Iron in PDB 9e15: Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1

All present enzymatic activity of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1:
1.12.1.3;

The structure of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1, PDB code: 9e15 was solved by W.N.Lanzilotta, P.M.Mcternan, M.W.W.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.84 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	94.235, 111.148, 141.091, 90.06, 90.02, 90
R / Rfree (%)	26.7 / 30.6

The structure of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 also contains other interesting chemical elements:

Nickel	(Ni)	8 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 104;

Binding sites:

The binding sites of Iron atom in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 (pdb code 9e15). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 104 binding sites of Iron where determined in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1, PDB code: 9e15:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:46.4 occ:1.00 FE1 A:SF4501 0.0 46.4 1.0 S2 A:SF4501 2.2 37.5 1.0 S3 A:SF4501 2.3 34.4 1.0 S4 A:SF4501 2.3 41.4 1.0 SG A:CYS135 2.4 53.0 1.0 FE4 A:SF4501 2.7 44.2 1.0 FE3 A:SF4501 2.7 46.4 1.0 FE2 A:SF4501 2.8 39.6 1.0 NE2 B:HIS160 3.8 39.5 1.0 CB A:CYS135 3.8 36.9 1.0 S1 A:SF4501 3.9 35.9 1.0 CA A:CYS135 3.9 38.7 1.0 SG A:CYS13 4.0 35.0 1.0 C A:CYS135 4.2 37.5 1.0 CD2 B:HIS160 4.2 26.5 1.0 SG A:CYS85 4.3 47.3 1.0 N A:PRO136 4.5 24.6 1.0 CD B:ARG63 4.5 28.5 1.0 SG A:CYS16 4.6 41.7 1.0 NH1 B:ARG63 4.6 47.2 1.0 O A:CYS135 4.7 42.7 1.0 CA A:PRO136 4.7 34.8 1.0 CE1 B:HIS160 5.0 38.1 1.0

Iron binding site 2 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:39.6 occ:1.00 FE2 A:SF4501 0.0 39.6 1.0 SG A:CYS13 1.7 35.0 1.0 S4 A:SF4501 2.2 41.4 1.0 S1 A:SF4501 2.3 35.9 1.0 S3 A:SF4501 2.3 34.4 1.0 FE3 A:SF4501 2.7 46.4 1.0 FE4 A:SF4501 2.8 44.2 1.0 FE1 A:SF4501 2.8 46.4 1.0 CB A:CYS13 3.2 36.2 1.0 N A:CYS13 3.4 36.4 1.0 N A:GLY15 3.5 35.3 1.0 CA A:CYS13 3.7 38.0 1.0 C A:CYS13 3.9 42.3 1.0 S2 A:SF4501 3.9 37.5 1.0 N A:TYR14 3.9 40.9 1.0 NE2 B:HIS160 4.0 39.5 1.0 CA A:GLY15 4.1 34.5 1.0 O A:CYS13 4.4 42.6 1.0 N A:CYS16 4.5 35.4 1.0 SG A:CYS85 4.6 47.3 1.0 SG A:CYS16 4.6 41.7 1.0 C A:TYR14 4.6 39.0 1.0 C A:SER12 4.6 42.3 1.0 CB A:SER12 4.6 37.6 1.0 CE1 B:HIS160 4.7 38.1 1.0 CA A:TYR14 4.8 41.5 1.0 C A:GLY15 4.8 34.7 1.0 CA A:SER12 4.9 39.2 1.0 O B:ARG63 4.9 40.5 1.0

Iron binding site 3 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:46.4 occ:1.00 FE3 A:SF4501 0.0 46.4 1.0 SG A:CYS85 2.1 47.3 1.0 S4 A:SF4501 2.2 41.4 1.0 S1 A:SF4501 2.3 35.9 1.0 S2 A:SF4501 2.3 37.5 1.0 FE2 A:SF4501 2.7 39.6 1.0 FE1 A:SF4501 2.7 46.4 1.0 FE4 A:SF4501 2.8 44.2 1.0 CB A:CYS85 3.4 42.5 1.0 S3 A:SF4501 3.9 34.4 1.0 N A:CYS85 4.2 49.4 1.0 SG A:CYS13 4.3 35.0 1.0 CB A:SER12 4.4 37.6 1.0 CA A:CYS85 4.4 42.3 1.0 SG A:CYS16 4.4 41.7 1.0 N A:CYS13 4.5 36.4 1.0 CA A:SER12 4.6 39.2 1.0 SG A:CYS135 4.6 53.0 1.0

Iron binding site 4 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:44.2 occ:1.00 FE4 A:SF4501 0.0 44.2 1.0 SG A:CYS16 2.0 41.7 1.0 S3 A:SF4501 2.2 34.4 1.0 S2 A:SF4501 2.3 37.5 1.0 S1 A:SF4501 2.3 35.9 1.0 FE1 A:SF4501 2.7 46.4 1.0 FE2 A:SF4501 2.8 39.6 1.0 FE3 A:SF4501 2.8 46.4 1.0 CB A:CYS16 3.5 32.3 1.0 N A:CYS16 3.5 35.4 1.0 S4 A:SF4501 3.9 41.4 1.0 CA A:CYS16 4.0 38.4 1.0 SG A:CYS13 4.3 35.0 1.0 C A:GLY15 4.3 34.7 1.0 CA A:PRO136 4.4 34.8 1.0 CB A:PRO136 4.4 36.5 1.0 N A:GLY15 4.4 35.3 1.0 OE2 A:GLU57 4.5 37.2 1.0 CA A:GLY15 4.5 34.5 1.0 SG A:CYS85 4.7 47.3 1.0 CA A:GLY83 4.8 31.7 1.0 SG A:CYS135 4.8 53.0 1.0 CG A:GLU57 4.8 36.7 1.0 CD A:GLU57 4.8 38.2 1.0 CD A:PRO137 4.9 36.0 1.0 CA A:CYS135 4.9 38.7 1.0 N A:PRO136 4.9 24.6 1.0

Iron binding site 5 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:34.2 occ:1.00 FE1 A:SF4502 0.0 34.2 1.0 S3 A:SF4502 2.2 31.9 1.0 S2 A:SF4502 2.3 40.8 1.0 S4 A:SF4502 2.3 43.2 1.0 SG A:CYS202 2.3 30.0 1.0 FE3 A:SF4502 2.7 40.9 1.0 FE2 A:SF4502 2.7 31.9 1.0 FE4 A:SF4502 2.7 47.6 1.0 CB A:CYS202 3.5 30.5 1.0 CA A:CYS202 3.8 34.5 1.0 S1 A:SF4502 3.8 46.7 1.0 N A:GLY204 4.0 36.8 1.0 N A:ILE203 4.0 33.7 1.0 N A:CYS205 4.2 41.2 1.0 CG2 A:THR187 4.3 37.6 1.0 C A:CYS202 4.3 38.8 1.0 CG2 A:VAL162 4.4 33.9 1.0 CA A:GLY204 4.5 33.6 1.0 C A:GLY204 4.6 30.7 1.0 SG A:CYS191 4.7 33.5 1.0 CG1 A:VAL162 4.7 35.1 1.0 SG A:CYS205 4.8 48.5 1.0 SG A:CYS195 4.9 32.1 1.0 CB A:THR187 4.9 37.4 1.0 C A:ILE203 5.0 36.6 1.0

Iron binding site 6 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:31.9 occ:1.00 FE2 A:SF4502 0.0 31.9 1.0 SG A:CYS191 2.2 33.5 1.0 S4 A:SF4502 2.3 43.2 1.0 S1 A:SF4502 2.3 46.7 1.0 S3 A:SF4502 2.3 31.9 1.0 FE1 A:SF4502 2.7 34.2 1.0 FE3 A:SF4502 2.8 40.9 1.0 FE4 A:SF4502 2.8 47.6 1.0 CB A:CYS191 3.2 50.1 1.0 S2 A:SF4502 3.9 40.8 1.0 CD A:ARG206 4.4 41.8 1.0 CG1 A:VAL162 4.4 35.1 1.0 CG A:ARG206 4.6 41.6 1.0 N A:ARG194 4.6 46.5 1.0 CA A:CYS191 4.6 46.2 1.0 CG2 A:VAL162 4.7 33.9 1.0 SG A:CYS205 4.7 48.5 1.0 SG A:CYS195 4.7 32.1 1.0 SG A:CYS202 4.7 30.0 1.0 CB A:ARG194 4.9 39.0 1.0 N A:CYS195 4.9 33.2 1.0

Iron binding site 7 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:40.9 occ:1.00 FE3 A:SF4502 0.0 40.9 1.0 S4 A:SF4502 2.3 43.2 1.0 S2 A:SF4502 2.3 40.8 1.0 S1 A:SF4502 2.3 46.7 1.0 SG A:CYS195 2.4 32.1 1.0 FE1 A:SF4502 2.7 34.2 1.0 FE2 A:SF4502 2.8 31.9 1.0 FE4 A:SF4502 2.8 47.6 1.0 CB A:CYS195 3.2 45.3 1.0 S3 A:SF4502 3.9 31.9 1.0 N A:CYS195 4.1 33.2 1.0 CA A:CYS195 4.3 36.7 1.0 CA A:CYS202 4.4 34.5 1.0 SG A:CYS202 4.6 30.0 1.0 N A:ILE203 4.6 33.7 1.0 SG A:CYS191 4.7 33.5 1.0 SG A:CYS205 4.8 48.5 1.0 CB A:CYS202 4.9 30.5 1.0 CB A:ARG194 4.9 39.0 1.0 CG A:PRO196 5.0 46.8 1.0 C A:ARG194 5.0 38.9 1.0

Iron binding site 8 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:47.6 occ:1.00 FE4 A:SF4502 0.0 47.6 1.0 SG A:CYS205 2.2 48.5 1.0 S2 A:SF4502 2.2 40.8 1.0 S3 A:SF4502 2.3 31.9 1.0 S1 A:SF4502 2.3 46.7 1.0 FE1 A:SF4502 2.7 34.2 1.0 FE3 A:SF4502 2.8 40.9 1.0 FE2 A:SF4502 2.8 31.9 1.0 CB A:CYS205 3.3 38.0 1.0 N A:CYS205 3.5 41.2 1.0 CA A:CYS205 3.9 43.1 1.0 S4 A:SF4502 3.9 43.2 1.0 N A:ARG206 4.0 35.9 1.0 CG A:ARG206 4.2 41.6 1.0 NH2 B:ARG157 4.3 25.9 1.0 C A:CYS205 4.3 39.7 1.0 C A:GLY204 4.6 30.7 1.0 CB A:ARG206 4.8 42.6 1.0 N A:GLY204 4.8 36.8 1.0 CD A:ARG206 4.8 41.8 1.0 SG A:CYS191 4.9 33.5 1.0 SG A:CYS202 4.9 30.0 1.0 SG A:CYS195 4.9 32.1 1.0 CA A:ARG206 5.0 41.6 1.0

Iron binding site 9 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:47.0 occ:1.00 FE1 A:SF4503 0.0 47.0 1.0 S2 A:SF4503 2.3 39.2 1.0 S4 A:SF4503 2.3 40.5 1.0 S3 A:SF4503 2.3 45.6 1.0 FE4 A:SF4503 2.7 61.9 1.0 SG A:CYS173 2.7 55.1 1.0 FE3 A:SF4503 2.7 36.5 1.0 FE2 A:SF4503 2.7 42.0 1.0 CA A:CYS173 3.2 38.2 1.0 CB A:CYS173 3.5 43.2 1.0 S1 A:SF4503 3.8 45.8 1.0 C A:CYS173 4.0 46.0 1.0 CZ A:PHE216 4.0 38.6 1.0 CB A:LEU175 4.1 42.3 1.0 N A:ILE174 4.1 48.3 1.0 N A:LEU175 4.1 43.1 1.0 N A:CYS173 4.3 44.1 1.0 SG A:CYS166 4.6 41.1 1.0 SG A:CYS182 4.6 36.8 1.0 CA A:LEU175 4.7 44.6 1.0 CE2 A:PHE216 4.8 48.0 1.0 CE1 A:PHE216 4.9 41.1 1.0 CB A:CYS182 4.9 40.6 1.0 O A:CYS173 5.0 42.9 1.0

Iron binding site 10 out of 104 in the Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Alpha-Delta Heterodimeric Form of Soluble Hydrogenase I From Pyrococcus Furiosus. Data Processed and Model Refined in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:42.0 occ:1.00 FE2 A:SF4503 0.0 42.0 1.0 SG A:CYS182 2.1 36.8 1.0 S3 A:SF4503 2.2 45.6 1.0 S4 A:SF4503 2.3 40.5 1.0 S1 A:SF4503 2.3 45.8 1.0 FE1 A:SF4503 2.7 47.0 1.0 FE4 A:SF4503 2.7 61.9 1.0 FE3 A:SF4503 2.8 36.5 1.0 CB A:CYS182 3.1 40.6 1.0 S2 A:SF4503 3.9 39.2 1.0 CD A:PRO196 4.0 45.1 1.0 CA A:GLY184 4.4 35.9 1.0 CB A:PRO196 4.5 33.3 1.0 CA A:CYS182 4.5 33.2 1.0 SG A:CYS163 4.5 39.2 1.0 N A:GLY184 4.6 34.9 1.0 SG A:CYS166 4.8 41.1 1.0 CD A:PRO185 4.8 41.1 1.0 CB A:LEU175 4.8 42.3 1.0 CD1 A:ILE174 4.9 39.0 1.0 C A:CYS182 5.0 34.4 1.0

X.Xiao, G.J.Schut, X.Feng, P.M.Mcternan, D.K.Haja, W.N.Lanzilotta, M.W.W.Adams, H.Li. Structural Insights Into the Biotechnologically Relevant Reversible Nadph-Oxidizing Nife-Hydrogenase From P.Furiosus. Structure 2025.
ISSN: ISSN 0969-2126
PubMed: 40570843
DOI: 10.1016/J.STR.2025.05.017