Iron in PDB 4ci0: Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh

All present enzymatic activity of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh:
1.12.98.1;

The structure of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Zinc	(Zn)	1 atom

Pages:

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

Binding sites:

The binding sites of Iron atom in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh (pdb code 4ci0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh, PDB code: 4ci0:
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 Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1387 b:23.8 occ:1.00 SG A:CYS66 2.2 20.0 1.0 SG A:CYS383 2.4 20.0 1.0 NI A:NI1388 2.5 24.9 1.0 CB A:CYS66 3.1 20.0 1.0 CD A:PRO350 3.4 20.0 1.0 CB A:CYS383 3.6 20.0 1.0 CG1 A:VAL349 3.8 20.0 1.0 CB A:ALA326 3.9 20.0 1.0 CE1 A:HIS70 4.0 20.0 1.0 NE2 A:HIS70 4.1 20.0 1.0 CG A:PRO350 4.1 20.0 1.0 SG A:CYS380 4.3 20.0 1.0 SG A:CYS63 4.5 20.0 1.0 CG A:ARG328 4.5 20.0 1.0 CD A:PRO327 4.5 20.0 1.0 CA A:CYS66 4.6 14.8 1.0 O A:CYS66 4.6 22.9 1.0 N A:PRO350 4.7 18.9 1.0 ND1 A:HIS70 4.8 20.0 1.0 CG A:PRO69 4.9 20.0 1.0 CB A:VAL349 4.9 20.0 1.0 CB A:ARG328 4.9 20.0 1.0 CB A:CYS63 4.9 20.0 1.0 CB A:PRO350 4.9 20.0 1.0 CA A:CYS383 5.0 19.1 1.0

Iron binding site 2 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1389 b:27.1 occ:1.00 O A:ALA347 2.2 22.2 1.0 NE2 A:HIS386 2.2 18.0 1.0 OE2 A:GLU44 2.3 20.0 1.0 OE1 A:GLU44 2.6 20.0 1.0 CD A:GLU44 2.6 20.0 1.0 CE1 A:HIS386 2.9 17.1 1.0 CD2 A:HIS386 3.4 20.8 1.0 C A:ALA347 3.4 15.2 1.0 CG A:GLU44 3.9 20.0 1.0 N A:ALA347 4.0 18.0 1.0 OE2 A:GLU229 4.1 20.0 1.0 ND1 A:HIS386 4.2 19.6 1.0 CA A:ALA347 4.2 17.6 1.0 N A:LEU348 4.4 17.5 1.0 CG A:HIS386 4.4 21.9 1.0 CA A:LEU348 4.6 18.3 1.0 CB A:ALA347 4.6 20.0 1.0 OE1 A:GLU229 4.9 20.0 1.0 CD A:GLU229 5.0 20.0 1.0 OG A:SER346 5.0 20.0 1.0

Iron binding site 3 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1274 b:20.0 occ:1.00 FE1 B:SF41274 0.0 20.0 1.0 SG B:CYS57 2.1 19.8 1.0 S4 B:SF41274 2.3 20.0 1.0 S2 B:SF41274 2.3 20.0 1.0 S3 B:SF41274 2.3 20.0 1.0 CB B:CYS57 2.4 18.7 1.0 FE3 B:SF41274 2.7 20.0 1.0 FE4 B:SF41274 2.7 20.0 1.0 FE2 B:SF41274 2.7 20.0 1.0 N B:CYS57 3.1 20.1 1.0 CA B:CYS57 3.3 18.8 1.0 S1 B:SF41274 3.9 20.0 1.0 N B:THR58 3.9 18.6 1.0 C B:CYS57 3.9 19.1 1.0 OD1 B:ASP60 3.9 20.0 1.0 N B:GLY59 4.1 2.9 1.0 SG B:CYS171 4.2 19.4 1.0 NE2 A:HIS150 4.3 20.0 1.0 C B:GLY56 4.3 20.6 1.0 CE1 A:HIS150 4.4 20.0 1.0 SG B:CYS132 4.4 20.0 1.0 CG B:ASP60 4.8 20.0 1.0 CA B:GLY59 4.8 2.9 1.0 O A:ARG61 4.8 19.3 1.0 CA B:GLY56 4.8 20.2 1.0 OD2 B:ASP60 4.8 20.0 1.0 O B:CYS57 4.9 18.5 1.0 CG A:ARG61 4.9 20.0 1.0

Iron binding site 4 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1274 b:20.0 occ:1.00 FE2 B:SF41274 0.0 20.0 1.0 SG B:CYS132 2.1 20.0 1.0 S3 B:SF41274 2.3 20.0 1.0 S4 B:SF41274 2.3 20.0 1.0 S1 B:SF41274 2.3 20.0 1.0 CB B:CYS132 2.5 20.0 1.0 FE3 B:SF41274 2.7 20.0 1.0 FE1 B:SF41274 2.7 20.0 1.0 FE4 B:SF41274 2.7 20.0 1.0 CA B:CYS132 3.6 17.8 1.0 N B:CYS132 3.6 17.2 1.0 S2 B:SF41274 3.9 20.0 1.0 OD2 B:ASP60 4.1 20.0 1.0 N B:CYS57 4.2 20.1 1.0 OD1 B:ASP60 4.3 20.0 1.0 O B:GLU102 4.4 21.7 1.0 SG B:CYS171 4.5 19.4 1.0 SG B:CYS137 4.6 20.0 1.0 CA B:GLY56 4.6 20.2 1.0 CG B:ASP60 4.7 20.0 1.0 CB B:CYS137 4.7 20.0 1.0 CB B:CYS57 4.7 18.7 1.0 SG B:CYS57 4.8 19.8 1.0 C B:CYS132 4.8 16.6 1.0 C B:SER131 4.8 18.1 1.0 C B:GLY56 5.0 20.6 1.0

Iron binding site 5 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1274 b:20.0 occ:1.00 FE3 B:SF41274 0.0 20.0 1.0 SG B:CYS171 2.2 19.4 1.0 S1 B:SF41274 2.3 20.0 1.0 S2 B:SF41274 2.3 20.0 1.0 S4 B:SF41274 2.3 20.0 1.0 FE1 B:SF41274 2.7 20.0 1.0 FE2 B:SF41274 2.7 20.0 1.0 FE4 B:SF41274 2.7 20.0 1.0 CB B:CYS171 3.1 19.5 1.0 CA B:CYS171 3.4 18.2 1.0 S3 B:SF41274 3.9 20.0 1.0 C B:CYS171 4.0 18.9 1.0 SG B:CYS57 4.2 19.8 1.0 SG B:CYS137 4.3 20.0 1.0 OD2 B:ASP60 4.3 20.0 1.0 SG B:CYS132 4.3 20.0 1.0 O B:GLY170 4.4 16.7 1.0 N B:PRO172 4.5 17.6 1.0 O B:CYS171 4.5 19.1 1.0 CA B:PRO172 4.6 17.8 1.0 N B:CYS171 4.6 18.8 1.0 OD1 B:ASP60 4.7 20.0 1.0 N B:CYS132 4.7 17.2 1.0 CG B:ASP60 4.8 20.0 1.0 CB B:CYS132 4.9 20.0 1.0 N B:SER131 4.9 17.2 1.0 C B:GLY170 5.0 17.1 1.0

Iron binding site 6 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1274 b:20.0 occ:1.00 FE4 B:SF41274 0.0 20.0 1.0 OD1 B:ASP60 2.0 20.0 1.0 OD2 B:ASP60 2.1 20.0 1.0 CG B:ASP60 2.3 20.0 1.0 S1 B:SF41274 2.3 20.0 1.0 S3 B:SF41274 2.3 20.0 1.0 S2 B:SF41274 2.3 20.0 1.0 FE1 B:SF41274 2.7 20.0 1.0 FE2 B:SF41274 2.7 20.0 1.0 FE3 B:SF41274 2.7 20.0 1.0 N B:ASP60 3.7 3.1 1.0 CB B:ASP60 3.7 20.0 1.0 S4 B:SF41274 3.9 20.0 1.0 SG B:CYS57 4.0 19.8 1.0 CA B:ASP60 4.2 3.1 1.0 N B:GLY59 4.2 2.9 1.0 CG B:GLU102 4.3 20.0 1.0 O B:GLU102 4.4 21.7 1.0 N B:THR58 4.6 18.6 1.0 CB B:CYS132 4.6 20.0 1.0 C B:GLY59 4.6 2.9 1.0 N B:CYS57 4.6 20.1 1.0 CA B:GLY59 4.6 2.9 1.0 CA B:GLY130 4.7 16.0 1.0 SG B:CYS132 4.8 20.0 1.0 CA B:PRO172 4.8 17.8 1.0 SG B:CYS171 4.9 19.4 1.0 CB B:CYS57 4.9 18.7 1.0 N B:CYS132 4.9 17.2 1.0 CD B:GLU102 4.9 20.0 1.0

Iron binding site 7 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1275 b:8.7 occ:1.00 FE1 B:SF41275 0.0 8.7 1.0 S4 B:SF41275 2.2 8.3 1.0 SG B:CYS249 2.2 9.2 1.0 S2 B:SF41275 2.2 8.8 1.0 S3 B:SF41275 2.3 7.9 1.0 FE4 B:SF41275 2.7 8.7 1.0 FE3 B:SF41275 2.7 9.6 1.0 FE2 B:SF41275 2.7 9.6 1.0 CB B:CYS249 3.2 10.8 1.0 CA B:CYS249 3.7 10.8 1.0 S1 B:SF41275 3.8 8.4 1.0 N B:ILE250 4.0 11.3 1.0 N B:LYS251 4.0 11.4 1.0 CA B:GLY207 4.1 30.0 1.0 C B:CYS249 4.2 11.0 1.0 CB B:ALA234 4.4 20.0 1.0 N B:GLY207 4.4 30.0 1.0 CA B:LYS251 4.7 11.5 1.0 SG B:CYS255 4.7 9.4 1.0 SG B:CYS252 4.7 10.8 1.0 SG B:CYS230 4.7 8.3 1.0 N B:CYS252 4.8 9.6 1.0 CD1 B:LEU235 4.9 20.0 1.0 C B:ILE250 5.0 11.2 1.0

Iron binding site 8 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1275 b:9.6 occ:1.00 FE2 B:SF41275 0.0 9.6 1.0 S1 B:SF41275 2.1 8.4 1.0 SG B:CYS252 2.2 10.8 1.0 S4 B:SF41275 2.2 8.3 1.0 S3 B:SF41275 2.2 7.9 1.0 FE3 B:SF41275 2.6 9.6 1.0 FE4 B:SF41275 2.6 8.7 1.0 FE1 B:SF41275 2.7 8.7 1.0 CB B:CYS252 3.6 10.2 1.0 N B:CYS252 3.7 9.6 1.0 S2 B:SF41275 3.8 8.8 1.0 N B:GLY253 3.9 11.2 1.0 CA B:CYS252 4.2 10.8 1.0 N B:ILE254 4.3 11.4 1.0 CG1 B:ILE250 4.4 11.0 1.0 SG B:CYS230 4.5 8.3 1.0 C B:CYS252 4.5 11.1 1.0 SG B:CYS249 4.5 9.2 1.0 SG B:CYS255 4.5 9.4 1.0 N B:LYS251 4.7 11.4 1.0 OG1 B:THR232 4.7 20.0 1.0 CA B:GLY253 4.8 11.6 1.0 CB B:ILE254 4.8 20.0 1.0 C B:LYS251 4.8 10.5 1.0 N B:CYS255 4.8 9.4 1.0 C B:GLY253 4.9 11.3 1.0 CG1 B:ILE254 5.0 20.0 1.0

Iron binding site 9 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1275 b:9.6 occ:1.00 FE3 B:SF41275 0.0 9.6 1.0 SG B:CYS230 2.2 8.3 1.0 S2 B:SF41275 2.2 8.8 1.0 S4 B:SF41275 2.3 8.3 1.0 S1 B:SF41275 2.3 8.4 1.0 FE2 B:SF41275 2.6 9.6 1.0 FE1 B:SF41275 2.7 8.7 1.0 FE4 B:SF41275 2.7 8.7 1.0 CB B:CYS230 3.4 10.1 1.0 S3 B:SF41275 3.8 7.9 1.0 CA B:CYS230 4.0 10.7 1.0 CB B:ALA234 4.1 20.0 1.0 CB B:THR232 4.2 20.0 1.0 N B:LEU235 4.3 10.6 1.0 N B:ALA234 4.3 13.9 1.0 CD1 B:LEU235 4.6 20.0 1.0 OG1 B:THR232 4.6 20.0 1.0 SG B:CYS252 4.6 10.8 1.0 N B:THR232 4.7 12.7 1.0 CA B:ALA234 4.7 12.9 1.0 N B:ARG233 4.7 14.0 1.0 C B:CYS230 4.7 11.6 1.0 CB B:LEU235 4.8 20.0 1.0 SG B:CYS255 4.8 9.4 1.0 SG B:CYS249 4.8 9.2 1.0 N B:GLN231 4.9 11.2 1.0 CA B:THR232 5.0 12.8 1.0 O B:ALA229 5.0 13.0 1.0 C B:ALA234 5.0 12.0 1.0

Iron binding site 10 out of 18 in the Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Electron Cryo-Microscopy of F420-Reducing Nife Hydrogenase Frh within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1275 b:8.7 occ:1.00 FE4 B:SF41275 0.0 8.7 1.0 S3 B:SF41275 2.1 7.9 1.0 S1 B:SF41275 2.2 8.4 1.0 SG B:CYS255 2.2 9.4 1.0 S2 B:SF41275 2.3 8.8 1.0 FE2 B:SF41275 2.6 9.6 1.0 FE1 B:SF41275 2.7 8.7 1.0 FE3 B:SF41275 2.7 9.6 1.0 CB B:CYS255 3.2 7.9 1.0 S4 B:SF41275 3.8 8.3 1.0 N B:CYS255 3.9 9.4 1.0 CD1 B:LEU235 4.1 20.0 1.0 CA B:GLY207 4.1 30.0 1.0 CA B:CYS255 4.2 9.1 1.0 SG B:CYS252 4.4 10.8 1.0 SG B:CYS249 4.5 9.2 1.0 SG B:CYS230 4.8 8.3 1.0 N B:ILE254 4.8 11.4 1.0 N B:GLY253 4.8 11.2 1.0 N B:GLY207 4.8 30.0 1.0

M.Allegretti, D.J.Mills, G.Mcmullan, W.Kuehlbrandt, J.Vonck. Atomic Model of the F420-Reducing [Nife] Hydrogenase By Electron Cryo-Electron Microscopy Using A Direct Electron Detector. Elife V. 3 01963 2014.
ISSN: ISSN 2050-084X
PubMed: 24569482
DOI: 10.7554/ELIFE.01963