Iron in PDB 4ud6: Structure of Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

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

The structure of Structure of Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ud6 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)	19.99 / 2.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.940, 99.560, 183.940, 90.00, 91.31, 90.00
R / Rfree (%)	15.223 / 19.594

The structure of Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4ud6). 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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ud6:
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 Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:17.8 occ:1.00 FE1 A:SF41265 0.0 17.8 1.0 S3 A:SF41265 2.3 17.3 1.0 S2 A:SF41265 2.3 17.2 1.0 S4 A:SF41265 2.3 18.4 1.0 SG A:CYS218 2.3 16.7 1.0 FE3 A:SF41265 2.6 18.3 1.0 FE4 A:SF41265 2.7 18.5 1.0 FE2 A:SF41265 2.8 18.3 1.0 CB A:CYS218 3.2 16.4 1.0 S1 A:SF41265 3.9 20.7 1.0 CG2 A:VAL239 4.3 15.2 1.0 CD A:PRO221 4.5 17.2 1.0 CA A:CYS218 4.6 16.0 1.0 CA A:GLY220 4.6 16.2 1.0 N A:GLY220 4.6 16.1 1.0 SG A:CYS212 4.7 18.7 1.0 ND1 A:HIS184 4.7 19.1 1.0 SG A:CYS187 4.7 19.0 1.0 N A:LEU213 4.8 18.9 1.0 N A:TYR214 4.9 18.9 1.0 C A:CYS218 4.9 15.9 1.0 CB A:LEU213 4.9 18.9 1.0

Iron binding site 2 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:18.3 occ:1.00 FE2 A:SF41265 0.0 18.3 1.0 S4 A:SF41265 2.3 18.4 1.0 S1 A:SF41265 2.3 20.7 1.0 SG A:CYS212 2.3 18.7 1.0 S3 A:SF41265 2.3 17.3 1.0 FE4 A:SF41265 2.7 18.5 1.0 FE3 A:SF41265 2.7 18.3 1.0 FE1 A:SF41265 2.8 17.8 1.0 CB A:CYS212 3.4 19.2 1.0 N A:LEU213 3.7 18.9 1.0 CA A:CYS212 3.8 19.4 1.0 S2 A:SF41265 4.0 17.2 1.0 CB A:PHE193 4.3 19.6 1.0 C A:CYS212 4.3 18.8 1.0 N A:TYR214 4.3 18.9 1.0 CD1 A:PHE193 4.4 18.8 1.0 CB A:ARG189 4.4 18.8 1.0 ND1 A:HIS184 4.5 19.1 1.0 CE1 A:HIS184 4.6 19.7 1.0 CB A:TYR214 4.7 19.2 1.0 CG A:PHE193 4.7 19.6 1.0 CA A:LEU213 4.8 18.7 1.0 SG A:CYS187 4.8 19.0 1.0 O A:ARG189 4.8 19.7 1.0 C A:LEU213 4.9 18.8 1.0 SG A:CYS218 4.9 16.7 1.0 CA A:TYR214 4.9 18.9 1.0 C A:ARG189 4.9 19.5 1.0

Iron binding site 3 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:18.3 occ:1.00 FE3 A:SF41265 0.0 18.3 1.0 S4 A:SF41265 2.3 18.4 1.0 S1 A:SF41265 2.3 20.7 1.0 S2 A:SF41265 2.3 17.2 1.0 SG A:CYS187 2.3 19.0 1.0 FE4 A:SF41265 2.6 18.5 1.0 FE1 A:SF41265 2.6 17.8 1.0 FE2 A:SF41265 2.7 18.3 1.0 CB A:CYS187 3.1 18.9 1.0 S3 A:SF41265 3.8 17.3 1.0 CB A:ARG189 3.9 18.8 1.0 CG1 A:VAL239 4.3 16.5 1.0 ND1 A:HIS184 4.5 19.1 1.0 CA A:CYS187 4.5 19.4 1.0 CG2 A:VAL239 4.6 15.2 1.0 CA A:ARG189 4.6 19.0 1.0 N A:LEU190 4.7 19.4 1.0 C A:ARG189 4.7 19.5 1.0 N A:ARG189 4.7 18.9 1.0 CG A:ARG189 4.7 18.8 1.0 SG A:CYS218 4.8 16.7 1.0 SG A:CYS212 5.0 18.7 1.0 CB A:VAL239 5.0 16.7 1.0 CD A:ARG189 5.0 18.3 1.0

Iron binding site 4 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:18.5 occ:1.00 FE4 A:SF41265 0.0 18.5 1.0 ND1 A:HIS184 2.1 19.1 1.0 S2 A:SF41265 2.3 17.2 1.0 S3 A:SF41265 2.3 17.3 1.0 S1 A:SF41265 2.3 20.7 1.0 FE3 A:SF41265 2.6 18.3 1.0 FE2 A:SF41265 2.7 18.3 1.0 FE1 A:SF41265 2.7 17.8 1.0 CE1 A:HIS184 2.9 19.7 1.0 CG A:HIS184 3.3 19.3 1.0 CB A:HIS184 3.8 18.3 1.0 S4 A:SF41265 3.8 18.4 1.0 CA A:HIS184 4.0 18.7 1.0 NE2 A:HIS184 4.1 20.2 1.0 CD A:PRO221 4.2 17.2 1.0 CG A:PRO221 4.2 17.8 1.0 CD2 A:HIS184 4.3 19.6 1.0 CB A:CYS187 4.4 18.9 1.0 SG A:CYS187 4.6 19.0 1.0 SG A:CYS212 4.6 18.7 1.0 CD1 A:PHE193 4.6 18.8 1.0 O A:HIS184 4.6 20.6 1.0 N A:PRO221 4.7 17.2 1.0 SG A:CYS218 4.8 16.7 1.0 C A:HIS184 4.8 20.2 1.0 CG A:PHE193 4.9 19.6 1.0 CB A:PHE193 4.9 19.6 1.0

Iron binding site 5 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:16.3 occ:1.00 FE1 A:F3S1266 0.0 16.3 1.0 S3 A:F3S1266 2.2 15.9 1.0 S2 A:F3S1266 2.2 17.7 1.0 S1 A:F3S1266 2.2 15.2 1.0 SG A:CYS248 2.3 16.1 1.0 FE4 A:F3S1266 2.7 16.7 1.0 FE3 A:F3S1266 2.7 15.4 1.0 CB A:CYS248 3.4 15.4 1.0 O A:HOH2301 3.6 21.1 1.0 S4 A:F3S1266 3.8 16.7 1.0 N A:CYS248 3.8 15.9 1.0 CA A:CYS248 4.1 15.9 1.0 O A:HOH2200 4.1 19.0 1.0 ND2 A:ASN225 4.5 14.9 1.0 C A:CYS248 4.7 15.4 1.0 SG A:CYS245 4.7 15.9 1.0 N A:SER249 4.7 15.2 1.0 SG A:CYS227 4.7 19.0 1.0 O A:HOH2199 4.8 19.9 1.0 CE Q:LYS225 4.9 15.1 1.0 N A:GLY247 5.0 15.2 1.0 C A:GLY247 5.0 16.1 1.0

Iron binding site 6 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:15.4 occ:1.00 FE3 A:F3S1266 0.0 15.4 1.0 S4 A:F3S1266 2.2 16.7 1.0 S1 A:F3S1266 2.2 15.2 1.0 S3 A:F3S1266 2.2 15.9 1.0 SG A:CYS245 2.3 15.9 1.0 FE1 A:F3S1266 2.7 16.3 1.0 FE4 A:F3S1266 2.7 16.7 1.0 CB A:CYS245 3.3 15.3 1.0 CA A:CYS245 3.7 14.9 1.0 S2 A:F3S1266 3.9 17.7 1.0 N A:LEU246 4.0 14.6 1.0 N A:GLY247 4.1 15.2 1.0 C A:CYS245 4.3 14.7 1.0 N A:CYS248 4.5 15.9 1.0 NE2 Q:GLN230 4.6 14.3 1.0 CG2 A:THR223 4.7 14.7 1.0 CA A:GLY247 4.7 15.8 1.0 CG2 A:VAL183 4.7 15.1 1.0 SG A:CYS248 4.8 16.1 1.0 SG A:CYS227 4.8 19.0 1.0

Iron binding site 7 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:16.7 occ:1.00 FE4 A:F3S1266 0.0 16.7 1.0 S4 A:F3S1266 2.2 16.7 1.0 S2 A:F3S1266 2.2 17.7 1.0 S3 A:F3S1266 2.3 15.9 1.0 SG A:CYS227 2.3 19.0 1.0 FE1 A:F3S1266 2.7 16.3 1.0 FE3 A:F3S1266 2.7 15.4 1.0 CB A:CYS227 3.4 17.5 1.0 S1 A:F3S1266 3.9 15.2 1.0 ND2 A:ASN225 4.0 14.9 1.0 CE2 A:PHE232 4.3 14.9 1.0 CZ A:PHE232 4.4 14.4 1.0 O A:HOH2200 4.4 19.0 1.0 CG A:ASN225 4.5 15.9 1.0 CB A:ASN225 4.6 16.4 1.0 CG2 A:VAL183 4.7 15.1 1.0 SG A:CYS245 4.7 15.9 1.0 SG A:CYS248 4.7 16.1 1.0 CA A:CYS227 4.8 17.9 1.0 CD A:PRO238 4.9 15.4 1.0 CG A:PRO238 5.0 15.1 1.0

Iron binding site 8 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:15.4 occ:1.00 FE1 A:SF41267 0.0 15.4 1.0 S3 A:SF41267 2.3 14.8 1.0 SG A:CYS17 2.3 14.4 1.0 S2 A:SF41267 2.3 14.7 1.0 S4 A:SF41267 2.3 14.5 1.0 FE2 A:SF41267 2.7 14.3 1.0 FE4 A:SF41267 2.7 14.3 1.0 FE3 A:SF41267 2.7 14.8 1.0 CB A:CYS17 3.4 14.6 1.0 N A:CYS17 3.7 15.6 1.0 S1 A:SF41267 3.8 14.9 1.0 CA A:CYS17 4.0 15.6 1.0 N A:GLY19 4.1 14.5 1.0 NE2 Q:HIS228 4.2 15.2 1.0 CA A:GLY19 4.4 14.0 1.0 N A:THR18 4.4 15.7 1.0 C A:CYS17 4.5 15.9 1.0 O A:HOH2021 4.6 18.2 1.0 SG A:CYS147 4.7 14.5 1.0 CG Q:ARG70 4.7 13.9 1.0 N A:CYS20 4.7 13.8 1.0 SG A:CYS114 4.7 14.6 1.0 C A:GLU16 4.8 15.8 1.0 CD2 Q:HIS228 4.8 15.8 1.0 SG A:CYS20 4.9 16.6 1.0 C A:GLY19 5.0 14.0 1.0

Iron binding site 9 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:14.3 occ:1.00 FE2 A:SF41267 0.0 14.3 1.0 SG A:CYS147 2.3 14.5 1.0 S4 A:SF41267 2.3 14.5 1.0 S1 A:SF41267 2.3 14.9 1.0 S3 A:SF41267 2.3 14.8 1.0 FE4 A:SF41267 2.6 14.3 1.0 FE1 A:SF41267 2.7 15.4 1.0 FE3 A:SF41267 2.8 14.8 1.0 CB A:CYS147 3.4 15.0 1.0 CA A:CYS147 3.5 15.0 1.0 O A:HOH2165 3.8 16.6 1.0 S2 A:SF41267 3.9 14.7 1.0 C A:CYS147 3.9 15.4 1.0 CG Q:ARG70 4.2 13.9 1.0 O A:CYS147 4.3 15.5 1.0 N A:PRO148 4.4 15.8 1.0 CD2 Q:HIS228 4.5 15.8 1.0 SG A:CYS114 4.5 14.6 1.0 SG A:CYS17 4.5 14.4 1.0 NE2 Q:HIS228 4.6 15.2 1.0 O A:GLY146 4.6 15.7 1.0 CA A:PRO148 4.7 15.5 1.0 NE Q:ARG70 4.7 14.9 1.0 N A:CYS147 4.7 15.2 1.0 SG A:CYS20 4.8 16.6 1.0

Iron binding site 10 out of 36 in the Structure of Methylviologen-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 Methylviologen-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:14.8 occ:1.00 FE3 A:SF41267 0.0 14.8 1.0 S4 A:SF41267 2.3 14.5 1.0 S1 A:SF41267 2.3 14.9 1.0 SG A:CYS20 2.3 16.6 1.0 S2 A:SF41267 2.3 14.7 1.0 FE1 A:SF41267 2.7 15.4 1.0 FE2 A:SF41267 2.8 14.3 1.0 FE4 A:SF41267 2.8 14.3 1.0 CB A:CYS20 3.6 14.6 1.0 N A:CYS20 3.7 13.8 1.0 O A:HOH2120 3.9 17.5 1.0 S3 A:SF41267 4.0 14.8 1.0 CA A:CYS20 4.1 14.1 1.0 CA A:GLY112 4.4 15.0 1.0 C A:GLY19 4.4 14.0 1.0 CB A:PRO148 4.5 15.5 1.0 CA A:PRO148 4.5 15.5 1.0 SG A:CYS17 4.6 14.4 1.0 CA A:GLY19 4.7 14.0 1.0 O A:GLY146 4.8 15.7 1.0 N A:GLY19 4.8 14.5 1.0 CA A:CYS147 4.9 15.0 1.0 SG A:CYS147 4.9 14.5 1.0 N A:PRO148 4.9 15.8 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