Iron in PDB 4upv: Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant

All present enzymatic activity of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant:
1.12.2.1;

The structure of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4upv 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)	30.00 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.690, 100.850, 116.700, 90.00, 105.96, 90.00
R / Rfree (%)	12.001 / 15.39

The structure of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant (pdb code 4upv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4upv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:8.0 occ:1.00 FE1 A:SF41265 0.0 8.0 1.0 S4 A:SF41265 2.3 8.6 1.0 SG A:CYS212 2.3 9.4 1.0 S3 A:SF41265 2.3 7.4 1.0 S2 A:SF41265 2.3 7.7 1.0 FE3 A:SF41265 2.7 8.0 1.0 FE2 A:SF41265 2.7 7.4 1.0 FE4 A:SF41265 2.7 7.5 1.0 CB A:CYS212 3.4 8.5 1.0 N A:LEU213 3.8 6.4 1.0 CA A:CYS212 3.9 8.1 1.0 S1 A:SF41265 3.9 7.5 1.0 N A:TYR214 4.3 8.2 1.0 CB A:PHE193 4.3 9.3 1.0 C A:CYS212 4.3 7.2 1.0 CD2 A:PHE193 4.4 10.8 1.0 ND1 A:HIS184 4.4 8.2 1.0 CB A:ARG189 4.6 7.2 1.0 O A:ARG189 4.6 8.5 1.0 CE1 A:HIS184 4.7 10.5 1.0 CB A:TYR214 4.8 9.8 1.0 CG A:PHE193 4.8 10.2 1.0 CA A:LEU213 4.8 6.9 1.0 SG A:CYS218 4.8 7.2 1.0 SG A:CYS187 4.8 7.6 1.0 C A:LEU213 4.9 7.1 1.0 CA A:TYR214 4.9 8.6 1.0 C A:ARG189 4.9 7.7 1.0

Iron binding site 2 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:7.4 occ:1.00 FE2 A:SF41265 0.0 7.4 1.0 S3 A:SF41265 2.3 7.4 1.0 SG A:CYS187 2.3 7.6 1.0 S4 A:SF41265 2.3 8.6 1.0 S1 A:SF41265 2.3 7.5 1.0 FE3 A:SF41265 2.7 8.0 1.0 FE1 A:SF41265 2.7 8.0 1.0 FE4 A:SF41265 2.7 7.5 1.0 CB A:CYS187 3.1 7.5 1.0 S2 A:SF41265 3.9 7.7 1.0 CB A:ARG189 4.0 7.2 1.0 CG1 A:VAL239 4.3 8.1 1.0 ND1 A:HIS184 4.5 8.2 1.0 CA A:CYS187 4.5 7.8 1.0 C A:ARG189 4.6 7.7 1.0 CG2 A:VAL239 4.6 7.4 1.0 CA A:ARG189 4.6 7.8 1.0 N A:ARG189 4.7 7.3 1.0 N A:LEU190 4.7 7.8 1.0 SG A:CYS218 4.8 7.2 1.0 CG A:ARG189 4.9 7.3 1.0 CH2 A:TRP237 4.9 6.4 1.0 SG A:CYS212 4.9 9.4 1.0 CB A:VAL239 5.0 6.2 1.0 O A:ARG189 5.0 8.5 1.0 C A:CYS187 5.0 7.3 1.0

Iron binding site 3 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:8.0 occ:1.00 FE3 A:SF41265 0.0 8.0 1.0 ND1 A:HIS184 2.1 8.2 1.0 S2 A:SF41265 2.3 7.7 1.0 S1 A:SF41265 2.3 7.5 1.0 S4 A:SF41265 2.3 8.6 1.0 FE1 A:SF41265 2.7 8.0 1.0 FE2 A:SF41265 2.7 7.4 1.0 FE4 A:SF41265 2.7 7.5 1.0 CE1 A:HIS184 2.9 10.5 1.0 CG A:HIS184 3.2 8.2 1.0 CB A:HIS184 3.6 7.7 1.0 S3 A:SF41265 3.9 7.4 1.0 CA A:HIS184 4.0 7.3 1.0 NE2 A:HIS184 4.1 12.0 1.0 CG A:PRO221 4.2 7.8 1.0 CD A:PRO221 4.2 7.3 1.0 CD2 A:HIS184 4.2 10.7 1.0 CB A:CYS187 4.5 7.5 1.0 O A:HIS184 4.5 8.2 1.0 SG A:CYS212 4.6 9.4 1.0 SG A:CYS187 4.6 7.6 1.0 CD2 A:PHE193 4.7 10.8 1.0 C A:HIS184 4.8 7.3 1.0 SG A:CYS218 4.8 7.2 1.0 N A:PRO221 4.8 7.7 1.0 CA A:GLY220 4.9 7.6 1.0 CB A:PHE193 4.9 9.3 1.0 CG A:PHE193 4.9 10.2 1.0

Iron binding site 4 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1265 b:7.5 occ:1.00 FE4 A:SF41265 0.0 7.5 1.0 S1 A:SF41265 2.3 7.5 1.0 S2 A:SF41265 2.3 7.7 1.0 SG A:CYS218 2.3 7.2 1.0 S3 A:SF41265 2.3 7.4 1.0 FE2 A:SF41265 2.7 7.4 1.0 FE3 A:SF41265 2.7 8.0 1.0 FE1 A:SF41265 2.7 8.0 1.0 CB A:CYS218 3.2 7.4 1.0 S4 A:SF41265 3.9 8.6 1.0 CG2 A:VAL239 4.4 7.4 1.0 N A:GLY220 4.5 7.1 1.0 CA A:GLY220 4.5 7.6 1.0 CA A:CYS218 4.6 6.8 1.0 CD A:PRO221 4.6 7.3 1.0 SG A:CYS212 4.7 9.4 1.0 ND1 A:HIS184 4.7 8.2 1.0 SG A:CYS187 4.8 7.6 1.0 C A:CYS218 4.8 6.2 1.0 N A:LEU213 4.9 6.4 1.0 N A:TYR214 4.9 8.2 1.0 CB A:LEU213 5.0 6.8 1.0

Iron binding site 5 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:6.6 occ:1.00 FE1 A:F3S1266 0.0 6.6 1.0 S1 A:F3S1266 2.2 7.0 1.0 S2 A:F3S1266 2.3 7.1 1.0 S3 A:F3S1266 2.3 6.9 1.0 SG A:CYS248 2.3 7.0 1.0 FE4 A:F3S1266 2.7 7.0 1.0 FE3 A:F3S1266 2.7 6.9 1.0 CB A:CYS248 3.5 7.0 1.0 O Q:HOH2717 3.7 6.9 1.0 N A:CYS248 3.8 6.0 1.0 S4 A:F3S1266 3.8 7.7 1.0 CA A:CYS248 4.1 6.0 1.0 O A:HOH2417 4.1 6.8 1.0 ND2 A:ASN225 4.4 8.1 1.0 C A:CYS248 4.6 6.6 1.0 N A:SER249 4.7 6.0 1.0 SG A:CYS245 4.7 7.0 1.0 SG A:CYS227 4.7 6.7 1.0 O A:HOH2404 4.8 6.8 1.0 CE Q:LYS225 4.9 5.7 1.0 C A:GLY247 5.0 6.1 1.0

Iron binding site 6 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:6.9 occ:1.00 FE3 A:F3S1266 0.0 6.9 1.0 S4 A:F3S1266 2.2 7.7 1.0 S1 A:F3S1266 2.3 7.0 1.0 S3 A:F3S1266 2.3 6.9 1.0 SG A:CYS227 2.3 6.7 1.0 FE1 A:F3S1266 2.7 6.6 1.0 FE4 A:F3S1266 2.7 7.0 1.0 CB A:CYS227 3.3 6.6 1.0 ND2 A:ASN225 3.9 8.1 1.0 S2 A:F3S1266 4.0 7.1 1.0 CE2 A:PHE232 4.3 6.4 1.0 O A:HOH2417 4.4 6.8 1.0 CZ A:PHE232 4.5 6.9 1.0 CG A:ASN225 4.5 6.8 1.0 CB A:ASN225 4.6 7.1 1.0 CG2 A:VAL183 4.7 8.5 1.0 CA A:CYS227 4.7 6.4 1.0 SG A:CYS245 4.7 7.0 1.0 SG A:CYS248 4.8 7.0 1.0 CD A:PRO238 4.9 6.4 1.0

Iron binding site 7 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1266 b:7.0 occ:1.00 FE4 A:F3S1266 0.0 7.0 1.0 S4 A:F3S1266 2.2 7.7 1.0 S2 A:F3S1266 2.3 7.1 1.0 SG A:CYS245 2.3 7.0 1.0 S3 A:F3S1266 2.3 6.9 1.0 FE1 A:F3S1266 2.7 6.6 1.0 FE3 A:F3S1266 2.7 6.9 1.0 CB A:CYS245 3.2 6.4 1.0 CA A:CYS245 3.6 5.8 1.0 S1 A:F3S1266 3.9 7.0 1.0 N A:LEU246 4.0 6.1 1.0 N A:GLY247 4.2 5.9 1.0 C A:CYS245 4.3 5.7 1.0 N A:CYS248 4.5 6.0 1.0 NE2 Q:GLN230 4.7 6.0 1.0 CG2 A:THR223 4.7 7.2 1.0 SG A:CYS248 4.8 7.0 1.0 CG2 A:VAL183 4.8 8.5 1.0 SG A:CYS227 4.8 6.7 1.0 CA A:GLY247 4.8 6.8 1.0 N A:CYS245 5.0 6.3 1.0

Iron binding site 8 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:6.5 occ:1.00 FE1 A:SF41267 0.0 6.5 1.0 SG A:CYS147 2.3 6.7 1.0 S3 A:SF41267 2.3 6.6 1.0 S4 A:SF41267 2.3 6.7 1.0 S2 A:SF41267 2.3 6.7 1.0 FE3 A:SF41267 2.6 6.9 1.0 FE4 A:SF41267 2.7 6.5 1.0 FE2 A:SF41267 2.8 6.8 1.0 CB A:CYS147 3.4 6.0 1.0 CA A:CYS147 3.4 6.0 1.0 O A:HOH2415 3.8 7.2 1.0 C A:CYS147 3.9 5.3 1.0 S1 A:SF41267 3.9 6.7 1.0 CG Q:ARG70 4.2 6.2 1.0 O A:CYS147 4.3 6.3 1.0 SG A:CYS114 4.4 7.1 1.0 N A:PRO148 4.4 5.3 1.0 SG A:CYS17 4.6 6.5 1.0 CD2 Q:HIS228 4.6 5.8 1.0 O A:GLY146 4.6 6.1 1.0 CA A:PRO148 4.7 5.2 1.0 NE2 Q:HIS228 4.7 6.1 1.0 NE Q:ARG70 4.7 5.4 1.0 N A:CYS147 4.7 5.5 1.0 SG A:CYS20 4.8 7.3 1.0

Iron binding site 9 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:6.8 occ:1.00 FE2 A:SF41267 0.0 6.8 1.0 S4 A:SF41267 2.2 6.7 1.0 SG A:CYS20 2.3 7.3 1.0 S3 A:SF41267 2.3 6.6 1.0 S1 A:SF41267 2.3 6.7 1.0 FE4 A:SF41267 2.7 6.5 1.0 FE3 A:SF41267 2.8 6.9 1.0 FE1 A:SF41267 2.8 6.5 1.0 CB A:CYS20 3.5 6.7 1.0 N A:CYS20 3.7 6.0 1.0 O A:HOH2414 3.9 6.6 1.0 S2 A:SF41267 3.9 6.7 1.0 CA A:CYS20 4.1 6.8 1.0 CB A:PRO148 4.4 5.4 1.0 CA A:PRO148 4.4 5.2 1.0 CA A:GLY112 4.4 6.1 1.0 C A:GLY19 4.4 6.1 1.0 SG A:CYS17 4.7 6.5 1.0 O A:GLY146 4.7 6.1 1.0 CA A:CYS147 4.8 6.0 1.0 CA A:GLY19 4.8 6.8 1.0 N A:PRO148 4.9 5.3 1.0 N A:GLY19 4.9 5.8 1.0 SG A:CYS114 4.9 7.1 1.0 SG A:CYS147 4.9 6.7 1.0

Iron binding site 10 out of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1267 b:6.9 occ:1.00 FE3 A:SF41267 0.0 6.9 1.0 SG A:CYS114 2.3 7.1 1.0 S2 A:SF41267 2.3 6.7 1.0 S1 A:SF41267 2.3 6.7 1.0 S4 A:SF41267 2.3 6.7 1.0 FE1 A:SF41267 2.6 6.5 1.0 FE4 A:SF41267 2.7 6.5 1.0 FE2 A:SF41267 2.8 6.8 1.0 CB A:CYS114 3.3 6.9 1.0 S3 A:SF41267 3.9 6.6 1.0 O A:HOH2414 3.9 6.6 1.0 O A:HOH2415 3.9 7.2 1.0 N A:CYS114 4.1 6.3 1.0 O A:HOH2405 4.2 7.4 1.0 CA A:CYS114 4.3 6.3 1.0 SG A:CYS147 4.5 6.7 1.0 SG A:CYS20 4.7 7.3 1.0 N A:CYS17 4.8 6.0 1.0 SG A:CYS17 4.8 6.5 1.0 CA A:GLU16 4.9 6.3 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