Iron in PDB 3zfs: Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate

All present enzymatic activity of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate:
1.12.98.1;

The structure of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate (pdb code 3zfs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate, PDB code: 3zfs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2989 b:23.8 occ:1.00 NI A:NI2990 2.5 24.9 1.0 CA A:CYS383 4.8 19.1 1.0 CA A:CYS66 4.9 14.8 1.0

Iron binding site 2 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2991 b:27.1 occ:1.00 CA A:ALA347 3.8 17.6 1.0 CA A:LEU348 4.1 18.3 1.0 CA A:SER346 4.6 17.4 1.0

Iron binding site 3 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:20.0 occ:1.00 FE1 B:SF4300 0.0 20.0 1.0 S4 B:SF4300 2.3 20.0 1.0 S2 B:SF4300 2.3 20.0 1.0 S3 B:SF4300 2.3 20.0 1.0 FE3 B:SF4300 2.7 20.0 1.0 FE4 B:SF4300 2.7 20.0 1.0 FE2 B:SF4300 2.7 20.0 1.0 CA B:CYS57 3.8 18.8 1.0 S1 B:SF4300 3.9 20.0 1.0 CA B:GLY59 4.0 2.9 1.0 CA B:GLY56 4.8 20.2 1.0

Iron binding site 4 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:20.0 occ:1.00 FE2 B:SF4300 0.0 20.0 1.0 S1 B:SF4300 2.3 20.0 1.0 S4 B:SF4300 2.3 20.0 1.0 S3 B:SF4300 2.3 20.0 1.0 FE3 B:SF4300 2.7 20.0 1.0 FE4 B:SF4300 2.7 20.0 1.0 FE1 B:SF4300 2.7 20.0 1.0 CA B:CYS132 3.5 17.8 1.0 S2 B:SF4300 3.9 20.0 1.0 CA B:GLY56 4.4 20.2 1.0

Iron binding site 5 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:20.0 occ:1.00 FE3 B:SF4300 0.0 20.0 1.0 S1 B:SF4300 2.3 20.0 1.0 S4 B:SF4300 2.3 20.0 1.0 S2 B:SF4300 2.3 20.0 1.0 FE1 B:SF4300 2.7 20.0 1.0 FE2 B:SF4300 2.7 20.0 1.0 FE4 B:SF4300 2.7 20.0 1.0 CA B:CYS171 3.6 18.2 1.0 S3 B:SF4300 3.9 20.0 1.0 CA B:PRO172 4.7 17.8 1.0

Iron binding site 6 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:20.0 occ:1.00 FE4 B:SF4300 0.0 20.0 1.0 S1 B:SF4300 2.3 20.0 1.0 S2 B:SF4300 2.3 20.0 1.0 S3 B:SF4300 2.3 20.0 1.0 FE1 B:SF4300 2.7 20.0 1.0 FE2 B:SF4300 2.7 20.0 1.0 FE3 B:SF4300 2.7 20.0 1.0 CA B:GLY59 3.6 2.9 1.0 S4 B:SF4300 3.9 20.0 1.0 CA B:ASP60 4.5 3.1 1.0 CA B:GLY130 4.6 16.0 1.0 CA B:PRO172 4.9 17.8 1.0

Iron binding site 7 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:20.0 occ:1.00 FE1 B:SF4301 0.0 20.0 1.0 S4 B:SF4301 2.3 20.0 1.0 S3 B:SF4301 2.3 20.0 1.0 S2 B:SF4301 2.3 20.0 1.0 FE3 B:SF4301 2.7 20.0 1.0 FE4 B:SF4301 2.7 20.0 1.0 FE2 B:SF4301 2.7 20.0 1.0 CA B:CYS252 3.7 10.8 1.0 CA B:ILE254 3.7 12.5 1.0 S1 B:SF4301 3.9 20.0 1.0 CA B:CYS255 4.3 9.1 1.0 CA B:GLY253 4.4 11.6 1.0 CA B:CYS230 4.8 10.7 1.0

Iron binding site 8 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:20.0 occ:1.00 FE2 B:SF4301 0.0 20.0 1.0 S1 B:SF4301 2.3 20.0 1.0 S4 B:SF4301 2.3 20.0 1.0 S3 B:SF4301 2.3 20.0 1.0 FE3 B:SF4301 2.7 20.0 1.0 FE1 B:SF4301 2.7 20.0 1.0 FE4 B:SF4301 2.7 20.0 1.0 CA B:LYS251 3.0 11.5 1.0 CA B:CYS249 3.5 10.8 1.0 S2 B:SF4301 3.9 20.0 1.0 CA B:CYS252 4.0 10.8 1.0 CA B:ILE250 4.7 11.0 1.0

Iron binding site 9 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:20.0 occ:1.00 FE3 B:SF4301 0.0 20.0 1.0 S2 B:SF4301 2.3 20.0 1.0 S4 B:SF4301 2.3 20.0 1.0 S1 B:SF4301 2.3 20.0 1.0 FE1 B:SF4301 2.7 20.0 1.0 FE2 B:SF4301 2.7 20.0 1.0 FE4 B:SF4301 2.7 20.0 1.0 S3 B:SF4301 3.9 20.0 1.0 CA B:CYS230 4.2 10.7 1.0 CA B:CYS249 4.7 10.8 1.0

Iron binding site 10 out of 18 in the Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of the F420-Reducing Nife-Hydrogenase From A Methanogenic Archaeon with Bound Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:20.0 occ:1.00 FE4 B:SF4301 0.0 20.0 1.0 S3 B:SF4301 2.3 20.0 1.0 S2 B:SF4301 2.3 20.0 1.0 S1 B:SF4301 2.3 20.0 1.0 FE1 B:SF4301 2.7 20.0 1.0 FE2 B:SF4301 2.7 20.0 1.0 FE3 B:SF4301 2.7 20.0 1.0 S4 B:SF4301 3.9 20.0 1.0 CA B:CYS255 4.6 9.1 1.0

D.J.Mills, S.Vitt, M.Strauss, S.Shima, J.Vonck. De Novo Modeling of the F420-Reducing [Nife]-Hydrogenase From A Methanogenic Archaeon By Cryo-Electron Microscopy Elife V. 2 218 2013.
ISSN: ESSN 2050-084X
PubMed: 23483797
DOI: 10.7554/ELIFE.00218