Iron in PDB 1yrq: Structure of the Ready Oxidized Form of [Nife]-Hydrogenase

All present enzymatic activity of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase:
1.12.2.1;

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq was solved by A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	127.500, 99.700, 183.200, 90.00, 91.80, 90.00
R / Rfree (%)	17.1 / 22

The structure of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	12 atoms
Magnesium	(Mg)	12 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 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 72;

Binding sites:

The binding sites of Iron atom in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase (pdb code 1yrq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 72 binding sites of Iron where determined in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase, PDB code: 1yrq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:9.8 occ:1.00 FE1 A:SF4265 0.0 9.8 1.0 S3 A:SF4265 2.3 10.2 1.0 S4 A:SF4265 2.3 12.1 1.0 SG A:CYS212 2.3 12.0 1.0 S2 A:SF4265 2.3 8.9 1.0 FE3 A:SF4265 2.6 9.8 1.0 FE4 A:SF4265 2.6 7.4 1.0 FE2 A:SF4265 2.7 7.4 1.0 CB A:CYS212 3.4 8.5 1.0 N A:LEU213 3.8 6.4 1.0 S1 A:SF4265 3.9 10.5 1.0 CA A:CYS212 4.0 7.3 1.0 N A:TYR214 4.2 7.2 1.0 CB A:PHE193 4.3 11.9 1.0 C A:CYS212 4.4 6.8 1.0 ND1 A:HIS184 4.4 9.7 1.0 CD1 A:PHE193 4.6 11.9 1.0 O A:ARG189 4.6 8.9 1.0 CB A:ARG189 4.6 8.0 1.0 CB A:TYR214 4.6 8.9 1.0 CE1 A:HIS184 4.7 6.9 1.0 SG A:CYS218 4.8 11.6 1.0 CA A:TYR214 4.8 7.7 1.0 CG A:PHE193 4.8 12.8 1.0 CA A:LEU213 4.8 8.0 1.0 SG A:CYS187 4.9 11.7 1.0 C A:LEU213 4.9 7.2 1.0 C A:ARG189 4.9 8.1 1.0 CB A:CYS218 5.0 9.0 1.0

Iron binding site 2 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:7.4 occ:1.00 FE2 A:SF4265 0.0 7.4 1.0 S3 A:SF4265 2.3 10.2 1.0 S4 A:SF4265 2.3 12.1 1.0 SG A:CYS187 2.3 11.7 1.0 S1 A:SF4265 2.3 10.5 1.0 FE4 A:SF4265 2.7 7.4 1.0 FE1 A:SF4265 2.7 9.8 1.0 FE3 A:SF4265 2.7 9.8 1.0 CB A:CYS187 3.1 9.9 1.0 S2 A:SF4265 3.9 8.9 1.0 CB A:ARG189 4.0 8.0 1.0 CG1 A:VAL239 4.4 2.2 1.0 CA A:CYS187 4.5 11.6 1.0 C A:ARG189 4.6 8.1 1.0 ND1 A:HIS184 4.6 9.7 1.0 CA A:ARG189 4.6 6.4 1.0 N A:LEU190 4.6 9.2 1.0 N A:ARG189 4.6 8.3 1.0 CG2 A:VAL239 4.7 6.5 1.0 SG A:CYS218 4.7 11.6 1.0 CG A:ARG189 4.8 5.3 1.0 SG A:CYS212 4.9 12.0 1.0 CH2 A:TRP237 4.9 12.6 1.0 O A:ARG189 5.0 8.9 1.0

Iron binding site 3 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:9.8 occ:1.00 FE3 A:SF4265 0.0 9.8 1.0 ND1 A:HIS184 2.2 9.7 1.0 S2 A:SF4265 2.3 8.9 1.0 S1 A:SF4265 2.3 10.5 1.0 S4 A:SF4265 2.3 12.1 1.0 FE1 A:SF4265 2.6 9.8 1.0 FE2 A:SF4265 2.7 7.4 1.0 FE4 A:SF4265 2.7 7.4 1.0 CE1 A:HIS184 3.0 6.9 1.0 CG A:HIS184 3.2 8.4 1.0 CB A:HIS184 3.6 8.1 1.0 S3 A:SF4265 3.9 10.2 1.0 CA A:HIS184 3.9 9.9 1.0 NE2 A:HIS184 4.2 7.8 1.0 CG A:PRO221 4.2 8.9 1.0 CD2 A:HIS184 4.3 8.4 1.0 O A:HIS184 4.4 7.8 1.0 CD A:PRO221 4.4 8.5 1.0 CB A:CYS187 4.5 9.9 1.0 SG A:CYS212 4.6 12.0 1.0 SG A:CYS187 4.6 11.7 1.0 C A:HIS184 4.7 9.2 1.0 SG A:CYS218 4.7 11.6 1.0 N A:PRO221 4.8 8.8 1.0 CD1 A:PHE193 4.9 11.9 1.0 CA A:GLY220 5.0 6.3 1.0 CB A:PHE193 5.0 11.9 1.0 CD1 A:LEU190 5.0 5.4 1.0

Iron binding site 4 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:7.4 occ:1.00 FE4 A:SF4265 0.0 7.4 1.0 S1 A:SF4265 2.3 10.5 1.0 S2 A:SF4265 2.3 8.9 1.0 S3 A:SF4265 2.3 10.2 1.0 SG A:CYS218 2.3 11.6 1.0 FE1 A:SF4265 2.6 9.8 1.0 FE2 A:SF4265 2.7 7.4 1.0 FE3 A:SF4265 2.7 9.8 1.0 CB A:CYS218 3.2 9.0 1.0 S4 A:SF4265 3.9 12.1 1.0 CG2 A:VAL239 4.4 6.5 1.0 SG A:CYS212 4.5 12.0 1.0 CA A:CYS218 4.6 6.7 1.0 CA A:GLY220 4.6 6.3 1.0 N A:GLY220 4.6 7.5 1.0 CD A:PRO221 4.7 8.5 1.0 ND1 A:HIS184 4.7 9.7 1.0 SG A:CYS187 4.7 11.7 1.0 N A:TYR214 4.8 7.2 1.0 N A:LEU213 4.8 6.4 1.0 C A:CYS218 4.8 7.1 1.0 O A:CYS218 5.0 8.3 1.0

Iron binding site 5 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:6.3 occ:1.00 FE1 A:F3S266 0.0 6.3 1.0 S3 A:F3S266 2.2 10.1 1.0 S1 A:F3S266 2.2 7.9 1.0 SG A:CYS248 2.3 9.3 1.0 S2 A:F3S266 2.3 6.7 1.0 FE3 A:F3S266 2.6 9.1 1.0 FE4 A:F3S266 2.8 9.1 1.0 CB A:CYS248 3.5 2.0 1.0 S4 A:F3S266 3.7 13.2 1.0 N A:CYS248 3.8 6.3 1.0 O H:HOH590 3.8 5.6 1.0 CA A:CYS248 4.1 6.4 1.0 O A:HOH280 4.2 13.0 1.0 ND2 A:ASN225 4.5 7.1 1.0 N A:SER249 4.6 6.7 1.0 SG A:CYS245 4.6 11.4 1.0 C A:CYS248 4.6 7.1 1.0 N A:GLY247 4.8 12.5 1.0 SG A:CYS227 4.8 13.1 1.0 O A:HOH319 4.8 5.3 1.0 C A:GLY247 4.8 9.5 1.0 CE H:LYS225 4.8 5.7 1.0

Iron binding site 6 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:9.1 occ:1.00 FE3 A:F3S266 0.0 9.1 1.0 S3 A:F3S266 2.2 10.1 1.0 S4 A:F3S266 2.2 13.2 1.0 S1 A:F3S266 2.2 7.9 1.0 SG A:CYS245 2.3 11.4 1.0 FE1 A:F3S266 2.6 6.3 1.0 FE4 A:F3S266 2.8 9.1 1.0 CB A:CYS245 3.2 9.5 1.0 CA A:CYS245 3.7 11.0 1.0 N A:GLY247 3.8 12.5 1.0 N A:LEU246 3.9 11.0 1.0 S2 A:F3S266 3.9 6.7 1.0 C A:CYS245 4.2 11.1 1.0 CA A:GLY247 4.3 11.1 1.0 N A:CYS248 4.5 6.3 1.0 NE2 H:GLN230 4.6 2.0 1.0 CG2 A:THR223 4.7 6.8 1.0 SG A:CYS248 4.7 9.3 1.0 SG A:CYS227 4.9 13.1 1.0 C A:LEU246 4.9 13.1 1.0 CG2 A:VAL183 4.9 6.8 1.0 CA A:LEU246 4.9 11.4 1.0 C A:GLY247 5.0 9.5 1.0

Iron binding site 7 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:9.1 occ:1.00 FE4 A:F3S266 0.0 9.1 1.0 S4 A:F3S266 2.2 13.2 1.0 S2 A:F3S266 2.2 6.7 1.0 S3 A:F3S266 2.2 10.1 1.0 SG A:CYS227 2.3 13.1 1.0 FE1 A:F3S266 2.8 6.3 1.0 FE3 A:F3S266 2.8 9.1 1.0 CB A:CYS227 3.3 5.0 1.0 ND2 A:ASN225 4.0 7.1 1.0 S1 A:F3S266 4.0 7.9 1.0 CE1 A:PHE232 4.4 8.8 1.0 O A:HOH280 4.4 13.0 1.0 CZ A:PHE232 4.5 9.8 1.0 CG A:ASN225 4.5 10.1 1.0 CG2 A:VAL183 4.7 6.8 1.0 CB A:ASN225 4.7 9.8 1.0 CA A:CYS227 4.7 7.9 1.0 SG A:CYS248 4.8 9.3 1.0 SG A:CYS245 4.8 11.4 1.0 CD A:PRO238 4.9 5.8 1.0 CG A:PRO238 4.9 6.8 1.0

Iron binding site 8 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:9.5 occ:1.00 FE1 A:SF4267 0.0 9.5 1.0 S3 A:SF4267 2.3 7.2 1.0 SG A:CYS147 2.3 12.2 1.0 S4 A:SF4267 2.3 9.9 1.0 S2 A:SF4267 2.3 8.0 1.0 FE4 A:SF4267 2.6 7.7 1.0 FE3 A:SF4267 2.6 8.4 1.0 FE2 A:SF4267 2.8 10.9 1.0 CB A:CYS147 3.5 8.7 1.0 CA A:CYS147 3.6 9.0 1.0 S1 A:SF4267 3.8 12.0 1.0 O A:HOH307 3.9 4.4 1.0 C A:CYS147 4.0 7.4 1.0 CG H:ARG70 4.2 7.3 1.0 SG A:CYS114 4.4 6.0 1.0 O A:CYS147 4.4 7.0 1.0 N A:PRO148 4.4 7.9 1.0 SG A:CYS17 4.5 8.9 1.0 CD2 H:HIS228 4.6 7.0 1.0 O A:GLY146 4.6 9.4 1.0 NE2 H:HIS228 4.6 9.2 1.0 NE H:ARG70 4.7 5.2 1.0 CA A:PRO148 4.7 7.9 1.0 SG A:CYS20 4.9 8.2 1.0 N A:CYS147 4.9 6.1 1.0

Iron binding site 9 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:10.9 occ:1.00 FE2 A:SF4267 0.0 10.9 1.0 S4 A:SF4267 2.3 9.9 1.0 S1 A:SF4267 2.3 12.0 1.0 SG A:CYS20 2.3 8.2 1.0 S3 A:SF4267 2.3 7.2 1.0 FE4 A:SF4267 2.7 7.7 1.0 FE1 A:SF4267 2.8 9.5 1.0 FE3 A:SF4267 2.8 8.4 1.0 CB A:CYS20 3.5 6.2 1.0 N A:CYS20 3.6 8.7 1.0 O A:HOH296 3.9 5.3 1.0 S2 A:SF4267 4.0 8.0 1.0 CA A:CYS20 4.0 7.7 1.0 CB A:PRO148 4.4 8.0 1.0 CA A:PRO148 4.4 7.9 1.0 C A:GLY19 4.4 8.8 1.0 CA A:GLY112 4.4 6.9 1.0 SG A:CYS17 4.7 8.9 1.0 O A:GLY146 4.7 9.4 1.0 CA A:GLY19 4.8 8.4 1.0 N A:GLY19 4.8 8.9 1.0 N A:PRO148 4.8 7.9 1.0 CA A:CYS147 4.9 9.0 1.0 SG A:CYS147 4.9 12.2 1.0 SG A:CYS114 5.0 6.0 1.0

Iron binding site 10 out of 72 in the Structure of the Ready Oxidized Form of [Nife]-Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Ready Oxidized Form of [Nife]-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:8.4 occ:1.00 FE3 A:SF4267 0.0 8.4 1.0 S2 A:SF4267 2.3 8.0 1.0 SG A:CYS114 2.3 6.0 1.0 S1 A:SF4267 2.3 12.0 1.0 S4 A:SF4267 2.3 9.9 1.0 FE1 A:SF4267 2.6 9.5 1.0 FE4 A:SF4267 2.7 7.7 1.0 FE2 A:SF4267 2.8 10.9 1.0 CB A:CYS114 3.2 4.0 1.0 S3 A:SF4267 3.9 7.2 1.0 O A:HOH296 3.9 5.3 1.0 O A:HOH307 4.0 4.4 1.0 N A:CYS114 4.1 7.7 1.0 CA A:CYS114 4.2 7.2 1.0 O A:HOH278 4.3 12.9 1.0 SG A:CYS147 4.5 12.2 1.0 SG A:CYS20 4.8 8.2 1.0 SG A:CYS17 4.8 8.9 1.0 N A:CYS17 4.9 11.7 1.0 CA A:GLU16 5.0 11.2 1.0

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X