Iron in PDB 4uew: Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

The structure of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4uew was solved by A.Volbeda, L.Martin, P.-P.Liebgott, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.98 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.770, 100.400, 183.430, 90.00, 91.55, 90.00
R / Rfree (%)	19.475 / 23.499

The structure of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Magnesium	(Mg)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4uew). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4uew:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:13.8 occ:1.00 FE1 A:SF41265 0.0 13.8 1.0 S3 A:SF41265 2.2 14.7 1.0 S2 A:SF41265 2.3 13.9 1.0 S4 A:SF41265 2.3 14.3 1.0 SG A:CYS218 2.3 13.2 1.0 FE3 A:SF41265 2.7 14.6 1.0 FE4 A:SF41265 2.7 14.8 1.0 FE2 A:SF41265 2.8 15.6 1.0 CB A:CYS218 3.3 13.2 1.0 S1 A:SF41265 3.9 15.6 1.0 CG2 A:VAL239 4.5 13.9 1.0 CD A:PRO221 4.5 13.0 1.0 CA A:GLY220 4.6 11.9 1.0 N A:GLY220 4.6 11.8 1.0 CA A:CYS218 4.6 12.7 1.0 ND1 A:HIS184 4.7 15.4 1.0 SG A:CYS212 4.7 17.1 1.0 SG A:CYS187 4.8 15.3 1.0 N A:LEU213 4.8 16.2 1.0 C A:CYS218 4.9 12.4 1.0 N A:TYR214 5.0 15.7 1.0 O A:CYS218 5.0 12.8 1.0

Iron binding site 2 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:15.6 occ:1.00 FE2 A:SF41265 0.0 15.6 1.0 SG A:CYS212 2.3 17.1 1.0 S1 A:SF41265 2.3 15.6 1.0 S3 A:SF41265 2.3 14.7 1.0 S4 A:SF41265 2.3 14.3 1.0 FE3 A:SF41265 2.7 14.6 1.0 FE4 A:SF41265 2.7 14.8 1.0 FE1 A:SF41265 2.8 13.8 1.0 CB A:CYS212 3.4 17.7 1.0 N A:LEU213 3.7 16.2 1.0 CA A:CYS212 3.8 17.6 1.0 S2 A:SF41265 3.9 13.9 1.0 C A:CYS212 4.2 17.1 1.0 CB A:PHE193 4.3 17.9 1.0 N A:TYR214 4.4 15.7 1.0 CD2 A:PHE193 4.4 16.9 1.0 ND1 A:HIS184 4.5 15.4 1.0 CB A:ARG189 4.5 16.9 1.0 CE1 A:HIS184 4.6 15.9 1.0 O A:ARG189 4.7 18.6 1.0 CG A:PHE193 4.8 17.6 1.0 CB A:TYR214 4.8 15.9 1.0 CA A:LEU213 4.8 15.7 1.0 SG A:CYS187 4.9 15.3 1.0 SG A:CYS218 4.9 13.2 1.0 C A:ARG189 4.9 18.1 1.0 C A:LEU213 4.9 15.5 1.0

Iron binding site 3 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:14.6 occ:1.00 FE3 A:SF41265 0.0 14.6 1.0 S1 A:SF41265 2.3 15.6 1.0 S4 A:SF41265 2.3 14.3 1.0 S2 A:SF41265 2.3 13.9 1.0 SG A:CYS187 2.3 15.3 1.0 FE4 A:SF41265 2.7 14.8 1.0 FE2 A:SF41265 2.7 15.6 1.0 FE1 A:SF41265 2.7 13.8 1.0 CB A:CYS187 3.1 15.8 1.0 S3 A:SF41265 3.8 14.7 1.0 CB A:ARG189 3.8 16.9 1.0 CG1 A:VAL239 4.3 14.8 1.0 ND1 A:HIS184 4.4 15.4 1.0 CA A:ARG189 4.5 17.7 1.0 C A:ARG189 4.5 18.1 1.0 CA A:CYS187 4.6 16.6 1.0 N A:ARG189 4.6 17.4 1.0 N A:LEU190 4.7 18.0 1.0 CG A:ARG189 4.8 16.7 1.0 CG2 A:VAL239 4.8 13.9 1.0 SG A:CYS218 4.9 13.2 1.0 SG A:CYS212 4.9 17.1 1.0 C A:CYS187 4.9 17.1 1.0 O A:ARG189 5.0 18.6 1.0

Iron binding site 4 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:14.8 occ:1.00 FE4 A:SF41265 0.0 14.8 1.0 ND1 A:HIS184 2.1 15.4 1.0 S2 A:SF41265 2.3 13.9 1.0 S3 A:SF41265 2.3 14.7 1.0 S1 A:SF41265 2.3 15.6 1.0 FE3 A:SF41265 2.7 14.6 1.0 FE2 A:SF41265 2.7 15.6 1.0 FE1 A:SF41265 2.7 13.8 1.0 CE1 A:HIS184 2.8 15.9 1.0 CG A:HIS184 3.2 15.4 1.0 CB A:HIS184 3.7 14.9 1.0 S4 A:SF41265 3.9 14.3 1.0 CA A:HIS184 4.0 15.3 1.0 NE2 A:HIS184 4.0 16.2 1.0 CD A:PRO221 4.1 13.0 1.0 CG A:PRO221 4.2 13.6 1.0 CD2 A:HIS184 4.2 15.8 1.0 CB A:CYS187 4.4 15.8 1.0 O A:HIS184 4.6 16.7 1.0 SG A:CYS187 4.6 15.3 1.0 SG A:CYS212 4.6 17.1 1.0 CD2 A:PHE193 4.7 16.9 1.0 N A:PRO221 4.8 12.9 1.0 C A:HIS184 4.8 16.6 1.0 SG A:CYS218 4.8 13.2 1.0 CA A:GLY220 4.9 11.9 1.0 CG A:PHE193 5.0 17.6 1.0

Iron binding site 5 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:9.5 occ:1.00 FE1 A:F3S1266 0.0 9.5 1.0 S3 A:F3S1266 2.2 10.1 1.0 S2 A:F3S1266 2.2 10.2 1.0 S1 A:F3S1266 2.2 9.6 1.0 SG A:CYS248 2.3 10.1 1.0 FE4 A:F3S1266 2.7 10.3 1.0 FE3 A:F3S1266 2.7 10.1 1.0 CB A:CYS248 3.5 10.1 1.0 O A:HOH2286 3.7 15.1 1.0 S4 A:F3S1266 3.8 10.3 1.0 N A:CYS248 3.9 10.2 1.0 CA A:CYS248 4.2 10.1 1.0 O A:HOH2190 4.2 14.1 1.0 ND2 A:ASN225 4.5 11.2 1.0 SG A:CYS245 4.7 10.9 1.0 C A:CYS248 4.7 10.3 1.0 SG A:CYS227 4.7 11.3 1.0 N A:SER249 4.7 10.5 1.0 CE Q:LYS225 4.8 12.4 1.0 O A:HOH2189 4.8 20.0 1.0

Iron binding site 6 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:10.1 occ:1.00 FE3 A:F3S1266 0.0 10.1 1.0 S1 A:F3S1266 2.2 9.6 1.0 S3 A:F3S1266 2.2 10.1 1.0 SG A:CYS245 2.2 10.9 1.0 S4 A:F3S1266 2.2 10.3 1.0 FE1 A:F3S1266 2.7 9.5 1.0 FE4 A:F3S1266 2.8 10.3 1.0 CB A:CYS245 3.3 11.2 1.0 CA A:CYS245 3.7 11.2 1.0 N A:LEU246 3.9 10.9 1.0 S2 A:F3S1266 3.9 10.2 1.0 N A:GLY247 4.2 10.8 1.0 C A:CYS245 4.3 11.2 1.0 N A:CYS248 4.5 10.2 1.0 CG2 A:THR223 4.7 11.4 1.0 NE2 Q:GLN230 4.7 12.2 1.0 CG2 A:VAL183 4.7 12.4 1.0 CA A:GLY247 4.8 10.8 1.0 SG A:CYS248 4.8 10.1 1.0 SG A:CYS227 4.8 11.3 1.0 CA A:LEU246 5.0 10.8 1.0

Iron binding site 7 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:10.3 occ:1.00 FE4 A:F3S1266 0.0 10.3 1.0 S2 A:F3S1266 2.2 10.2 1.0 S3 A:F3S1266 2.2 10.1 1.0 S4 A:F3S1266 2.2 10.3 1.0 SG A:CYS227 2.3 11.3 1.0 FE1 A:F3S1266 2.7 9.5 1.0 FE3 A:F3S1266 2.8 10.1 1.0 CB A:CYS227 3.3 12.3 1.0 S1 A:F3S1266 3.9 9.6 1.0 ND2 A:ASN225 4.0 11.2 1.0 CE1 A:PHE232 4.3 11.3 1.0 CZ A:PHE232 4.4 11.0 1.0 CG A:ASN225 4.5 11.9 1.0 CB A:ASN225 4.6 12.3 1.0 O A:HOH2190 4.6 14.1 1.0 CG2 A:VAL183 4.7 12.4 1.0 SG A:CYS245 4.8 10.9 1.0 CA A:CYS227 4.8 13.2 1.0 SG A:CYS248 4.8 10.1 1.0 CD A:PRO238 4.9 12.1 1.0

Iron binding site 8 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:8.9 occ:1.00 FE1 A:SF41267 0.0 8.9 1.0 S4 A:SF41267 2.2 9.1 1.0 S2 A:SF41267 2.3 8.8 1.0 SG A:CYS17 2.3 9.2 1.0 S3 A:SF41267 2.4 8.7 1.0 FE2 A:SF41267 2.6 8.6 1.0 FE3 A:SF41267 2.7 9.1 1.0 FE4 A:SF41267 2.8 8.9 1.0 CB A:CYS17 3.4 9.6 1.0 N A:CYS17 3.7 10.1 1.0 S1 A:SF41267 3.8 8.8 1.0 CA A:CYS17 4.0 9.9 1.0 N A:GLY19 4.2 9.8 1.0 NE2 Q:HIS228 4.3 9.6 1.0 O A:HOH2021 4.4 13.6 1.0 CA A:GLY19 4.5 9.5 1.0 N A:THR18 4.5 10.2 1.0 C A:CYS17 4.5 10.1 1.0 SG A:CYS147 4.6 9.0 1.0 CG Q:ARG70 4.7 9.3 1.0 SG A:CYS114 4.8 8.9 1.0 N A:CYS20 4.8 9.2 1.0 C A:GLU16 4.8 10.6 1.0 CD2 Q:HIS228 4.9 9.8 1.0 SG A:CYS20 4.9 9.0 1.0

Iron binding site 9 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:8.6 occ:1.00 FE2 A:SF41267 0.0 8.6 1.0 S3 A:SF41267 2.3 8.7 1.0 SG A:CYS147 2.3 9.0 1.0 S1 A:SF41267 2.3 8.8 1.0 S2 A:SF41267 2.3 8.8 1.0 FE1 A:SF41267 2.6 8.9 1.0 FE3 A:SF41267 2.6 9.1 1.0 FE4 A:SF41267 2.7 8.9 1.0 CB A:CYS147 3.4 9.0 1.0 CA A:CYS147 3.4 9.0 1.0 S4 A:SF41267 3.8 9.1 1.0 C A:CYS147 3.9 9.1 1.0 O A:HOH2158 4.0 14.1 1.0 O A:CYS147 4.3 9.0 1.0 CG Q:ARG70 4.3 9.3 1.0 N A:PRO148 4.4 9.4 1.0 SG A:CYS114 4.5 8.9 1.0 CD2 Q:HIS228 4.6 9.8 1.0 O A:GLY146 4.6 9.2 1.0 SG A:CYS17 4.6 9.2 1.0 CA A:PRO148 4.6 9.7 1.0 NE2 Q:HIS228 4.6 9.6 1.0 N A:CYS147 4.7 9.1 1.0 SG A:CYS20 4.8 9.0 1.0 NE Q:ARG70 4.8 9.5 1.0

Iron binding site 10 out of 36 in the Structure of H2-Treated Anaerobically Purified D. Fructosovorans 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:9.1 occ:1.00 FE3 A:SF41267 0.0 9.1 1.0 S4 A:SF41267 2.3 9.1 1.0 S2 A:SF41267 2.3 8.8 1.0 S1 A:SF41267 2.3 8.8 1.0 SG A:CYS114 2.3 8.9 1.0 FE2 A:SF41267 2.6 8.6 1.0 FE1 A:SF41267 2.7 8.9 1.0 FE4 A:SF41267 2.8 8.9 1.0 CB A:CYS114 3.2 9.2 1.0 S3 A:SF41267 3.9 8.7 1.0 O A:HOH2113 4.0 12.0 1.0 O A:HOH2158 4.0 14.1 1.0 O A:HOH2021 4.1 13.6 1.0 N A:CYS114 4.1 9.1 1.0 CA A:CYS114 4.2 9.2 1.0 SG A:CYS147 4.4 9.0 1.0 SG A:CYS20 4.8 9.0 1.0 N A:CYS17 4.8 10.1 1.0 CA A:GLU16 4.9 10.7 1.0 SG A:CYS17 4.9 9.2 1.0

A.Volbeda, L.Martin, P.-P.Liebgott, A.L.De Lacey, J.C.Fontecilla-Camps. [Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H