 2.2 17.6 1.0 SG A:CYS59 2.3 20.8 1.0 S3 A:SF4700 2.3 16.3 1.0 S4 A:SF4700 2.3 16.6 1.0 FE3 A:SF4700 2.7 18.0 1.0 FE4 A:SF4700 2.8 20.6 1.0 FE1 A:SF4700 2.8 17.4 1.0 CB A:CYS59 3.1 22.4 1.0 S2 A:SF4700 3.9 18.7 1.0 N A:GLY62 4.3 21.1 1.0 CA A:CYS59 4.6 22.5 1.0 CB A:ILE61 4.6 22.6 1.0 CA A:GLY62 4.8 20.6 1.0 SG B:CYS59 4.8 20.5 1.0 SG B:CYS67 4.8 18.1 1.0 CD1 A:ILE61 4.8 28.2 1.0 O A:HOH787 4.8 21.8 1.0 SG A:CYS67 4.9 17.6 1.0

Iron binding site 3 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:18.0 occ:1.00 FE3 A:SF4700 0.0 18.0 1.0 SG A:CYS67 2.2 17.6 1.0 S4 A:SF4700 2.3 16.6 1.0 S2 A:SF4700 2.3 18.7 1.0 S1 A:SF4700 2.4 17.6 1.0 FE1 A:SF4700 2.7 17.4 1.0 FE2 A:SF4700 2.7 19.4 1.0 FE4 A:SF4700 2.8 20.6 1.0 CB A:CYS67 3.1 15.2 1.0 O A:HOH758 3.8 20.0 1.0 S3 A:SF4700 3.9 16.3 1.0 NE B:ARG69 4.3 21.9 1.0 NE A:ARG69 4.5 19.5 1.0 NH2 B:ARG69 4.5 25.7 1.0 CA A:CYS67 4.5 18.4 1.0 SG B:CYS59 4.7 20.5 1.0 SG B:CYS67 4.7 18.1 1.0 SG A:CYS59 4.8 20.8 1.0 CB B:CYS59 4.8 21.3 1.0 CZ B:ARG69 4.9 25.7 1.0 N A:GLY62 5.0 21.1 1.0

Iron binding site 4 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:20.6 occ:1.00 FE4 A:SF4700 0.0 20.6 1.0 SG B:CYS59 2.2 20.5 1.0 S3 A:SF4700 2.3 16.3 1.0 S2 A:SF4700 2.3 18.7 1.0 S1 A:SF4700 2.4 17.6 1.0 FE1 A:SF4700 2.8 17.4 1.0 FE2 A:SF4700 2.8 19.4 1.0 FE3 A:SF4700 2.8 18.0 1.0 CB B:CYS59 3.1 21.3 1.0 S4 A:SF4700 4.0 16.6 1.0 N B:GLY62 4.2 22.4 1.0 CB B:ILE61 4.5 22.9 1.0 CA B:CYS59 4.6 21.9 1.0 SG A:CYS67 4.7 17.6 1.0 CA B:GLY62 4.7 21.2 1.0 O A:HOH758 4.9 20.0 1.0 CD1 B:ILE61 4.9 25.6 1.0 SG B:CYS67 4.9 18.1 1.0 SG A:CYS59 4.9 20.8 1.0 CG2 B:ILE61 5.0 22.0 1.0 CB B:CYS67 5.0 14.4 1.0

Iron binding site 5 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe750 b:18.9 occ:1.00 FE1 A:SF4750 0.0 18.9 1.0 S3 A:SF4750 2.3 18.2 1.0 S2 A:SF4750 2.3 17.7 1.0 SG A:CYS76 2.3 16.7 1.0 S4 A:SF4750 2.4 19.1 1.0 FE2 A:SF4750 2.7 17.5 1.0 FE4 A:SF4750 2.7 18.4 1.0 FE3 A:SF4750 2.8 17.3 1.0 CB A:CYS76 3.2 18.9 1.0 S1 A:SF4750 3.9 17.4 1.0 N A:ILE89 4.1 16.7 1.0 CA A:CYS76 4.4 20.0 1.0 CA A:GLY74 4.4 18.9 1.0 N A:CYS76 4.4 19.2 1.0 N A:GLY74 4.5 19.4 1.0 CA A:GLY88 4.5 17.5 1.0 SG A:CYS68 4.6 16.8 1.0 CB A:CYS68 4.6 18.0 1.0 O A:CYS68 4.7 16.6 1.0 SG A:CYS90 4.7 17.6 1.0 CB A:ILE89 4.7 16.2 1.0 C A:GLY88 4.7 17.9 1.0 SG A:CYS71 4.8 16.9 1.0 CB A:ALA73 4.8 21.6 1.0 N A:CYS90 4.9 16.7 1.0 CA A:ILE89 4.9 16.2 1.0 C A:ALA73 4.9 20.5 1.0

Iron binding site 6 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe750 b:17.5 occ:1.00 FE2 A:SF4750 0.0 17.5 1.0 S1 A:SF4750 2.2 17.4 1.0 SG A:CYS68 2.3 16.8 1.0 S4 A:SF4750 2.3 19.1 1.0 S3 A:SF4750 2.3 18.2 1.0 FE4 A:SF4750 2.7 18.4 1.0 FE1 A:SF4750 2.7 18.9 1.0 FE3 A:SF4750 2.7 17.3 1.0 CB A:CYS68 3.2 18.0 1.0 NH1 A:ARG100 3.7 14.5 1.0 S2 A:SF4750 3.8 17.7 1.0 N A:PHE70 4.1 17.4 1.0 C A:CYS68 4.3 16.9 1.0 O A:CYS68 4.3 16.6 1.0 CB A:PHE70 4.4 16.6 1.0 CA A:CYS68 4.4 17.6 1.0 N A:CYS71 4.5 16.4 1.0 CZ A:ARG100 4.5 21.4 1.0 CA A:PHE70 4.6 18.7 1.0 N A:ARG69 4.7 15.8 1.0 SG A:CYS76 4.7 16.7 1.0 SG A:CYS90 4.8 17.6 1.0 CB A:CYS76 4.8 18.9 1.0 C A:PHE70 4.8 18.0 1.0 SG A:CYS71 4.9 16.9 1.0

Iron binding site 7 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe750 b:17.3 occ:1.00 FE3 A:SF4750 0.0 17.3 1.0 SG A:CYS71 2.2 16.9 1.0 S4 A:SF4750 2.3 19.1 1.0 S1 A:SF4750 2.4 17.4 1.0 S2 A:SF4750 2.4 17.7 1.0 FE2 A:SF4750 2.7 17.5 1.0 FE4 A:SF4750 2.7 18.4 1.0 FE1 A:SF4750 2.8 18.9 1.0 CB A:CYS71 3.3 14.8 1.0 N A:CYS71 3.6 16.4 1.0 CA A:CYS71 3.8 17.2 1.0 S3 A:SF4750 4.0 18.2 1.0 O A:CYS71 4.1 19.1 1.0 C A:CYS71 4.1 18.5 1.0 CG A:MET221 4.2 12.2 1.0 CB A:ALA73 4.2 21.6 1.0 C A:PHE70 4.4 18.0 1.0 CB A:MET221 4.5 14.2 1.0 N A:GLY74 4.5 19.4 1.0 N A:ALA73 4.6 19.9 1.0 SG A:CYS90 4.7 17.6 1.0 CE B:MET584 4.8 13.2 1.0 SG A:CYS68 4.8 16.8 1.0 CA A:ALA73 4.9 20.1 1.0 N A:PHE70 4.9 17.4 1.0 SG A:CYS76 5.0 16.7 1.0 N A:MET72 5.0 18.1 1.0

Iron binding site 8 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe750 b:18.4 occ:1.00 FE4 A:SF4750 0.0 18.4 1.0 SG A:CYS90 2.3 17.6 1.0 S2 A:SF4750 2.3 17.7 1.0 S1 A:SF4750 2.3 17.4 1.0 S3 A:SF4750 2.3 18.2 1.0 FE2 A:SF4750 2.7 17.5 1.0 FE1 A:SF4750 2.7 18.9 1.0 FE3 A:SF4750 2.7 17.3 1.0 CB A:CYS90 3.4 18.1 1.0 S4 A:SF4750 3.9 19.1 1.0 N A:CYS90 4.0 16.7 1.0 NH1 A:ARG100 4.1 14.5 1.0 CG A:MET221 4.2 12.2 1.0 CA A:CYS90 4.3 19.1 1.0 O A:HOH708 4.4 19.5 1.0 CB A:ALA92 4.5 14.5 1.0 SG A:CYS71 4.7 16.9 1.0 SG A:CYS68 4.7 16.8 1.0 N A:ILE89 4.7 16.7 1.0 NH2 A:ARG100 4.8 17.9 1.0 SG A:CYS76 4.8 16.7 1.0 CZ A:ARG100 4.8 21.4 1.0 CA A:GLY88 4.8 17.5 1.0 C A:GLY88 5.0 17.9 1.0 CB A:MET221 5.0 14.2 1.0

Iron binding site 9 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:21.2 occ:1.00 FE1 A:XCC800 0.0 21.2 1.0 SG A:CYS355 2.3 18.4 1.0 S2 A:XCC800 2.3 21.8 1.0 S3 A:XCC800 2.4 22.7 1.0 S4 A:XCC800 2.4 24.9 1.0 FE3 A:XCC800 2.7 21.9 1.0 FE4 A:XCC800 2.8 22.6 1.0 CB A:CYS355 3.2 18.6 1.0 FE2 A:XCC800 3.4 25.6 1.0 NI A:XCC800 3.7 26.9 1.0 S1 A:XCC800 3.8 22.9 1.0 NZ A:LYS587 3.9 14.0 1.0 NE2 A:HIS283 4.1 15.9 1.0 CE1 A:HIS283 4.1 18.7 1.0 O A:HOH2513 4.2 24.7 1.0 CE A:LYS587 4.6 11.7 1.0 OG A:SER585 4.6 14.8 1.0 CA A:CYS355 4.6 19.0 1.0 SG A:CYS470 4.7 19.1 1.0 CB A:SER585 4.8 17.4 1.0 CD1 A:PHE334 4.9 20.7 1.0 C A:CYN900 5.0 31.2 1.0 SG A:CYS500 5.0 21.0 1.0

Iron binding site 10 out of 56 in the Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cyanide-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase From Moorella Thermoacetica, Cyanide-Bound C-Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:25.6 occ:1.00 FE2 A:XCC800 0.0 25.6 1.0 O A:HOH2513 2.1 24.7 1.0 NE2 A:HIS283 2.2 15.9 1.0 S3 A:XCC800 2.3 22.7 1.0 SG A:CYS317 2.3 23.4 1.0 CD2 A:HIS283 3.0 14.4 1.0 NI A:XCC800 3.1 26.9 1.0 SG A:CYS550 3.2 24.0 1.0 CE1 A:HIS283 3.3 18.7 1.0 CB A:CYS317 3.3 21.6 1.0 FE1 A:XCC800 3.4 21.2 1.0 S4 A:XCC800 3.7 24.9 1.0 NZ A:LYS587 3.8 14.0 1.0 CB A:CYS550 3.9 19.5 1.0 FE4 A:XCC800 4.0 22.6 1.0 S1 A:XCC800 4.1 22.9 1.0 CG A:HIS283 4.2 20.3 1.0 O A:HOH709 4.2 22.7 1.0 N A:CYS317 4.2 21.0 1.0 O A:HOH710 4.2 27.4 1.0 ND1 A:HIS283 4.3 16.5 1.0 N A:CYN900 4.3 32.2 1.0 CA A:CYS317 4.3 20.7 1.0 O A:HOH693 4.3 22.7 1.0 C A:CYN900 4.4 31.2 1.0 FE3 A:XCC800 4.7 21.9 1.0 N A:CYS550 4.7 20.7 1.0 SG A:CYS355 4.7 18.4 1.0 CA A:CYS550 5.0 20.7 1.0 CE A:LYS587 5.0 11.7 1.0

Y.Kung, T.I.Doukov, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Crystallographic Snapshots of Cyanide- and Water-Bound C-Clusters From Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase. Biochemistry V. 48 7432 2009.
ISSN: ISSN 0006-2960
PubMed: 19583207
DOI: 10.1021/BI900574H