Iron in PDB 3cus: Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution

All present enzymatic activity of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution:
1.12.2.1;

The structure of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.400, 99.960, 182.690, 90.00, 92.23, 90.00
R / Rfree (%)	18.5 / 22.2

The structure of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution 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 A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution (pdb code 3cus). 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 A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution, PDB code: 3cus:
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 A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:13.9 occ:1.00 FE1 A:SF4265 0.0 13.9 1.0 S4 A:SF4265 2.3 12.6 1.0 SG A:CYS212 2.3 14.2 1.0 S3 A:SF4265 2.3 13.9 1.0 S2 A:SF4265 2.3 13.1 1.0 FE2 A:SF4265 2.7 14.0 1.0 FE3 A:SF4265 2.7 13.4 1.0 FE4 A:SF4265 2.9 13.2 1.0 CB A:CYS212 3.3 13.7 1.0 N A:LEU213 3.7 14.6 1.0 CA A:CYS212 3.8 13.8 1.0 S1 A:SF4265 3.9 14.0 1.0 N A:TYR214 4.2 15.6 1.0 C A:CYS212 4.2 13.8 1.0 CB A:PHE193 4.3 13.9 1.0 CD2 A:PHE193 4.4 12.1 1.0 ND1 A:HIS184 4.6 14.5 1.0 CB A:ARG189 4.6 15.2 1.0 CE1 A:HIS184 4.6 14.8 1.0 CA A:LEU213 4.7 15.0 1.0 CB A:TYR214 4.7 15.3 1.0 CG A:PHE193 4.8 12.9 1.0 O A:ARG189 4.8 15.4 1.0 C A:LEU213 4.8 15.1 1.0 SG A:CYS187 4.8 14.7 1.0 CA A:TYR214 4.9 15.2 1.0 SG A:CYS218 4.9 14.5 1.0 C A:ARG189 5.0 14.7 1.0

Iron binding site 2 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:14.0 occ:1.00 FE2 A:SF4265 0.0 14.0 1.0 S3 A:SF4265 2.3 13.9 1.0 SG A:CYS187 2.3 14.7 1.0 S1 A:SF4265 2.3 14.0 1.0 S4 A:SF4265 2.3 12.6 1.0 FE3 A:SF4265 2.7 13.4 1.0 FE1 A:SF4265 2.7 13.9 1.0 FE4 A:SF4265 2.7 13.2 1.0 CB A:CYS187 3.1 14.0 1.0 S2 A:SF4265 3.8 13.1 1.0 CB A:ARG189 4.0 15.2 1.0 CG1 A:VAL239 4.3 14.4 1.0 ND1 A:HIS184 4.4 14.5 1.0 CA A:CYS187 4.6 14.6 1.0 CG2 A:VAL239 4.6 13.5 1.0 N A:LEU190 4.7 14.3 1.0 CA A:ARG189 4.7 15.0 1.0 C A:ARG189 4.7 14.7 1.0 N A:ARG189 4.8 14.9 1.0 CG A:ARG189 4.8 14.4 1.0 SG A:CYS218 4.8 14.5 1.0 SG A:CYS212 4.9 14.2 1.0

Iron binding site 3 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:13.4 occ:1.00 FE3 A:SF4265 0.0 13.4 1.0 ND1 A:HIS184 2.1 14.5 1.0 S1 A:SF4265 2.3 14.0 1.0 S2 A:SF4265 2.3 13.1 1.0 S4 A:SF4265 2.3 12.6 1.0 FE2 A:SF4265 2.7 14.0 1.0 FE1 A:SF4265 2.7 13.9 1.0 FE4 A:SF4265 2.7 13.2 1.0 CE1 A:HIS184 2.7 14.8 1.0 CG A:HIS184 3.3 14.8 1.0 S3 A:SF4265 3.9 13.9 1.0 CB A:HIS184 3.9 14.1 1.0 NE2 A:HIS184 4.0 13.6 1.0 CA A:HIS184 4.1 14.7 1.0 CD A:PRO221 4.2 13.9 1.0 CD2 A:HIS184 4.3 14.2 1.0 CG A:PRO221 4.3 13.9 1.0 CB A:CYS187 4.5 14.0 1.0 SG A:CYS187 4.6 14.7 1.0 O A:HIS184 4.6 14.7 1.0 SG A:CYS212 4.6 14.2 1.0 CD2 A:PHE193 4.6 12.1 1.0 SG A:CYS218 4.7 14.5 1.0 N A:PRO221 4.8 13.6 1.0 C A:HIS184 4.8 14.8 1.0 CB A:PHE193 4.9 13.9 1.0 CG A:PHE193 4.9 12.9 1.0 CA A:GLY220 5.0 14.0 1.0

Iron binding site 4 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:13.2 occ:1.00 FE4 A:SF4265 0.0 13.2 1.0 S2 A:SF4265 2.3 13.1 1.0 S1 A:SF4265 2.3 14.0 1.0 SG A:CYS218 2.3 14.5 1.0 S3 A:SF4265 2.3 13.9 1.0 FE2 A:SF4265 2.7 14.0 1.0 FE3 A:SF4265 2.7 13.4 1.0 FE1 A:SF4265 2.9 13.9 1.0 CB A:CYS218 3.2 14.7 1.0 S4 A:SF4265 4.0 12.6 1.0 CG2 A:VAL239 4.4 13.5 1.0 N A:GLY220 4.5 14.2 1.0 CD A:PRO221 4.5 13.9 1.0 CA A:CYS218 4.6 14.6 1.0 CA A:GLY220 4.6 14.0 1.0 ND1 A:HIS184 4.6 14.5 1.0 SG A:CYS212 4.7 14.2 1.0 SG A:CYS187 4.7 14.7 1.0 C A:CYS218 4.8 13.8 1.0 N A:LEU213 4.8 14.6 1.0 N A:TYR214 4.8 15.6 1.0

Iron binding site 5 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:14.1 occ:1.00 FE1 A:F3S266 0.0 14.1 1.0 S3 A:F3S266 2.2 14.2 1.0 S2 A:F3S266 2.2 13.4 1.0 S1 A:F3S266 2.3 14.9 1.0 SG A:CYS248 2.3 15.1 1.0 FE4 A:F3S266 2.7 13.5 1.0 FE3 A:F3S266 2.7 14.5 1.0 CB A:CYS248 3.5 14.2 1.0 O Q:HOH589 3.8 4.0 1.0 S4 A:F3S266 3.8 14.7 1.0 N A:CYS248 3.9 15.3 1.0 CA A:CYS248 4.1 15.0 1.0 O A:HOH301 4.2 8.2 1.0 ND2 A:ASN225 4.3 15.0 1.0 C A:CYS248 4.6 15.0 1.0 N A:SER249 4.7 14.8 1.0 SG A:CYS227 4.7 14.1 1.0 SG A:CYS245 4.7 14.5 1.0 O Q:HOH572 4.9 6.4 1.0 CE Q:LYS225 5.0 14.4 1.0 N A:GLY247 5.0 13.9 1.0

Iron binding site 6 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:14.5 occ:1.00 FE3 A:F3S266 0.0 14.5 1.0 S1 A:F3S266 2.2 14.9 1.0 S4 A:F3S266 2.2 14.7 1.0 S3 A:F3S266 2.3 14.2 1.0 SG A:CYS227 2.3 14.1 1.0 FE1 A:F3S266 2.7 14.1 1.0 FE4 A:F3S266 2.8 13.5 1.0 CB A:CYS227 3.3 13.8 1.0 ND2 A:ASN225 3.9 15.0 1.0 S2 A:F3S266 3.9 13.4 1.0 CE1 A:PHE232 4.3 13.7 1.0 CZ A:PHE232 4.4 14.1 1.0 CG A:ASN225 4.5 14.4 1.0 O A:HOH301 4.6 8.2 1.0 CB A:ASN225 4.6 13.7 1.0 CG2 A:VAL183 4.7 14.1 1.0 CA A:CYS227 4.8 14.1 1.0 SG A:CYS245 4.8 14.5 1.0 SG A:CYS248 4.8 15.1 1.0 CD A:PRO238 4.9 14.7 1.0

Iron binding site 7 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:13.5 occ:1.00 FE4 A:F3S266 0.0 13.5 1.0 S2 A:F3S266 2.2 13.4 1.0 S3 A:F3S266 2.2 14.2 1.0 S4 A:F3S266 2.2 14.7 1.0 SG A:CYS245 2.3 14.5 1.0 FE1 A:F3S266 2.7 14.1 1.0 FE3 A:F3S266 2.8 14.5 1.0 CB A:CYS245 3.3 13.8 1.0 CA A:CYS245 3.7 14.3 1.0 N A:LEU246 3.9 13.9 1.0 S1 A:F3S266 3.9 14.9 1.0 N A:GLY247 4.1 13.9 1.0 C A:CYS245 4.2 13.8 1.0 N A:CYS248 4.5 15.3 1.0 CA A:GLY247 4.7 14.5 1.0 SG A:CYS248 4.8 15.1 1.0 CG2 A:VAL183 4.8 14.1 1.0 NE2 Q:GLN230 4.8 14.4 1.0 CG2 A:THR223 4.8 14.0 1.0 SG A:CYS227 4.8 14.1 1.0 CA A:LEU246 4.9 13.8 1.0 C A:LEU246 5.0 14.4 1.0

Iron binding site 8 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:14.5 occ:1.00 FE1 A:SF4267 0.0 14.5 1.0 SG A:CYS147 2.3 13.6 1.0 S4 A:SF4267 2.3 13.3 1.0 S3 A:SF4267 2.3 12.7 1.0 S2 A:SF4267 2.3 15.7 1.0 FE4 A:SF4267 2.6 13.7 1.0 FE2 A:SF4267 2.7 13.5 1.0 FE3 A:SF4267 2.7 13.8 1.0 CB A:CYS147 3.4 14.2 1.0 CA A:CYS147 3.4 14.4 1.0 S1 A:SF4267 3.8 13.9 1.0 C A:CYS147 3.9 14.1 1.0 O A:HOH274 4.0 4.1 1.0 O A:CYS147 4.3 13.8 1.0 CG Q:ARG70 4.3 14.0 1.0 N A:PRO148 4.4 14.5 1.0 CD2 Q:HIS228 4.4 14.1 1.0 NE2 Q:HIS228 4.5 14.8 1.0 SG A:CYS17 4.5 13.4 1.0 SG A:CYS114 4.6 13.8 1.0 CA A:PRO148 4.7 14.6 1.0 O A:GLY146 4.7 15.5 1.0 N A:CYS147 4.8 14.7 1.0 NE Q:ARG70 4.8 14.9 1.0 SG A:CYS20 4.8 15.1 1.0

Iron binding site 9 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:13.5 occ:1.00 FE2 A:SF4267 0.0 13.5 1.0 S4 A:SF4267 2.3 13.3 1.0 SG A:CYS20 2.3 15.1 1.0 S3 A:SF4267 2.3 12.7 1.0 S1 A:SF4267 2.3 13.9 1.0 FE4 A:SF4267 2.7 13.7 1.0 FE1 A:SF4267 2.7 14.5 1.0 FE3 A:SF4267 2.8 13.8 1.0 CB A:CYS20 3.6 14.4 1.0 N A:CYS20 3.7 14.4 1.0 O A:HOH276 3.9 7.1 1.0 S2 A:SF4267 4.0 15.7 1.0 CA A:CYS20 4.1 14.6 1.0 CB A:PRO148 4.3 14.8 1.0 CA A:PRO148 4.3 14.6 1.0 CA A:GLY112 4.4 14.2 1.0 C A:GLY19 4.4 14.7 1.0 SG A:CYS17 4.7 13.4 1.0 O A:GLY146 4.7 15.5 1.0 CA A:CYS147 4.8 14.4 1.0 CA A:GLY19 4.8 14.7 1.0 N A:PRO148 4.8 14.5 1.0 N A:GLY19 4.8 14.4 1.0 SG A:CYS147 4.9 13.6 1.0

Iron binding site 10 out of 36 in the Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of A Double Ile/Phe Mutant of Ni-Fe Hydrogenase Refined at 2.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:13.8 occ:1.00 FE3 A:SF4267 0.0 13.8 1.0 S1 A:SF4267 2.3 13.9 1.0 S2 A:SF4267 2.3 15.7 1.0 SG A:CYS114 2.3 13.8 1.0 S4 A:SF4267 2.3 13.3 1.0 FE1 A:SF4267 2.7 14.5 1.0 FE4 A:SF4267 2.7 13.7 1.0 FE2 A:SF4267 2.8 13.5 1.0 CB A:CYS114 3.1 14.0 1.0 O A:HOH276 3.9 7.1 1.0 O A:HOH274 3.9 4.1 1.0 S3 A:SF4267 4.0 12.7 1.0 N A:CYS114 4.0 14.0 1.0 CA A:CYS114 4.2 14.8 1.0 O A:HOH272 4.2 6.3 1.0 SG A:CYS147 4.5 13.6 1.0 SG A:CYS20 4.8 15.1 1.0 N A:CYS17 4.9 13.9 1.0 SG A:CYS17 4.9 13.4 1.0 CA A:GLU16 4.9 14.7 1.0

F.Leroux, S.Dementin, B.Burlat, L.Cournac, A.Volbeda, S.Champ, L.Martin, B.Guigliarelli, P.Bertrand, J.Fontecilla-Camps, M.Rousset. Experimental Approaches to Kinetics of Gas Diffusion in Hydrogenase Proc.Natl.Acad.Sci.Usa V. 105 11188 2008.
ISSN: ISSN 0027-8424
PubMed: 18685111
DOI: 10.1073/PNAS.0803689105