Iron in PDB 4ucq: Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

The structure of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucq was solved by A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.Delacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.800, 99.900, 183.300, 90.00, 91.90, 90.00
R / Rfree (%)	19.777 / 24.133

The structure of Structure of the T18D Small Subunit Mutant of 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 the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ucq). 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucq:
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 T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:42.6 occ:1.00 FE1 A:SF41265 0.0 42.6 1.0 S2 A:SF41265 2.2 44.2 1.0 S3 A:SF41265 2.3 44.8 1.0 S4 A:SF41265 2.3 45.0 1.0 SG A:CYS218 2.3 41.3 1.0 FE3 A:SF41265 2.7 43.2 1.0 FE4 A:SF41265 2.7 43.5 1.0 FE2 A:SF41265 2.8 45.6 1.0 CB A:CYS218 3.2 42.0 1.0 S1 A:SF41265 3.9 46.2 1.0 CD A:PRO221 4.4 42.2 1.0 CG2 A:VAL239 4.5 38.3 1.0 CA A:CYS218 4.6 41.1 1.0 CA A:GLY220 4.6 39.8 1.0 N A:GLY220 4.6 39.2 1.0 ND1 A:HIS184 4.7 45.7 1.0 SG A:CYS187 4.7 44.1 1.0 N A:LEU213 4.7 44.0 1.0 SG A:CYS212 4.7 46.1 1.0 C A:CYS218 4.8 41.1 1.0 N A:TYR214 4.8 45.1 1.0 CB A:LEU213 5.0 43.5 1.0 C A:LEU213 5.0 44.8 1.0

Iron binding site 2 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:45.6 occ:1.00 FE2 A:SF41265 0.0 45.6 1.0 S1 A:SF41265 2.2 46.2 1.0 S4 A:SF41265 2.3 45.0 1.0 S3 A:SF41265 2.3 44.8 1.0 SG A:CYS212 2.4 46.1 1.0 FE4 A:SF41265 2.7 43.5 1.0 FE3 A:SF41265 2.7 43.2 1.0 FE1 A:SF41265 2.8 42.6 1.0 CB A:CYS212 3.4 47.1 1.0 N A:LEU213 3.7 44.0 1.0 S2 A:SF41265 3.8 44.2 1.0 CA A:CYS212 3.9 46.5 1.0 C A:CYS212 4.2 45.5 1.0 N A:TYR214 4.2 45.1 1.0 CB A:PHE193 4.3 48.3 1.0 CB A:ARG189 4.3 45.7 1.0 CD1 A:PHE193 4.4 46.7 1.0 ND1 A:HIS184 4.5 45.7 1.0 CE1 A:HIS184 4.7 46.9 1.0 CB A:TYR214 4.7 46.4 1.0 CA A:LEU213 4.7 43.7 1.0 CG A:PHE193 4.8 48.0 1.0 C A:LEU213 4.8 44.8 1.0 SG A:CYS187 4.8 44.1 1.0 SG A:CYS218 4.9 41.3 1.0 CA A:TYR214 4.9 45.2 1.0 CB A:CYS218 5.0 42.0 1.0

Iron binding site 3 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:43.2 occ:1.00 FE3 A:SF41265 0.0 43.2 1.0 S1 A:SF41265 2.2 46.2 1.0 S2 A:SF41265 2.3 44.2 1.0 S4 A:SF41265 2.3 45.0 1.0 SG A:CYS187 2.3 44.1 1.0 FE4 A:SF41265 2.7 43.5 1.0 FE1 A:SF41265 2.7 42.6 1.0 FE2 A:SF41265 2.7 45.6 1.0 CB A:CYS187 3.1 44.5 1.0 CB A:ARG189 3.8 45.7 1.0 S3 A:SF41265 3.8 44.8 1.0 CG1 A:VAL239 4.4 41.3 1.0 ND1 A:HIS184 4.5 45.7 1.0 CG A:ARG189 4.6 45.1 1.0 CA A:CYS187 4.6 44.6 1.0 CA A:ARG189 4.6 47.3 1.0 N A:ARG189 4.6 46.5 1.0 C A:ARG189 4.7 48.3 1.0 N A:LEU190 4.8 48.4 1.0 CG2 A:VAL239 4.8 38.3 1.0 SG A:CYS218 4.8 41.3 1.0 C A:CYS187 5.0 46.4 1.0 SG A:CYS212 5.0 46.1 1.0 CD A:ARG189 5.0 44.4 1.0

Iron binding site 4 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:43.5 occ:1.00 FE4 A:SF41265 0.0 43.5 1.0 ND1 A:HIS184 2.1 45.7 1.0 S2 A:SF41265 2.2 44.2 1.0 S3 A:SF41265 2.3 44.8 1.0 S1 A:SF41265 2.3 46.2 1.0 FE3 A:SF41265 2.7 43.2 1.0 FE2 A:SF41265 2.7 45.6 1.0 FE1 A:SF41265 2.7 42.6 1.0 CE1 A:HIS184 2.9 46.9 1.0 CG A:HIS184 3.2 45.1 1.0 CB A:HIS184 3.7 43.6 1.0 S4 A:SF41265 3.9 45.0 1.0 CA A:HIS184 3.9 42.9 1.0 CD A:PRO221 4.0 42.2 1.0 NE2 A:HIS184 4.1 46.4 1.0 CG A:PRO221 4.2 43.1 1.0 CD2 A:HIS184 4.3 45.6 1.0 CB A:CYS187 4.5 44.5 1.0 O A:HIS184 4.5 44.6 1.0 SG A:CYS187 4.6 44.1 1.0 SG A:CYS212 4.7 46.1 1.0 N A:PRO221 4.7 42.2 1.0 C A:HIS184 4.7 44.3 1.0 SG A:CYS218 4.8 41.3 1.0 CD1 A:PHE193 4.8 46.7 1.0 CB A:PHE193 5.0 48.3 1.0 CG A:PHE193 5.0 48.0 1.0 CA A:GLY220 5.0 39.8 1.0

Iron binding site 5 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:35.4 occ:1.00 FE1 A:F3S1266 0.0 35.4 1.0 S2 A:F3S1266 2.2 34.2 1.0 S1 A:F3S1266 2.3 36.6 1.0 S3 A:F3S1266 2.3 36.3 1.0 SG A:CYS248 2.3 33.7 1.0 FE3 A:F3S1266 2.6 37.6 1.0 FE4 A:F3S1266 2.7 38.0 1.0 CB A:CYS248 3.5 34.0 1.0 O A:HOH2062 3.7 39.9 1.0 S4 A:F3S1266 3.8 37.2 1.0 N A:CYS248 3.9 36.1 1.0 CA A:CYS248 4.1 35.2 1.0 O A:HOH2049 4.2 37.5 1.0 ND2 A:ASN225 4.5 40.4 1.0 N A:SER249 4.6 35.0 1.0 C A:CYS248 4.6 35.3 1.0 SG A:CYS245 4.7 39.8 1.0 SG A:CYS227 4.8 38.4 1.0 CE Q:LYS225 4.9 37.1 1.0

Iron binding site 6 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:37.6 occ:1.00 FE3 A:F3S1266 0.0 37.6 1.0 S4 A:F3S1266 2.2 37.2 1.0 S1 A:F3S1266 2.2 36.6 1.0 S3 A:F3S1266 2.3 36.3 1.0 SG A:CYS245 2.3 39.8 1.0 FE1 A:F3S1266 2.6 35.4 1.0 FE4 A:F3S1266 2.7 38.0 1.0 CB A:CYS245 3.2 39.1 1.0 CA A:CYS245 3.7 38.4 1.0 S2 A:F3S1266 3.8 34.2 1.0 N A:LEU246 3.9 37.5 1.0 N A:GLY247 4.2 35.7 1.0 C A:CYS245 4.2 38.7 1.0 N A:CYS248 4.6 36.1 1.0 CG2 A:THR223 4.8 37.0 1.0 SG A:CYS248 4.8 33.7 1.0 CA A:GLY247 4.8 35.7 1.0 NE2 Q:GLN230 4.8 44.2 1.0 CG2 A:VAL183 4.8 38.6 1.0 SG A:CYS227 4.9 38.4 1.0 N A:CYS245 5.0 39.2 1.0

Iron binding site 7 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:38.0 occ:1.00 FE4 A:F3S1266 0.0 38.0 1.0 S2 A:F3S1266 2.2 34.2 1.0 S4 A:F3S1266 2.2 37.2 1.0 S3 A:F3S1266 2.2 36.3 1.0 SG A:CYS227 2.4 38.4 1.0 FE3 A:F3S1266 2.7 37.6 1.0 FE1 A:F3S1266 2.7 35.4 1.0 CB A:CYS227 3.4 38.5 1.0 S1 A:F3S1266 3.9 36.6 1.0 ND2 A:ASN225 4.0 40.4 1.0 CE1 A:PHE232 4.3 35.0 1.0 O A:HOH2049 4.4 37.5 1.0 CZ A:PHE232 4.5 34.0 1.0 CG A:ASN225 4.5 41.5 1.0 CB A:ASN225 4.6 40.4 1.0 SG A:CYS245 4.7 39.8 1.0 CA A:CYS227 4.8 38.5 1.0 CG2 A:VAL183 4.8 38.6 1.0 SG A:CYS248 4.8 33.7 1.0 CD A:PRO238 4.8 36.3 1.0 CG A:PRO238 4.9 36.1 1.0

Iron binding site 8 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:30.4 occ:1.00 FE1 A:SF41267 0.0 30.4 1.0 SG A:CYS17 2.3 31.7 1.0 S2 A:SF41267 2.3 31.4 1.0 S3 A:SF41267 2.3 30.8 1.0 S4 A:SF41267 2.3 31.1 1.0 FE4 A:SF41267 2.7 31.3 1.0 FE3 A:SF41267 2.7 31.6 1.0 FE2 A:SF41267 2.7 31.6 1.0 CB A:CYS17 3.3 32.6 1.0 N A:CYS17 3.7 32.3 1.0 S1 A:SF41267 3.9 30.9 1.0 CA A:CYS17 4.0 32.8 1.0 N A:GLY19 4.1 31.8 1.0 NE2 Q:HIS228 4.3 32.8 1.0 CA A:GLY19 4.3 31.7 1.0 O A:HOH2005 4.5 38.6 1.0 C A:CYS17 4.5 32.5 1.0 N A:ASP18 4.5 32.6 1.0 SG A:CYS114 4.7 32.0 1.0 SG A:CYS147 4.7 33.5 1.0 N A:CYS20 4.7 31.5 1.0 C A:GLU16 4.8 32.9 1.0 CG Q:ARG70 4.8 32.5 1.0 CD2 Q:HIS228 4.9 34.3 1.0 SG A:CYS20 4.9 31.6 1.0 C A:GLY19 4.9 31.1 1.0

Iron binding site 9 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:31.6 occ:1.00 FE2 A:SF41267 0.0 31.6 1.0 S1 A:SF41267 2.3 30.9 1.0 S4 A:SF41267 2.3 31.1 1.0 SG A:CYS20 2.3 31.6 1.0 S3 A:SF41267 2.3 30.8 1.0 FE1 A:SF41267 2.7 30.4 1.0 FE4 A:SF41267 2.7 31.3 1.0 FE3 A:SF41267 2.8 31.6 1.0 CB A:CYS20 3.6 30.1 1.0 N A:CYS20 3.8 31.5 1.0 O A:HOH2027 3.9 35.1 1.0 S2 A:SF41267 4.0 31.4 1.0 CA A:CYS20 4.1 31.6 1.0 CB A:PRO148 4.3 32.0 1.0 CA A:PRO148 4.4 33.3 1.0 C A:GLY19 4.5 31.1 1.0 CA A:GLY112 4.5 34.3 1.0 SG A:CYS17 4.7 31.7 1.0 O A:GLY146 4.7 33.9 1.0 CA A:CYS147 4.7 33.6 1.0 CA A:GLY19 4.7 31.7 1.0 N A:GLY19 4.8 31.8 1.0 SG A:CYS147 4.9 33.5 1.0 SG A:CYS114 4.9 32.0 1.0 N A:PRO148 5.0 34.3 1.0 O A:ILE111 5.0 33.8 1.0 OE2 A:GLU75 5.0 32.2 1.0

Iron binding site 10 out of 36 in the Structure of the T18D Small Subunit 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 T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:31.6 occ:1.00 FE3 A:SF41267 0.0 31.6 1.0 S4 A:SF41267 2.3 31.1 1.0 SG A:CYS114 2.3 32.0 1.0 S2 A:SF41267 2.3 31.4 1.0 S1 A:SF41267 2.3 30.9 1.0 FE4 A:SF41267 2.6 31.3 1.0 FE1 A:SF41267 2.7 30.4 1.0 FE2 A:SF41267 2.8 31.6 1.0 CB A:CYS114 3.1 32.6 1.0 S3 A:SF41267 3.9 30.8 1.0 N A:CYS114 4.0 33.4 1.0 O A:HOH2027 4.0 35.1 1.0 O A:HOH2036 4.0 36.2 1.0 O A:HOH2005 4.0 38.6 1.0 CA A:CYS114 4.1 33.0 1.0 SG A:CYS147 4.5 33.5 1.0 SG A:CYS20 4.8 31.6 1.0 N A:CYS17 4.8 32.3 1.0 SG A:CYS17 4.9 31.7 1.0 CA A:GLU16 4.9 33.1 1.0

A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.De Lacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin. A Threonine Stabilizes the Nic and Nir Catalytic Intermediates of [Nife]-Hydrogenase During Catalysis in Nife-Hydrogenase J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.630491