Iron in PDB 4ud2: Structure of Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

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

The structure of Structure of Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ud2 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)	25.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.010, 100.170, 183.980, 90.00, 91.42, 90.00
R / Rfree (%)	17.308 / 20.688

The structure of Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4ud2). 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ud2:
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 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:20.7 occ:1.00 FE1 A:SF41265 0.0 20.7 1.0 S3 A:SF41265 2.3 18.1 1.0 S2 A:SF41265 2.3 20.0 1.0 SG A:CYS218 2.3 20.9 1.0 S4 A:SF41265 2.3 22.2 1.0 FE4 A:SF41265 2.6 21.4 1.0 FE3 A:SF41265 2.8 21.1 1.0 FE2 A:SF41265 2.8 23.8 1.0 CB A:CYS218 3.2 20.0 1.0 S1 A:SF41265 3.8 20.7 1.0 CD A:PRO221 4.5 28.7 1.0 N A:GLY220 4.5 21.1 1.0 CA A:GLY220 4.5 21.0 1.0 ND1 A:HIS184 4.6 22.0 1.0 CA A:CYS218 4.6 19.6 1.0 CG2 A:VAL239 4.6 20.4 1.0 SG A:CYS212 4.7 23.9 1.0 C A:CYS218 4.8 20.0 1.0 N A:LEU213 4.9 22.9 1.0 SG A:CYS187 4.9 24.4 1.0 N A:TYR214 4.9 22.5 1.0

Iron binding site 2 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:23.8 occ:1.00 FE2 A:SF41265 0.0 23.8 1.0 S1 A:SF41265 2.2 20.7 1.0 S4 A:SF41265 2.3 22.2 1.0 SG A:CYS212 2.3 23.9 1.0 S3 A:SF41265 2.3 18.1 1.0 FE4 A:SF41265 2.8 21.4 1.0 FE1 A:SF41265 2.8 20.7 1.0 FE3 A:SF41265 2.8 21.1 1.0 CB A:CYS212 3.3 21.6 1.0 N A:LEU213 3.7 22.9 1.0 CA A:CYS212 3.7 24.1 1.0 S2 A:SF41265 3.9 20.0 1.0 C A:CYS212 4.1 22.9 1.0 N A:TYR214 4.3 22.5 1.0 CB A:PHE193 4.4 21.8 1.0 CB A:ARG189 4.5 24.4 1.0 CD2 A:PHE193 4.5 21.1 1.0 ND1 A:HIS184 4.6 22.0 1.0 O A:ARG189 4.7 31.2 1.0 CE1 A:HIS184 4.7 22.2 1.0 CB A:TYR214 4.7 23.2 1.0 CA A:LEU213 4.7 22.9 1.0 SG A:CYS218 4.8 20.9 1.0 C A:LEU213 4.9 23.5 1.0 CG A:PHE193 4.9 23.4 1.0 C A:ARG189 4.9 26.7 1.0 SG A:CYS187 4.9 24.4 1.0 CA A:TYR214 4.9 23.3 1.0

Iron binding site 3 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:21.1 occ:1.00 FE3 A:SF41265 0.0 21.1 1.0 S1 A:SF41265 2.3 20.7 1.0 SG A:CYS187 2.3 24.4 1.0 S4 A:SF41265 2.3 22.2 1.0 S2 A:SF41265 2.3 20.0 1.0 FE1 A:SF41265 2.8 20.7 1.0 FE2 A:SF41265 2.8 23.8 1.0 FE4 A:SF41265 2.9 21.4 1.0 CB A:CYS187 3.0 22.2 1.0 S3 A:SF41265 3.9 18.1 1.0 CB A:ARG189 4.0 24.4 1.0 CG1 A:VAL239 4.3 23.8 1.0 CA A:CYS187 4.5 25.7 1.0 ND1 A:HIS184 4.5 22.0 1.0 CA A:ARG189 4.6 24.0 1.0 N A:ARG189 4.6 25.8 1.0 C A:ARG189 4.6 26.7 1.0 N A:LEU190 4.7 25.0 1.0 CG2 A:VAL239 4.7 20.4 1.0 CG A:ARG189 4.7 20.8 1.0 SG A:CYS218 4.8 20.9 1.0 C A:CYS187 4.9 25.8 1.0 CH2 A:TRP237 5.0 21.9 1.0

Iron binding site 4 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:21.4 occ:1.00 FE4 A:SF41265 0.0 21.4 1.0 ND1 A:HIS184 2.0 22.0 1.0 S3 A:SF41265 2.2 18.1 1.0 S2 A:SF41265 2.3 20.0 1.0 S1 A:SF41265 2.3 20.7 1.0 FE1 A:SF41265 2.6 20.7 1.0 CE1 A:HIS184 2.8 22.2 1.0 FE2 A:SF41265 2.8 23.8 1.0 FE3 A:SF41265 2.9 21.1 1.0 CG A:HIS184 3.2 21.3 1.0 CB A:HIS184 3.8 20.7 1.0 S4 A:SF41265 3.8 22.2 1.0 NE2 A:HIS184 4.0 21.0 1.0 CA A:HIS184 4.1 21.8 1.0 CG A:PRO221 4.1 33.6 1.0 CD A:PRO221 4.2 28.7 1.0 CD2 A:HIS184 4.2 21.7 1.0 O A:HIS184 4.6 22.9 1.0 CB A:CYS187 4.6 22.2 1.0 SG A:CYS212 4.6 23.9 1.0 CD2 A:PHE193 4.7 21.1 1.0 N A:PRO221 4.7 27.3 1.0 SG A:CYS218 4.7 20.9 1.0 SG A:CYS187 4.8 24.4 1.0 C A:HIS184 4.8 23.0 1.0 CA A:GLY220 4.9 21.0 1.0 CG A:PHE193 5.0 23.4 1.0

Iron binding site 5 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:19.3 occ:1.00 FE1 A:F3S1266 0.0 19.3 1.0 S1 A:F3S1266 2.2 16.4 1.0 S3 A:F3S1266 2.2 19.2 1.0 S2 A:F3S1266 2.2 22.4 1.0 SG A:CYS248 2.3 16.6 1.0 FE3 A:F3S1266 2.6 18.9 1.0 FE4 A:F3S1266 2.8 20.0 1.0 CB A:CYS248 3.4 14.8 1.0 S4 A:F3S1266 3.7 20.9 1.0 N A:CYS248 3.8 17.0 1.0 O A:HOH2166 3.9 21.0 1.0 CA A:CYS248 4.1 16.2 1.0 O A:HOH2110 4.3 8.7 1.0 ND2 A:ASN225 4.6 25.1 1.0 C A:CYS248 4.7 18.4 1.0 N A:SER249 4.7 19.0 1.0 SG A:CYS245 4.7 18.7 1.0 SG A:CYS227 4.8 21.1 1.0 C A:GLY247 4.9 18.1 1.0 N A:GLY247 4.9 15.9 1.0

Iron binding site 6 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:18.9 occ:1.00 FE3 A:F3S1266 0.0 18.9 1.0 S4 A:F3S1266 2.2 20.9 1.0 S3 A:F3S1266 2.2 19.2 1.0 S1 A:F3S1266 2.2 16.4 1.0 SG A:CYS245 2.3 18.7 1.0 FE1 A:F3S1266 2.6 19.3 1.0 FE4 A:F3S1266 2.7 20.0 1.0 CB A:CYS245 3.3 17.8 1.0 CA A:CYS245 3.7 17.8 1.0 S2 A:F3S1266 3.9 22.4 1.0 N A:LEU246 3.9 16.7 1.0 N A:GLY247 4.1 15.9 1.0 C A:CYS245 4.2 17.4 1.0 N A:CYS248 4.6 17.0 1.0 CG2 A:THR223 4.7 16.6 1.0 CA A:GLY247 4.7 16.2 1.0 SG A:CYS248 4.8 16.6 1.0 NE2 Q:GLN230 4.8 21.8 1.0 SG A:CYS227 4.8 21.1 1.0 CG2 A:VAL183 4.8 16.0 1.0

Iron binding site 7 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:20.0 occ:1.00 FE4 A:F3S1266 0.0 20.0 1.0 S2 A:F3S1266 2.2 22.4 1.0 S4 A:F3S1266 2.2 20.9 1.0 S3 A:F3S1266 2.3 19.2 1.0 SG A:CYS227 2.3 21.1 1.0 FE3 A:F3S1266 2.7 18.9 1.0 FE1 A:F3S1266 2.8 19.3 1.0 CB A:CYS227 3.4 19.9 1.0 S1 A:F3S1266 3.9 16.4 1.0 ND2 A:ASN225 4.0 25.1 1.0 CE1 A:PHE232 4.4 15.7 1.0 CG A:ASN225 4.5 26.2 1.0 CZ A:PHE232 4.5 15.9 1.0 O A:HOH2110 4.5 8.7 1.0 CB A:ASN225 4.6 23.2 1.0 CG2 A:VAL183 4.7 16.0 1.0 SG A:CYS248 4.7 16.6 1.0 CA A:CYS227 4.8 22.6 1.0 SG A:CYS245 4.8 18.7 1.0 CD A:PRO238 5.0 19.7 1.0

Iron binding site 8 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:17.5 occ:1.00 FE1 A:SF41267 0.0 17.5 1.0 S3 A:SF41267 2.2 16.2 1.0 S2 A:SF41267 2.3 17.8 1.0 SG A:CYS17 2.3 17.6 1.0 S4 A:SF41267 2.3 16.6 1.0 FE4 A:SF41267 2.7 16.2 1.0 FE2 A:SF41267 2.7 17.1 1.0 FE3 A:SF41267 2.8 18.0 1.0 CB A:CYS17 3.3 17.4 1.0 N A:CYS17 3.7 20.8 1.0 S1 A:SF41267 3.9 15.6 1.0 CA A:CYS17 4.0 19.5 1.0 N A:GLY19 4.1 19.2 1.0 NE2 Q:HIS228 4.3 19.5 1.0 CA A:GLY19 4.4 18.0 1.0 C A:CYS17 4.4 19.7 1.0 N A:THR18 4.4 19.7 1.0 N A:CYS20 4.7 18.4 1.0 SG A:CYS147 4.7 17.0 1.0 SG A:CYS114 4.7 18.4 1.0 O A:HOH2093 4.7 19.9 1.0 C A:GLU16 4.8 22.7 1.0 CG Q:ARG70 4.9 16.9 1.0 SG A:CYS20 4.9 18.7 1.0 CD2 Q:HIS228 5.0 19.0 1.0 C A:GLY19 5.0 19.7 1.0

Iron binding site 9 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:17.1 occ:1.00 FE2 A:SF41267 0.0 17.1 1.0 S4 A:SF41267 2.2 16.6 1.0 SG A:CYS147 2.3 17.0 1.0 S3 A:SF41267 2.3 16.2 1.0 S1 A:SF41267 2.3 15.6 1.0 FE4 A:SF41267 2.6 16.2 1.0 FE1 A:SF41267 2.7 17.5 1.0 FE3 A:SF41267 2.8 18.0 1.0 CB A:CYS147 3.4 18.7 1.0 CA A:CYS147 3.5 17.7 1.0 S2 A:SF41267 3.8 17.8 1.0 C A:CYS147 3.9 17.6 1.0 O A:HOH2085 4.0 15.3 1.0 CG Q:ARG70 4.3 16.9 1.0 O A:CYS147 4.3 16.6 1.0 SG A:CYS114 4.4 18.4 1.0 N A:PRO148 4.4 20.2 1.0 SG A:CYS17 4.6 17.6 1.0 CA A:PRO148 4.6 18.0 1.0 CD2 Q:HIS228 4.6 19.0 1.0 O A:GLY146 4.6 19.0 1.0 NE2 Q:HIS228 4.7 19.5 1.0 NE Q:ARG70 4.7 19.2 1.0 N A:CYS147 4.8 19.4 1.0 SG A:CYS20 4.9 18.7 1.0

Iron binding site 10 out of 36 in the Structure of 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 Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:18.0 occ:1.00 FE3 A:SF41267 0.0 18.0 1.0 S4 A:SF41267 2.3 16.6 1.0 S1 A:SF41267 2.3 15.6 1.0 S2 A:SF41267 2.3 17.8 1.0 SG A:CYS20 2.3 18.7 1.0 FE1 A:SF41267 2.8 17.5 1.0 FE2 A:SF41267 2.8 17.1 1.0 FE4 A:SF41267 2.8 16.2 1.0 CB A:CYS20 3.6 17.3 1.0 O A:HOH2017 3.7 18.0 1.0 N A:CYS20 3.7 18.4 1.0 S3 A:SF41267 4.0 16.2 1.0 CA A:CYS20 4.1 17.9 1.0 CB A:PRO148 4.2 18.1 1.0 CA A:PRO148 4.4 18.0 1.0 C A:GLY19 4.5 19.7 1.0 CA A:GLY112 4.5 18.0 1.0 SG A:CYS17 4.7 17.6 1.0 O A:GLY146 4.8 19.0 1.0 CA A:GLY19 4.8 18.0 1.0 N A:GLY19 4.8 19.2 1.0 CA A:CYS147 4.8 17.7 1.0 N A:PRO148 4.9 20.2 1.0 SG A:CYS147 4.9 17.0 1.0 SG A:CYS114 5.0 18.4 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