Iron in PDB 3h3x: Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State

All present enzymatic activity of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State:
1.12.2.1;

The structure of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State, PDB code: 3h3x was solved by A.Volbeda, N.Martinez, L.Martin, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.400, 99.200, 182.300, 90.00, 92.80, 90.00
R / Rfree (%)	20.3 / 24.7

The structure of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State 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 the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State (pdb code 3h3x). 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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State, PDB code: 3h3x:
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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:35.7 occ:1.00 FE1 A:SF4265 0.0 35.7 1.0 S3 A:SF4265 2.3 34.1 1.0 SG A:CYS212 2.3 35.6 1.0 S2 A:SF4265 2.3 33.5 1.0 S4 A:SF4265 2.3 31.4 1.0 FE4 A:SF4265 2.6 33.0 1.0 FE2 A:SF4265 2.7 33.3 1.0 FE3 A:SF4265 2.7 32.7 1.0 CB A:CYS212 3.3 35.5 1.0 N A:LEU213 3.7 35.6 1.0 CA A:CYS212 3.8 35.6 1.0 S1 A:SF4265 3.9 29.5 1.0 C A:CYS212 4.1 35.7 1.0 CB A:PHE193 4.2 34.9 1.0 N A:TYR214 4.2 35.4 1.0 CD2 A:PHE193 4.2 34.4 1.0 CB A:TYR214 4.4 35.5 1.0 ND1 A:HIS184 4.5 34.4 1.0 CB A:ARG189 4.6 33.8 1.0 SG A:CYS218 4.7 34.6 1.0 CG A:PHE193 4.7 33.1 1.0 CE1 A:HIS184 4.7 33.7 1.0 CA A:LEU213 4.7 35.7 1.0 CA A:TYR214 4.7 35.6 1.0 C A:LEU213 4.8 35.7 1.0 O A:ARG189 4.9 35.1 1.0 SG A:CYS187 4.9 33.3 1.0

Iron binding site 2 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:33.3 occ:1.00 FE2 A:SF4265 0.0 33.3 1.0 SG A:CYS187 2.3 33.3 1.0 S3 A:SF4265 2.3 34.1 1.0 S4 A:SF4265 2.3 31.4 1.0 S1 A:SF4265 2.3 29.5 1.0 FE3 A:SF4265 2.7 32.7 1.0 FE1 A:SF4265 2.7 35.7 1.0 FE4 A:SF4265 2.8 33.0 1.0 CB A:CYS187 3.0 34.6 1.0 CB A:ARG189 3.7 33.8 1.0 S2 A:SF4265 3.9 33.5 1.0 N A:LEU190 4.3 34.8 1.0 C A:ARG189 4.4 34.7 1.0 ND1 A:HIS184 4.4 34.4 1.0 CA A:ARG189 4.4 34.2 1.0 CA A:CYS187 4.5 35.0 1.0 CG1 A:VAL239 4.5 35.8 1.0 N A:ARG189 4.6 34.9 1.0 CG A:ARG189 4.8 33.1 1.0 SG A:CYS218 4.9 34.6 1.0 SG A:CYS212 4.9 35.6 1.0 O A:ARG189 4.9 35.1 1.0 C A:CYS187 4.9 35.3 1.0

Iron binding site 3 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:32.7 occ:1.00 FE3 A:SF4265 0.0 32.7 1.0 ND1 A:HIS184 2.0 34.4 1.0 S1 A:SF4265 2.3 29.5 1.0 S2 A:SF4265 2.3 33.5 1.0 S4 A:SF4265 2.3 31.4 1.0 FE4 A:SF4265 2.6 33.0 1.0 FE2 A:SF4265 2.7 33.3 1.0 FE1 A:SF4265 2.7 35.7 1.0 CE1 A:HIS184 2.8 33.7 1.0 CG A:HIS184 3.2 35.2 1.0 CB A:HIS184 3.8 35.3 1.0 S3 A:SF4265 3.9 34.1 1.0 NE2 A:HIS184 4.0 33.7 1.0 CA A:HIS184 4.1 35.9 1.0 CG A:PRO221 4.2 33.8 1.0 CD2 A:HIS184 4.2 35.0 1.0 CD A:PRO221 4.2 35.6 1.0 CD2 A:PHE193 4.4 34.4 1.0 CB A:CYS187 4.4 34.6 1.0 O A:HIS184 4.6 37.4 1.0 SG A:CYS187 4.6 33.3 1.0 SG A:CYS218 4.6 34.6 1.0 SG A:CYS212 4.7 35.6 1.0 N A:PRO221 4.7 35.8 1.0 CG A:PHE193 4.8 33.1 1.0 C A:HIS184 4.8 36.3 1.0 CB A:PHE193 4.8 34.9 1.0 CA A:GLY220 5.0 34.8 1.0

Iron binding site 4 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe265 b:33.0 occ:1.00 FE4 A:SF4265 0.0 33.0 1.0 S1 A:SF4265 2.3 29.5 1.0 SG A:CYS218 2.3 34.6 1.0 S2 A:SF4265 2.3 33.5 1.0 S3 A:SF4265 2.4 34.1 1.0 FE3 A:SF4265 2.6 32.7 1.0 FE1 A:SF4265 2.6 35.7 1.0 FE2 A:SF4265 2.8 33.3 1.0 CB A:CYS218 3.4 34.7 1.0 S4 A:SF4265 3.9 31.4 1.0 ND1 A:HIS184 4.5 34.4 1.0 CA A:GLY220 4.6 34.8 1.0 CD A:PRO221 4.6 35.6 1.0 SG A:CYS187 4.7 33.3 1.0 SG A:CYS212 4.7 35.6 1.0 CG2 A:VAL239 4.7 34.3 1.0 N A:GLY220 4.7 34.9 1.0 CA A:CYS218 4.7 34.9 1.0 N A:LEU213 4.7 35.6 1.0 N A:TYR214 4.9 35.4 1.0 C A:CYS218 4.9 34.4 1.0 O A:CYS218 5.0 34.6 1.0 C A:LEU213 5.0 35.7 1.0

Iron binding site 5 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:35.4 occ:1.00 FE1 A:F3S266 0.0 35.4 1.0 S2 A:F3S266 2.2 34.1 1.0 S1 A:F3S266 2.2 34.8 1.0 S3 A:F3S266 2.3 32.3 1.0 SG A:CYS248 2.3 35.0 1.0 FE3 A:F3S266 2.7 35.0 1.0 FE4 A:F3S266 2.8 35.0 1.0 CB A:CYS248 3.4 34.6 1.0 O Q:HOH578 3.8 33.1 1.0 N A:CYS248 3.8 35.3 1.0 S4 A:F3S266 3.9 34.8 1.0 CA A:CYS248 4.1 34.8 1.0 O A:HOH268 4.3 33.0 1.0 ND2 A:ASN225 4.5 37.8 1.0 N A:SER249 4.6 35.2 1.0 C A:CYS248 4.6 35.1 1.0 SG A:CYS227 4.7 36.6 1.0 SG A:CYS245 4.8 35.5 1.0 CE Q:LYS225 4.8 34.6 1.0 C A:GLY247 4.9 35.2 1.0 O A:HOH286 4.9 35.7 1.0 N A:GLY247 5.0 35.8 1.0

Iron binding site 6 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:35.0 occ:1.00 FE3 A:F3S266 0.0 35.0 1.0 S4 A:F3S266 2.2 34.8 1.0 S3 A:F3S266 2.2 32.3 1.0 S1 A:F3S266 2.2 34.8 1.0 SG A:CYS227 2.3 36.6 1.0 FE4 A:F3S266 2.7 35.0 1.0 FE1 A:F3S266 2.7 35.4 1.0 CB A:CYS227 3.4 36.9 1.0 S2 A:F3S266 3.9 34.1 1.0 ND2 A:ASN225 3.9 37.8 1.0 CE2 A:PHE232 4.4 35.1 1.0 CG A:ASN225 4.5 36.0 1.0 CB A:ASN225 4.6 35.5 1.0 CZ A:PHE232 4.6 35.9 1.0 CG2 A:VAL183 4.6 36.0 1.0 O A:HOH268 4.6 33.0 1.0 SG A:CYS245 4.7 35.5 1.0 SG A:CYS248 4.8 35.0 1.0 CA A:CYS227 4.8 36.3 1.0 CD A:PRO238 4.9 36.0 1.0

Iron binding site 7 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe266 b:35.0 occ:1.00 FE4 A:F3S266 0.0 35.0 1.0 S3 A:F3S266 2.2 32.3 1.0 S4 A:F3S266 2.2 34.8 1.0 S2 A:F3S266 2.2 34.1 1.0 SG A:CYS245 2.3 35.5 1.0 FE3 A:F3S266 2.7 35.0 1.0 FE1 A:F3S266 2.8 35.4 1.0 CB A:CYS245 3.1 36.2 1.0 CA A:CYS245 3.7 35.7 1.0 S1 A:F3S266 3.8 34.8 1.0 N A:LEU246 3.9 36.0 1.0 N A:GLY247 4.2 35.8 1.0 C A:CYS245 4.2 35.7 1.0 N A:CYS248 4.6 35.3 1.0 CG2 A:VAL183 4.7 36.0 1.0 SG A:CYS227 4.7 36.6 1.0 CA A:GLY247 4.7 35.3 1.0 CG2 A:THR223 4.8 36.1 1.0 SG A:CYS248 4.9 35.0 1.0 NE2 Q:GLN230 4.9 34.5 1.0 N A:CYS245 5.0 35.6 1.0

Iron binding site 8 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:37.1 occ:1.00 FE1 A:SF4267 0.0 37.1 1.0 S3 A:SF4267 2.2 37.3 1.0 SG A:CYS147 2.3 34.2 1.0 S4 A:SF4267 2.3 38.2 1.0 S2 A:SF4267 2.4 38.8 1.0 FE4 A:SF4267 2.6 36.0 1.0 FE2 A:SF4267 2.6 37.8 1.0 FE3 A:SF4267 2.7 39.4 1.0 CB A:CYS147 3.3 34.9 1.0 CA A:CYS147 3.4 35.4 1.0 S1 A:SF4267 3.8 39.0 1.0 C A:CYS147 3.9 35.2 1.0 O A:HOH283 4.2 39.6 1.0 N A:PRO148 4.4 35.6 1.0 O A:CYS147 4.4 35.3 1.0 CG Q:ARG70 4.4 36.5 1.0 SG A:CYS114 4.6 34.4 1.0 O A:GLY146 4.6 35.0 1.0 SG A:CYS17 4.6 35.9 1.0 CD2 Q:HIS228 4.6 36.1 1.0 NE2 Q:HIS228 4.7 35.3 1.0 N A:CYS147 4.7 36.1 1.0 CA A:PRO148 4.7 35.5 1.0 SG A:CYS20 4.7 35.4 1.0 NE Q:ARG70 4.9 37.4 1.0

Iron binding site 9 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:37.8 occ:1.00 FE2 A:SF4267 0.0 37.8 1.0 S4 A:SF4267 2.2 38.2 1.0 S3 A:SF4267 2.3 37.3 1.0 SG A:CYS20 2.3 35.4 1.0 S1 A:SF4267 2.4 39.0 1.0 FE1 A:SF4267 2.6 37.1 1.0 FE3 A:SF4267 2.7 39.4 1.0 FE4 A:SF4267 2.8 36.0 1.0 CB A:CYS20 3.7 35.9 1.0 O A:HOH288 3.9 33.6 1.0 N A:CYS20 3.9 36.9 1.0 S2 A:SF4267 3.9 38.8 1.0 CA A:CYS20 4.3 36.0 1.0 CA A:PRO148 4.3 35.5 1.0 CB A:PRO148 4.4 35.1 1.0 CA A:GLY112 4.5 36.0 1.0 CA A:CYS147 4.6 35.4 1.0 O A:GLY146 4.6 35.0 1.0 C A:GLY19 4.6 36.4 1.0 SG A:CYS17 4.7 35.9 1.0 SG A:CYS147 4.7 34.2 1.0 N A:PRO148 4.8 35.6 1.0 CA A:GLY19 4.9 36.5 1.0 C A:CYS147 5.0 35.2 1.0 SG A:CYS114 5.0 34.4 1.0

Iron binding site 10 out of 36 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


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 V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe267 b:39.4 occ:1.00 FE3 A:SF4267 0.0 39.4 1.0 S1 A:SF4267 2.2 39.0 1.0 S4 A:SF4267 2.3 38.2 1.0 S2 A:SF4267 2.3 38.8 1.0 SG A:CYS114 2.3 34.4 1.0 FE4 A:SF4267 2.7 36.0 1.0 FE1 A:SF4267 2.7 37.1 1.0 FE2 A:SF4267 2.7 37.8 1.0 CB A:CYS114 3.1 34.8 1.0 O A:HOH288 3.9 33.6 1.0 S3 A:SF4267 3.9 37.3 1.0 N A:CYS114 4.0 35.7 1.0 CA A:CYS114 4.1 35.2 1.0 O A:HOH274 4.2 36.2 1.0 O A:HOH283 4.4 39.6 1.0 SG A:CYS147 4.6 34.2 1.0 SG A:CYS20 4.7 35.4 1.0 SG A:CYS17 4.8 35.9 1.0 N A:CYS17 4.9 37.1 1.0 CA A:GLU16 4.9 37.1 1.0

S.Dementin, F.Leroux, L.Cournac, A.L.De Lacey, A.Volbeda, C.Leger, B.Burlat, N.Martinez, S.Champ, L.Martin, O.Sanganas, M.Haumann, V.M.Fernandez, B.Guigliarelli, J.C.Fontecilla-Camps, M.Rousset. Introduction of Methionines in the Gas Channel Makes [Nife] Hydrogenase Aero-Tolerant J.Am.Chem.Soc. V. 131 10156 2009.
ISSN: ISSN 0002-7863
PubMed: 19580279
DOI: 10.1021/JA9018258