Iron in PDB 3cur: Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase

All present enzymatic activity of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase:
1.12.2.1;

The structure of Structure of A Double Methionine Mutant of Ni-Fe Hydrogenase, PDB code: 3cur was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.600, 99.900, 183.000, 90.00, 91.60, 90.00
R / Rfree (%)	15 / 19.4

The structure of Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase (pdb code 3cur). 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 Methionine Mutant of Ni-Fe Hydrogenase, PDB code: 3cur:
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 Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:39.0 occ:1.00 FE1 A:SF4265 0.0 39.0 1.0 S4 A:SF4265 2.3 37.0 1.0 S3 A:SF4265 2.3 38.1 1.0 SG A:CYS212 2.3 38.8 1.0 S2 A:SF4265 2.3 36.0 1.0 FE4 A:SF4265 2.7 40.4 1.0 FE3 A:SF4265 2.7 37.7 1.0 FE2 A:SF4265 2.8 40.4 1.0 CB A:CYS212 3.4 38.9 1.0 N A:LEU213 3.6 40.8 1.0 CA A:CYS212 3.9 39.5 1.0 S1 A:SF4265 3.9 39.4 1.0 C A:CYS212 4.2 40.1 1.0 N A:TYR214 4.2 42.1 1.0 CB A:PHE193 4.2 38.7 1.0 CD2 A:PHE193 4.4 35.8 1.0 ND1 A:HIS184 4.5 39.6 1.0 CB A:ARG189 4.5 39.0 1.0 CB A:TYR214 4.6 39.3 1.0 CE1 A:HIS184 4.6 41.1 1.0 CA A:LEU213 4.7 40.4 1.0 O A:ARG189 4.7 43.8 1.0 SG A:CYS218 4.8 38.8 1.0 CG A:PHE193 4.8 38.9 1.0 C A:LEU213 4.8 41.6 1.0 CA A:TYR214 4.8 41.0 1.0 SG A:CYS187 4.9 38.2 1.0 C A:ARG189 5.0 42.2 1.0 CB A:CYS218 5.0 40.2 1.0

Iron binding site 2 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:40.4 occ:1.00 FE2 A:SF4265 0.0 40.4 1.0 S4 A:SF4265 2.3 37.0 1.0 SG A:CYS187 2.3 38.2 1.0 S1 A:SF4265 2.3 39.4 1.0 S3 A:SF4265 2.3 38.1 1.0 FE3 A:SF4265 2.7 37.7 1.0 FE4 A:SF4265 2.7 40.4 1.0 FE1 A:SF4265 2.8 39.0 1.0 CB A:CYS187 3.0 39.9 1.0 CB A:ARG189 3.9 39.0 1.0 S2 A:SF4265 3.9 36.0 1.0 ND1 A:HIS184 4.3 39.6 1.0 CG1 A:VAL239 4.3 41.5 1.0 CA A:CYS187 4.5 40.2 1.0 C A:ARG189 4.6 42.2 1.0 CA A:ARG189 4.6 40.6 1.0 CG A:ARG189 4.6 38.7 1.0 N A:LEU190 4.6 41.4 1.0 N A:ARG189 4.6 41.2 1.0 SG A:CYS218 4.7 38.8 1.0 CG2 A:VAL239 4.8 40.1 1.0 O A:ARG189 5.0 43.8 1.0 SG A:CYS212 5.0 38.8 1.0 C A:CYS187 5.0 40.5 1.0

Iron binding site 3 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:37.7 occ:1.00 FE3 A:SF4265 0.0 37.7 1.0 ND1 A:HIS184 2.0 39.6 1.0 S1 A:SF4265 2.3 39.4 1.0 S2 A:SF4265 2.3 36.0 1.0 S4 A:SF4265 2.3 37.0 1.0 FE2 A:SF4265 2.7 40.4 1.0 FE4 A:SF4265 2.7 40.4 1.0 FE1 A:SF4265 2.7 39.0 1.0 CE1 A:HIS184 2.8 41.1 1.0 CG A:HIS184 3.2 40.5 1.0 CB A:HIS184 3.7 40.0 1.0 S3 A:SF4265 3.8 38.1 1.0 CA A:HIS184 4.0 40.6 1.0 NE2 A:HIS184 4.0 41.2 1.0 CD2 A:HIS184 4.2 40.6 1.0 CG A:PRO221 4.2 40.1 1.0 CD A:PRO221 4.2 41.1 1.0 CB A:CYS187 4.5 39.9 1.0 O A:HIS184 4.5 42.8 1.0 CD2 A:PHE193 4.6 35.8 1.0 SG A:CYS187 4.6 38.2 1.0 SG A:CYS212 4.6 38.8 1.0 SG A:CYS218 4.7 38.8 1.0 C A:HIS184 4.7 41.5 1.0 N A:PRO221 4.7 41.8 1.0 CG A:PHE193 4.9 38.9 1.0 CB A:PHE193 4.9 38.7 1.0 CA A:GLY220 4.9 39.0 1.0

Iron binding site 4 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:40.4 occ:1.00 FE4 A:SF4265 0.0 40.4 1.0 SG A:CYS218 2.3 38.8 1.0 S1 A:SF4265 2.3 39.4 1.0 S2 A:SF4265 2.3 36.0 1.0 S3 A:SF4265 2.3 38.1 1.0 FE3 A:SF4265 2.7 37.7 1.0 FE2 A:SF4265 2.7 40.4 1.0 FE1 A:SF4265 2.7 39.0 1.0 CB A:CYS218 3.2 40.2 1.0 S4 A:SF4265 3.9 37.0 1.0 CA A:GLY220 4.5 39.0 1.0 N A:GLY220 4.5 37.4 1.0 CD A:PRO221 4.5 41.1 1.0 CG2 A:VAL239 4.6 40.1 1.0 CA A:CYS218 4.6 38.5 1.0 ND1 A:HIS184 4.6 39.6 1.0 SG A:CYS187 4.7 38.2 1.0 SG A:CYS212 4.7 38.8 1.0 C A:CYS218 4.8 38.9 1.0 N A:LEU213 4.8 40.8 1.0 N A:TYR214 4.9 42.1 1.0 O A:CYS218 5.0 38.5 1.0 CB A:LEU213 5.0 40.6 1.0

Iron binding site 5 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:41.0 occ:1.00 FE1 A:F3S266 0.0 41.0 1.0 S1 A:F3S266 2.2 43.1 1.0 S2 A:F3S266 2.2 39.4 1.0 S3 A:F3S266 2.2 39.6 1.0 SG A:CYS248 2.3 39.7 1.0 FE4 A:F3S266 2.6 39.0 1.0 FE3 A:F3S266 2.6 40.9 1.0 CB A:CYS248 3.6 39.7 1.0 O H:HOH604 3.7 21.4 1.0 S4 A:F3S266 3.7 42.7 1.0 N A:CYS248 3.9 39.0 1.0 CA A:CYS248 4.2 40.2 1.0 O A:HOH285 4.2 22.9 1.0 ND2 A:ASN225 4.5 42.1 1.0 SG A:CYS245 4.6 39.7 1.0 C A:CYS248 4.7 40.7 1.0 N A:SER249 4.7 39.6 1.0 SG A:CYS227 4.8 40.8 1.0 CE H:LYS225 4.8 38.8 1.0 O A:HOH276 4.8 33.3 1.0 C A:GLY247 5.0 39.9 1.0

Iron binding site 6 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:40.9 occ:1.00 FE3 A:F3S266 0.0 40.9 1.0 S3 A:F3S266 2.2 39.6 1.0 S1 A:F3S266 2.2 43.1 1.0 S4 A:F3S266 2.2 42.7 1.0 SG A:CYS227 2.3 40.8 1.0 FE1 A:F3S266 2.6 41.0 1.0 FE4 A:F3S266 2.7 39.0 1.0 CB A:CYS227 3.4 39.8 1.0 ND2 A:ASN225 3.8 42.1 1.0 S2 A:F3S266 3.9 39.4 1.0 CE1 A:PHE232 4.2 39.3 1.0 O A:HOH285 4.4 22.9 1.0 CZ A:PHE232 4.4 40.5 1.0 CG A:ASN225 4.4 43.2 1.0 CB A:ASN225 4.6 41.4 1.0 CG2 A:VAL183 4.6 36.6 1.0 SG A:CYS248 4.7 39.7 1.0 SG A:CYS245 4.8 39.7 1.0 CA A:CYS227 4.8 40.9 1.0 CD A:PRO238 5.0 40.9 1.0

Iron binding site 7 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:39.0 occ:1.00 FE4 A:F3S266 0.0 39.0 1.0 S4 A:F3S266 2.2 42.7 1.0 S2 A:F3S266 2.2 39.4 1.0 S3 A:F3S266 2.2 39.6 1.0 SG A:CYS245 2.3 39.7 1.0 FE1 A:F3S266 2.6 41.0 1.0 FE3 A:F3S266 2.7 40.9 1.0 CB A:CYS245 3.2 40.3 1.0 CA A:CYS245 3.7 40.5 1.0 S1 A:F3S266 3.9 43.1 1.0 N A:LEU246 3.9 42.0 1.0 N A:GLY247 4.2 40.2 1.0 C A:CYS245 4.2 41.5 1.0 N A:CYS248 4.6 39.0 1.0 SG A:CYS248 4.7 39.7 1.0 CG2 A:THR223 4.7 41.1 1.0 CG2 A:VAL183 4.7 36.6 1.0 CA A:GLY247 4.8 39.2 1.0 NE2 H:GLN230 4.8 38.2 1.0 SG A:CYS227 4.8 40.8 1.0 N A:CYS245 5.0 39.3 1.0

Iron binding site 8 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:39.9 occ:1.00 FE1 A:SF4267 0.0 39.9 1.0 S3 A:SF4267 2.3 40.9 1.0 SG A:CYS147 2.3 43.7 1.0 S2 A:SF4267 2.3 40.8 1.0 S4 A:SF4267 2.3 40.6 1.0 FE3 A:SF4267 2.7 43.9 1.0 FE4 A:SF4267 2.7 41.5 1.0 FE2 A:SF4267 2.7 40.9 1.0 CB A:CYS147 3.4 41.3 1.0 CA A:CYS147 3.5 42.2 1.0 O A:HOH284 3.8 27.5 1.0 S1 A:SF4267 3.9 42.9 1.0 C A:CYS147 3.9 41.9 1.0 CG H:ARG70 4.3 39.0 1.0 N A:PRO148 4.4 42.1 1.0 O A:CYS147 4.4 44.0 1.0 SG A:CYS114 4.4 39.0 1.0 CD2 H:HIS228 4.5 39.0 1.0 O A:GLY146 4.6 42.2 1.0 CA A:PRO148 4.6 40.8 1.0 SG A:CYS17 4.6 38.8 1.0 NE2 H:HIS228 4.6 39.7 1.0 NE H:ARG70 4.8 39.4 1.0 N A:CYS147 4.8 42.4 1.0 SG A:CYS20 4.8 40.6 1.0

Iron binding site 9 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:40.9 occ:1.00 FE2 A:SF4267 0.0 40.9 1.0 S3 A:SF4267 2.3 40.9 1.0 S4 A:SF4267 2.3 40.6 1.0 SG A:CYS20 2.3 40.6 1.0 S1 A:SF4267 2.3 42.9 1.0 FE4 A:SF4267 2.7 41.5 1.0 FE1 A:SF4267 2.7 39.9 1.0 FE3 A:SF4267 2.8 43.9 1.0 CB A:CYS20 3.6 38.4 1.0 N A:CYS20 3.8 38.7 1.0 S2 A:SF4267 3.9 40.8 1.0 O A:HOH274 4.0 34.5 1.0 CA A:CYS20 4.1 38.2 1.0 CB A:PRO148 4.3 40.0 1.0 CA A:PRO148 4.4 40.8 1.0 C A:GLY19 4.5 40.2 1.0 CA A:GLY112 4.5 39.2 1.0 SG A:CYS17 4.7 38.8 1.0 N A:GLY19 4.8 40.9 1.0 CA A:GLY19 4.8 39.8 1.0 O A:GLY146 4.8 42.2 1.0 CA A:CYS147 4.9 42.2 1.0 N A:PRO148 4.9 42.1 1.0 SG A:CYS147 4.9 43.7 1.0 SG A:CYS114 5.0 39.0 1.0 CD A:PRO149 5.0 40.9 1.0

Iron binding site 10 out of 36 in the Structure of A Double Methionine Mutant of Ni-Fe 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 A Double Methionine Mutant of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:43.9 occ:1.00 FE3 A:SF4267 0.0 43.9 1.0 S2 A:SF4267 2.3 40.8 1.0 S1 A:SF4267 2.3 42.9 1.0 SG A:CYS114 2.3 39.0 1.0 S4 A:SF4267 2.3 40.6 1.0 FE1 A:SF4267 2.7 39.9 1.0 FE4 A:SF4267 2.7 41.5 1.0 FE2 A:SF4267 2.8 40.9 1.0 CB A:CYS114 3.1 40.6 1.0 S3 A:SF4267 3.9 40.9 1.0 O A:HOH284 4.0 27.5 1.0 O A:HOH274 4.0 34.5 1.0 N A:CYS114 4.0 39.2 1.0 CA A:CYS114 4.1 40.6 1.0 O A:HOH268 4.2 33.7 1.0 SG A:CYS147 4.5 43.7 1.0 SG A:CYS20 4.8 40.6 1.0 N A:CYS17 4.8 40.4 1.0 SG A:CYS17 4.8 38.8 1.0 CA A:GLU16 4.9 40.2 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