Iron in PDB 4upe: Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

The structure of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4upe was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, 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)	29.83 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.430, 98.960, 184.950, 90.00, 91.19, 90.00
R / Rfree (%)	15.09 / 18.977

The structure of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Calcium	(Ca)	4 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4upe). 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4upe:
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 the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:14.6 occ:1.00 FE1 A:SF41265 0.0 14.6 1.0 S4 A:SF41265 2.2 17.1 1.0 SG A:CYS212 2.3 15.8 1.0 S3 A:SF41265 2.3 15.4 1.0 S2 A:SF41265 2.4 13.7 1.0 FE4 A:SF41265 2.7 15.7 1.0 FE3 A:SF41265 2.7 14.5 1.0 FE2 A:SF41265 2.8 14.4 1.0 CB A:CYS212 3.4 15.2 1.0 N A:LEU213 3.7 12.7 1.0 CA A:CYS212 3.9 14.7 1.0 S1 A:SF41265 4.0 13.2 1.0 CB A:PHE193 4.2 16.8 1.0 C A:CYS212 4.3 14.2 1.0 N A:TYR214 4.3 12.7 1.0 CD2 A:PHE193 4.4 16.8 1.0 CB A:ARG189 4.5 13.6 1.0 ND1 A:HIS184 4.5 16.0 1.0 CB A:TYR214 4.7 12.4 1.0 CG A:PHE193 4.7 17.5 1.0 O A:ARG189 4.7 16.0 1.0 CE1 A:HIS184 4.7 17.0 1.0 CA A:LEU213 4.8 12.2 1.0 SG A:CYS218 4.9 11.8 1.0 C A:LEU213 4.9 12.3 1.0 SG A:CYS187 4.9 14.8 1.0 CA A:TYR214 4.9 12.9 1.0 C A:ARG189 4.9 15.7 1.0 CB A:CYS218 5.0 11.5 1.0

Iron binding site 2 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:14.4 occ:1.00 FE2 A:SF41265 0.0 14.4 1.0 S2 A:SF41265 2.2 13.7 1.0 SG A:CYS218 2.3 11.8 1.0 S1 A:SF41265 2.3 13.2 1.0 S3 A:SF41265 2.4 15.4 1.0 FE4 A:SF41265 2.7 15.7 1.0 FE3 A:SF41265 2.7 14.5 1.0 FE1 A:SF41265 2.8 14.6 1.0 CB A:CYS218 3.1 11.5 1.0 S4 A:SF41265 3.9 17.1 1.0 CG2 A:VAL239 4.4 13.2 1.0 N A:GLY220 4.5 12.8 1.0 CA A:CYS218 4.5 11.5 1.0 CA A:GLY220 4.6 13.2 1.0 CD A:PRO221 4.6 13.1 1.0 ND1 A:HIS184 4.7 16.0 1.0 SG A:CYS187 4.7 14.8 1.0 SG A:CYS212 4.7 15.8 1.0 C A:CYS218 4.8 11.6 1.0 N A:LEU213 4.9 12.7 1.0 O A:CYS218 5.0 11.4 1.0 N A:TYR214 5.0 12.7 1.0

Iron binding site 3 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:14.5 occ:1.00 FE3 A:SF41265 0.0 14.5 1.0 SG A:CYS187 2.3 14.8 1.0 S1 A:SF41265 2.3 13.2 1.0 S3 A:SF41265 2.3 15.4 1.0 S4 A:SF41265 2.3 17.1 1.0 FE4 A:SF41265 2.7 15.7 1.0 FE2 A:SF41265 2.7 14.4 1.0 FE1 A:SF41265 2.7 14.6 1.0 CB A:CYS187 3.1 15.7 1.0 S2 A:SF41265 3.9 13.7 1.0 CB A:ARG189 4.0 13.6 1.0 CG1 A:VAL239 4.4 15.1 1.0 ND1 A:HIS184 4.5 16.0 1.0 CA A:CYS187 4.5 16.4 1.0 CA A:ARG189 4.6 15.4 1.0 N A:ARG189 4.6 15.3 1.0 C A:ARG189 4.6 15.7 1.0 CG2 A:VAL239 4.7 13.2 1.0 CG A:ARG189 4.7 13.6 1.0 N A:LEU190 4.7 17.2 1.0 SG A:CYS218 4.8 11.8 1.0 SG A:CYS212 5.0 15.8 1.0 C A:CYS187 5.0 16.6 1.0

Iron binding site 4 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:15.7 occ:1.00 FE4 A:SF41265 0.0 15.7 1.0 ND1 A:HIS184 2.1 16.0 1.0 S2 A:SF41265 2.3 13.7 1.0 S4 A:SF41265 2.3 17.1 1.0 S1 A:SF41265 2.3 13.2 1.0 FE3 A:SF41265 2.7 14.5 1.0 FE2 A:SF41265 2.7 14.4 1.0 FE1 A:SF41265 2.7 14.6 1.0 CE1 A:HIS184 3.0 17.0 1.0 CG A:HIS184 3.2 15.8 1.0 CB A:HIS184 3.7 14.2 1.0 S3 A:SF41265 3.9 15.4 1.0 CA A:HIS184 4.0 13.5 1.0 NE2 A:HIS184 4.2 17.2 1.0 CD A:PRO221 4.3 13.1 1.0 CD2 A:HIS184 4.3 16.9 1.0 CG A:PRO221 4.3 13.6 1.0 CB A:CYS187 4.4 15.7 1.0 O A:HIS184 4.6 15.8 1.0 SG A:CYS187 4.6 14.8 1.0 SG A:CYS212 4.6 15.8 1.0 CD2 A:PHE193 4.7 16.8 1.0 SG A:CYS218 4.7 11.8 1.0 N A:PRO221 4.7 12.8 1.0 C A:HIS184 4.8 15.6 1.0 CG A:PHE193 5.0 17.5 1.0 CA A:GLY220 5.0 13.2 1.0 CB A:PHE193 5.0 16.8 1.0

Iron binding site 5 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:13.2 occ:1.00 FE1 A:F3S1266 0.0 13.2 1.0 S1 A:F3S1266 2.2 13.2 1.0 S2 A:F3S1266 2.2 13.0 1.0 SG A:CYS248 2.3 11.8 1.0 S3 A:F3S1266 2.3 11.9 1.0 FE3 A:F3S1266 2.7 13.9 1.0 FE4 A:F3S1266 2.7 12.7 1.0 CB A:CYS248 3.4 11.7 1.0 O Q:HOH2037 3.7 11.1 1.0 N A:CYS248 3.8 13.3 1.0 S4 A:F3S1266 3.9 15.9 1.0 CA A:CYS248 4.1 11.9 1.0 O A:HOH2017 4.2 10.7 1.0 ND2 A:ASN225 4.6 12.3 1.0 C A:CYS248 4.6 12.9 1.0 N A:SER249 4.6 11.5 1.0 SG A:CYS227 4.7 15.0 1.0 SG A:CYS245 4.8 11.9 1.0 O A:HOH2008 4.8 11.4 1.0 CE Q:LYS225 4.9 10.0 1.0 C A:GLY247 5.0 12.1 1.0

Iron binding site 6 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:13.9 occ:1.00 FE3 A:F3S1266 0.0 13.9 1.0 S4 A:F3S1266 2.2 15.9 1.0 S3 A:F3S1266 2.2 11.9 1.0 S1 A:F3S1266 2.3 13.2 1.0 SG A:CYS227 2.3 15.0 1.0 FE4 A:F3S1266 2.7 12.7 1.0 FE1 A:F3S1266 2.7 13.2 1.0 CB A:CYS227 3.4 13.3 1.0 S2 A:F3S1266 3.9 13.0 1.0 ND2 A:ASN225 4.0 12.3 1.0 CE2 A:PHE232 4.3 12.4 1.0 O A:HOH2017 4.4 10.7 1.0 CZ A:PHE232 4.5 11.8 1.0 CG A:ASN225 4.6 12.1 1.0 CB A:ASN225 4.7 11.4 1.0 SG A:CYS248 4.7 11.8 1.0 CG2 A:VAL183 4.7 10.9 1.0 SG A:CYS245 4.7 11.9 1.0 CA A:CYS227 4.8 13.8 1.0 CD A:PRO238 5.0 12.1 1.0

Iron binding site 7 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:12.7 occ:1.00 FE4 A:F3S1266 0.0 12.7 1.0 S4 A:F3S1266 2.3 15.9 1.0 S3 A:F3S1266 2.3 11.9 1.0 S2 A:F3S1266 2.3 13.0 1.0 SG A:CYS245 2.3 11.9 1.0 FE3 A:F3S1266 2.7 13.9 1.0 FE1 A:F3S1266 2.7 13.2 1.0 CB A:CYS245 3.3 10.9 1.0 CA A:CYS245 3.7 10.9 1.0 S1 A:F3S1266 3.9 13.2 1.0 N A:LEU246 3.9 14.1 1.0 N A:GLY247 4.2 12.4 1.0 C A:CYS245 4.3 11.3 1.0 N A:CYS248 4.5 13.3 1.0 CG2 A:THR223 4.7 11.5 1.0 NE2 Q:GLN230 4.8 13.5 1.0 CG2 A:VAL183 4.8 10.9 1.0 SG A:CYS227 4.8 15.0 1.0 CA A:GLY247 4.8 12.1 1.0 SG A:CYS248 4.8 11.8 1.0

Iron binding site 8 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:12.0 occ:1.00 FE1 A:SF41267 0.0 12.0 1.0 S3 A:SF41267 2.2 12.3 1.0 S4 A:SF41267 2.3 11.1 1.0 S2 A:SF41267 2.3 10.8 1.0 SG A:CYS147 2.3 12.1 1.0 FE3 A:SF41267 2.7 12.8 1.0 FE4 A:SF41267 2.7 12.8 1.0 FE2 A:SF41267 2.8 13.7 1.0 CB A:CYS147 3.4 9.4 1.0 CA A:CYS147 3.4 10.2 1.0 O A:HOH2011 3.9 9.7 1.0 S1 A:SF41267 3.9 12.1 1.0 C A:CYS147 3.9 10.6 1.0 CG Q:ARG70 4.3 10.8 1.0 O A:CYS147 4.3 9.8 1.0 N A:PRO148 4.4 11.5 1.0 SG A:CYS114 4.5 13.4 1.0 CD2 Q:HIS228 4.6 10.7 1.0 O A:GLY146 4.6 11.2 1.0 SG A:CYS17 4.6 11.8 1.0 NE2 Q:HIS228 4.7 10.3 1.0 CA A:PRO148 4.7 10.3 1.0 N A:CYS147 4.7 9.6 1.0 NE Q:ARG70 4.7 11.2 1.0 SG A:CYS20 4.8 13.7 1.0

Iron binding site 9 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:13.7 occ:1.00 FE2 A:SF41267 0.0 13.7 1.0 S1 A:SF41267 2.3 12.1 1.0 S4 A:SF41267 2.3 11.1 1.0 S3 A:SF41267 2.3 12.3 1.0 SG A:CYS20 2.3 13.7 1.0 FE4 A:SF41267 2.8 12.8 1.0 FE3 A:SF41267 2.8 12.8 1.0 FE1 A:SF41267 2.8 12.0 1.0 CB A:CYS20 3.5 11.0 1.0 N A:CYS20 3.7 9.8 1.0 S2 A:SF41267 3.9 10.8 1.0 O A:HOH2007 4.0 9.3 1.0 CA A:CYS20 4.1 11.0 1.0 CA A:GLY112 4.4 11.8 1.0 CA A:PRO148 4.4 10.3 1.0 CB A:PRO148 4.4 9.8 1.0 C A:GLY19 4.5 10.8 1.0 SG A:CYS17 4.7 11.8 1.0 O A:GLY146 4.8 11.2 1.0 CA A:GLY19 4.8 10.0 1.0 CA A:CYS147 4.8 10.2 1.0 N A:GLY19 4.9 11.4 1.0 N A:PRO148 4.9 11.5 1.0 SG A:CYS114 5.0 13.4 1.0

Iron binding site 10 out of 36 in the Structure of the Unready Ni-A State of the S499C Mutant of 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 the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:12.8 occ:1.00 FE3 A:SF41267 0.0 12.8 1.0 S2 A:SF41267 2.3 10.8 1.0 S4 A:SF41267 2.3 11.1 1.0 S1 A:SF41267 2.3 12.1 1.0 SG A:CYS114 2.3 13.4 1.0 FE1 A:SF41267 2.7 12.0 1.0 FE4 A:SF41267 2.7 12.8 1.0 FE2 A:SF41267 2.8 13.7 1.0 CB A:CYS114 3.3 10.1 1.0 S3 A:SF41267 3.8 12.3 1.0 O A:HOH2007 4.0 9.3 1.0 N A:CYS114 4.0 9.5 1.0 O A:HOH2011 4.0 9.7 1.0 CA A:CYS114 4.2 10.5 1.0 O A:HOH2005 4.3 13.3 1.0 SG A:CYS147 4.5 12.1 1.0 N A:CYS17 4.8 12.3 1.0 SG A:CYS20 4.8 13.7 1.0 SG A:CYS17 4.8 11.8 1.0 CA A:GLU16 5.0 11.7 1.0

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9