Iron in PDB 8tc3: Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii

The binding sites of Iron atom in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii (pdb code 8tc3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii, PDB code: 8tc3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:12.4 occ:1.00 FE1 B:SF4601 0.0 12.4 1.0 SG A:CYS97 2.3 16.7 1.0 S3 B:SF4601 2.3 9.7 1.0 S4 B:SF4601 2.3 9.2 1.0 S2 B:SF4601 2.3 9.8 1.0 FE2 B:SF4601 2.7 9.5 1.0 FE4 B:SF4601 2.7 12.3 1.0 FE3 B:SF4601 2.7 10.3 1.0 CB A:CYS97 3.3 19.8 1.0 CA A:CYS97 3.8 22.0 1.0 S1 B:SF4601 3.9 9.6 1.0 CA A:GLY134 4.2 15.1 1.0 N A:ALA98 4.2 27.6 1.0 N A:GLY134 4.4 13.7 1.0 C A:CYS97 4.5 24.8 1.0 SG A:CYS132 4.7 12.4 1.0 SG B:CYS97 4.8 19.3 1.0 CB B:CYS132 4.8 17.4 1.0 SG B:CYS132 4.8 17.1 1.0 N A:GLY99 4.9 31.5 1.0 N A:CYS97 5.0 27.2 1.0

Iron binding site 2 out of 4 in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:9.5 occ:1.00 FE2 B:SF4601 0.0 9.5 1.0 SG A:CYS132 2.3 12.4 1.0 S3 B:SF4601 2.3 9.7 1.0 S4 B:SF4601 2.3 9.2 1.0 S1 B:SF4601 2.3 9.6 1.0 FE1 B:SF4601 2.7 12.4 1.0 FE4 B:SF4601 2.7 12.3 1.0 FE3 B:SF4601 2.7 10.3 1.0 CB A:CYS132 3.2 13.4 1.0 S2 B:SF4601 3.9 9.8 1.0 N A:GLY134 4.0 13.7 1.0 CA A:GLY134 4.4 15.1 1.0 CA A:CYS132 4.5 13.5 1.0 N B:ALA98 4.6 29.0 1.0 CA B:CYS97 4.6 25.1 1.0 SG A:CYS97 4.7 16.7 1.0 N A:GLY133 4.7 10.6 1.0 SG B:CYS132 4.7 17.1 1.0 CD2 A:PHE135 4.8 36.7 1.0 SG B:CYS97 4.8 19.3 1.0 C A:CYS132 4.8 11.9 1.0 N A:PHE135 4.9 20.1 1.0 CB B:CYS97 4.9 21.6 1.0

Iron binding site 3 out of 4 in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:10.3 occ:1.00 FE3 B:SF4601 0.0 10.3 1.0 SG B:CYS97 2.3 19.3 1.0 S1 B:SF4601 2.3 9.6 1.0 S2 B:SF4601 2.3 9.8 1.0 S4 B:SF4601 2.3 9.2 1.0 FE4 B:SF4601 2.7 12.3 1.0 FE1 B:SF4601 2.7 12.4 1.0 FE2 B:SF4601 2.7 9.5 1.0 CB B:CYS97 3.0 21.6 1.0 CA B:CYS97 3.5 25.1 1.0 N B:ALA98 3.8 29.0 1.0 S3 B:SF4601 3.9 9.7 1.0 C B:CYS97 4.0 28.4 1.0 CA B:GLY134 4.1 18.7 1.0 N B:GLY134 4.4 18.4 1.0 N B:GLY99 4.5 33.9 1.0 SG B:CYS132 4.8 17.1 1.0 SG A:CYS97 4.8 16.7 1.0 SG A:CYS132 4.8 12.4 1.0 N B:CYS97 4.9 29.9 1.0 CA B:ALA98 4.9 35.7 1.0

Iron binding site 4 out of 4 in the Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Nucleotide-Free Form of the Nitrogenase Iron Protein From A. Vinelandii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:12.3 occ:1.00 FE4 B:SF4601 0.0 12.3 1.0 SG B:CYS132 2.3 17.1 1.0 S2 B:SF4601 2.3 9.8 1.0 S3 B:SF4601 2.3 9.7 1.0 S1 B:SF4601 2.3 9.6 1.0 FE3 B:SF4601 2.7 10.3 1.0 FE1 B:SF4601 2.7 12.4 1.0 FE2 B:SF4601 2.7 9.5 1.0 CB B:CYS132 3.0 17.4 1.0 S4 B:SF4601 3.9 9.2 1.0 N B:GLY134 4.0 18.4 1.0 CA B:GLY134 4.3 18.7 1.0 CA B:CYS132 4.4 18.1 1.0 N B:PHE135 4.6 22.5 1.0 N B:GLY133 4.7 18.1 1.0 C B:CYS132 4.7 19.1 1.0 SG B:CYS97 4.7 19.3 1.0 CD2 B:PHE135 4.7 37.0 1.0 SG A:CYS132 4.7 12.4 1.0 SG A:CYS97 4.8 16.7 1.0 C B:GLY134 5.0 20.7 1.0

R.A.Warmack, B.B.Wenke, T.Spatzal, D.C.Rees. Anaerobic Cryoem Protocols For Air-Sensitive Nitrogenase Proteins. Nat Protoc 2024.
ISSN: ESSN 1750-2799
PubMed: 38575747
DOI: 10.1038/S41596-024-00973-5