Iron in PDB 1frv: Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase

All present enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase:
1.12.2.1;

The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 1frv was solved by A.Volbeda, M.Frey, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.600, 93.900, 69.200, 89.80, 102.90, 90.80
R / Rfree (%)	17.8 / n/a

The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase (pdb code 1frv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 1frv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:11.8 occ:1.00 FE1 A:SF4265 0.0 11.8 1.0 S3 A:SF4265 2.3 13.9 1.0 S4 A:SF4265 2.3 13.7 1.0 SG A:CYS219 2.3 11.4 1.0 S2 A:SF4265 2.3 11.8 1.0 FE2 A:SF4265 2.7 11.8 1.0 FE3 A:SF4265 2.7 15.1 1.0 FE4 A:SF4265 2.7 15.5 1.0 CB A:CYS219 3.4 11.1 1.0 S1 A:SF4265 3.9 13.1 1.0 N A:GLY221 4.3 7.7 1.0 CD A:PRO222 4.4 11.9 1.0 CA A:GLY221 4.5 8.6 1.0 ND1 A:HIS185 4.5 16.1 1.0 CA A:CYS219 4.6 9.6 1.0 N A:TYR215 4.6 14.6 1.0 SG A:CYS213 4.7 14.1 1.0 CB A:LEU214 4.7 10.7 1.0 C A:CYS219 4.7 9.8 1.0 N A:LEU214 4.8 12.8 1.0 SG A:CYS188 4.9 11.5 1.0 C A:LEU214 4.9 14.7 1.0 N A:LYS220 5.0 8.3 1.0 CA A:LEU214 5.0 13.4 1.0

Iron binding site 2 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:11.8 occ:1.00 FE2 A:SF4265 0.0 11.8 1.0 S4 A:SF4265 2.3 13.7 1.0 S1 A:SF4265 2.3 13.1 1.0 SG A:CYS188 2.3 11.5 1.0 S3 A:SF4265 2.3 13.9 1.0 FE1 A:SF4265 2.7 11.8 1.0 FE3 A:SF4265 2.7 15.1 1.0 FE4 A:SF4265 2.8 15.5 1.0 CB A:CYS188 3.2 14.7 1.0 S2 A:SF4265 3.9 11.8 1.0 CG1 A:VAL240 4.2 11.1 1.0 CB A:ARG190 4.3 10.5 1.0 CA A:CYS188 4.6 17.2 1.0 SG A:CYS219 4.7 11.4 1.0 ND1 A:HIS185 4.7 16.1 1.0 CG A:ARG190 4.8 8.5 1.0 C A:ARG190 4.8 13.7 1.0 O A:ARG190 4.9 14.1 1.0 CA A:HIS185 4.9 19.5 1.0 CH2 A:TRP238 4.9 19.3 1.0 N A:ARG190 4.9 14.3 1.0 CG2 A:VAL240 4.9 13.0 1.0 CA A:ARG190 4.9 12.7 1.0 SG A:CYS213 5.0 14.1 1.0 C A:CYS188 5.0 17.6 1.0

Iron binding site 3 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:15.1 occ:1.00 FE3 A:SF4265 0.0 15.1 1.0 S2 A:SF4265 2.3 11.8 1.0 S1 A:SF4265 2.3 13.1 1.0 S4 A:SF4265 2.3 13.7 1.0 SG A:CYS213 2.4 14.1 1.0 FE4 A:SF4265 2.7 15.5 1.0 FE2 A:SF4265 2.7 11.8 1.0 FE1 A:SF4265 2.7 11.8 1.0 CB A:CYS213 3.4 13.5 1.0 N A:LEU214 3.9 12.8 1.0 S3 A:SF4265 3.9 13.9 1.0 O A:ARG190 4.1 14.1 1.0 CA A:CYS213 4.1 13.3 1.0 CD1 A:PHE194 4.2 7.8 1.0 N A:TYR215 4.2 14.6 1.0 CB A:PHE194 4.3 9.9 1.0 ND1 A:HIS185 4.4 16.1 1.0 C A:CYS213 4.5 13.1 1.0 CB A:ARG190 4.5 10.5 1.0 CE1 A:HIS185 4.6 15.8 1.0 CG A:PHE194 4.6 8.4 1.0 C A:ARG190 4.7 13.7 1.0 CA A:LEU214 4.8 13.4 1.0 SG A:CYS188 4.8 11.5 1.0 SG A:CYS219 4.9 11.4 1.0 C A:LEU214 4.9 14.7 1.0 CA A:TYR215 5.0 14.4 1.0

Iron binding site 4 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:15.5 occ:1.00 FE4 A:SF4265 0.0 15.5 1.0 ND1 A:HIS185 2.0 16.1 1.0 S1 A:SF4265 2.3 13.1 1.0 S2 A:SF4265 2.3 11.8 1.0 S3 A:SF4265 2.3 13.9 1.0 FE3 A:SF4265 2.7 15.1 1.0 FE1 A:SF4265 2.7 11.8 1.0 FE2 A:SF4265 2.8 11.8 1.0 CE1 A:HIS185 2.9 15.8 1.0 CG A:HIS185 3.0 17.2 1.0 CB A:HIS185 3.5 17.8 1.0 CA A:HIS185 3.8 19.5 1.0 S4 A:SF4265 3.9 13.7 1.0 NE2 A:HIS185 3.9 16.5 1.0 CD2 A:HIS185 4.0 16.9 1.0 CD A:PRO222 4.2 11.9 1.0 CG A:PRO222 4.4 12.3 1.0 N A:PRO222 4.6 11.5 1.0 SG A:CYS188 4.7 11.5 1.0 SG A:CYS213 4.7 14.1 1.0 CA A:GLY221 4.7 8.6 1.0 O A:HIS185 4.8 20.1 1.0 C A:HIS185 4.8 20.0 1.0 SG A:CYS219 4.8 11.4 1.0 CB A:CYS188 4.8 14.7 1.0 CD1 A:PHE194 4.8 7.8 1.0 N A:HIS185 4.9 20.0 1.0 C A:GLY221 4.9 10.5 1.0 CG A:PHE194 5.0 8.4 1.0

Iron binding site 5 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:15.7 occ:1.00 FE1 A:F3S266 0.0 15.7 1.0 S1 A:F3S266 2.3 13.0 1.0 S2 A:F3S266 2.3 13.5 1.0 S3 A:F3S266 2.3 10.5 1.0 SG A:CYS246 2.4 13.8 1.0 FE3 A:F3S266 2.7 12.6 1.0 FE4 A:F3S266 2.8 13.7 1.0 CB A:CYS246 3.4 13.6 1.0 CA A:CYS246 3.8 13.1 1.0 S4 A:F3S266 3.9 11.7 1.0 N A:ILE247 4.2 13.8 1.0 CG2 A:VAL184 4.3 20.8 1.0 C A:CYS246 4.4 13.2 1.0 N A:ALA248 4.6 14.2 1.0 SG A:CYS228 4.7 12.7 1.0 CG2 A:THR224 4.7 7.3 1.0 CG A:PRO239 4.8 13.4 1.0 NE2 B:GLN221 5.0 8.9 1.0 SG A:CYS249 5.0 12.9 1.0

Iron binding site 6 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:12.6 occ:1.00 FE3 A:F3S266 0.0 12.6 1.0 S1 A:F3S266 2.3 13.0 1.0 S4 A:F3S266 2.3 11.7 1.0 S3 A:F3S266 2.3 10.5 1.0 SG A:CYS249 2.3 12.9 1.0 FE1 A:F3S266 2.7 15.7 1.0 FE4 A:F3S266 2.7 13.7 1.0 CB A:CYS249 3.4 13.9 1.0 N A:CYS249 3.8 15.2 1.0 S2 A:F3S266 3.9 13.5 1.0 CA A:CYS249 4.0 15.0 1.0 C A:CYS249 4.6 15.2 1.0 SG A:CYS246 4.6 13.8 1.0 ND2 A:ASN226 4.7 9.7 1.0 SG A:CYS228 4.8 12.7 1.0 N A:SER250 4.8 15.1 1.0 C A:ALA248 4.9 15.5 1.0 N A:ALA248 5.0 14.2 1.0

Iron binding site 7 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:13.7 occ:1.00 FE4 A:F3S266 0.0 13.7 1.0 S4 A:F3S266 2.3 11.7 1.0 S3 A:F3S266 2.3 10.5 1.0 S2 A:F3S266 2.3 13.5 1.0 SG A:CYS228 2.3 12.7 1.0 FE3 A:F3S266 2.7 12.6 1.0 FE1 A:F3S266 2.8 15.7 1.0 CB A:CYS228 3.4 12.9 1.0 CZ A:PHE233 3.9 14.2 1.0 CE2 A:PHE233 3.9 14.7 1.0 S1 A:F3S266 3.9 13.0 1.0 ND2 A:ASN226 4.1 9.7 1.0 CG2 A:VAL184 4.5 20.8 1.0 CG A:ASN226 4.5 10.3 1.0 SG A:CYS249 4.6 12.9 1.0 CB A:ASN226 4.7 9.6 1.0 CG A:PRO239 4.7 13.4 1.0 CD A:PRO239 4.7 13.7 1.0 CA A:CYS228 4.8 12.8 1.0

Iron binding site 8 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:9.7 occ:1.00 FE1 A:SF4267 0.0 9.7 1.0 S4 A:SF4267 2.3 8.8 1.0 SG A:CYS17 2.3 8.4 1.0 S2 A:SF4267 2.3 12.0 1.0 S3 A:SF4267 2.3 11.2 1.0 FE3 A:SF4267 2.7 8.8 1.0 FE4 A:SF4267 2.8 10.1 1.0 FE2 A:SF4267 2.8 4.8 1.0 CB A:CYS17 3.4 9.4 1.0 N A:GLY19 3.8 6.1 1.0 S1 A:SF4267 4.0 9.3 1.0 CA A:GLY19 4.0 7.3 1.0 NE2 B:HIS219 4.0 13.1 1.0 N A:CYS17 4.1 7.6 1.0 CA A:CYS17 4.2 7.6 1.0 C A:CYS17 4.4 6.7 1.0 CD2 B:HIS219 4.6 13.5 1.0 N A:THR18 4.6 7.2 1.0 SG A:CYS148 4.7 4.8 1.0 N A:CYS20 4.8 9.2 1.0 O A:CYS17 4.8 6.0 1.0 SG A:CYS112 4.9 9.2 1.0 CG B:ARG63 4.9 4.1 1.0 C A:GLY19 5.0 8.7 1.0 SG A:CYS20 5.0 8.8 1.0

Iron binding site 9 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:4.8 occ:1.00 FE2 A:SF4267 0.0 4.8 1.0 S1 A:SF4267 2.2 9.3 1.0 S3 A:SF4267 2.3 11.2 1.0 SG A:CYS20 2.3 8.8 1.0 S4 A:SF4267 2.3 8.8 1.0 FE4 A:SF4267 2.7 10.1 1.0 FE3 A:SF4267 2.7 8.8 1.0 FE1 A:SF4267 2.8 9.7 1.0 CB A:CYS20 3.5 6.5 1.0 N A:CYS20 3.7 9.2 1.0 S2 A:SF4267 3.9 12.0 1.0 CA A:CYS20 4.2 8.2 1.0 CB A:PRO149 4.2 8.5 1.0 CA A:GLY110 4.3 10.1 1.0 CA A:PRO149 4.4 9.0 1.0 CA A:GLY19 4.5 7.3 1.0 C A:GLY19 4.5 8.7 1.0 N A:GLY19 4.6 6.1 1.0 O A:ILE109 4.8 12.4 1.0 CA A:CYS148 4.8 7.1 1.0 SG A:CYS112 4.9 9.2 1.0 N A:PRO149 4.9 7.7 1.0 SG A:CYS17 4.9 8.4 1.0 O A:GLY147 5.0 10.0 1.0 SG A:CYS148 5.0 4.8 1.0

Iron binding site 10 out of 24 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:8.8 occ:1.00 FE3 A:SF4267 0.0 8.8 1.0 S2 A:SF4267 2.3 12.0 1.0 S4 A:SF4267 2.3 8.8 1.0 S1 A:SF4267 2.3 9.3 1.0 SG A:CYS148 2.4 4.8 1.0 FE4 A:SF4267 2.7 10.1 1.0 FE1 A:SF4267 2.7 9.7 1.0 FE2 A:SF4267 2.7 4.8 1.0 CB A:CYS148 3.4 6.3 1.0 CA A:CYS148 3.4 7.1 1.0 C A:CYS148 3.8 7.8 1.0 S3 A:SF4267 3.9 11.2 1.0 O A:CYS148 4.3 9.1 1.0 N A:PRO149 4.3 7.7 1.0 SG A:CYS112 4.3 9.2 1.0 CA A:PRO149 4.6 9.0 1.0 CG B:ARG63 4.6 4.1 1.0 SG A:CYS20 4.7 8.8 1.0 N A:CYS148 4.7 8.0 1.0 CD2 B:HIS219 4.8 13.5 1.0 SG A:CYS17 4.8 8.4 1.0 NE2 B:HIS219 5.0 13.1 1.0 O A:GLY147 5.0 10.0 1.0 CB A:PRO149 5.0 8.5 1.0

A.Volbeda, M.H.Charon, C.Piras, E.C.Hatchikian, M.Frey, J.C.Fontecilla-Camps. Crystal Structure of the Nickel-Iron Hydrogenase From Desulfovibrio Gigas. Nature V. 373 580 1995.
ISSN: ISSN 0028-0836
PubMed: 7854413
DOI: 10.1038/373580A0