Iron in PDB 5aa5: Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution

All present enzymatic activity of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution:
1.12.99.6;

The structure of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution, PDB code: 5aa5 was solved by C.Schaefer, M.Bommer, S.Hennig, J.H.Jeoung, H.Dobbek, O.Lenz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.965 / 2.497
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.780, 267.971, 144.686, 90.00, 106.58, 90.00
R / Rfree (%)	18.7 / 24.2

The structure of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution also contains other interesting chemical elements:

Nickel

(Ni)

6 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 - 78;

Binding sites:

The binding sites of Iron atom in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution (pdb code 5aa5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 78 binding sites of Iron where determined in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution, PDB code: 5aa5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE1 A:SF4501 0.0 21.7 1.0 S3 A:SF4501 2.3 15.2 1.0 S2 A:SF4501 2.3 14.5 1.0 S4 A:SF4501 2.3 35.0 1.0 SG A:CYS257 2.3 30.1 1.0 FE4 A:SF4501 2.6 19.1 1.0 FE3 A:SF4501 2.7 30.6 1.0 FE2 A:SF4501 2.7 26.4 1.0 CB A:CYS257 3.3 19.7 1.0 S1 A:SF4501 3.9 21.3 1.0 CB A:PRO279 4.0 29.2 1.0 N A:GLY259 4.5 19.1 1.0 CA A:GLY259 4.5 23.0 1.0 SG A:CYS251 4.5 37.0 1.0 CG A:PRO279 4.6 30.4 1.0 CA A:CYS257 4.6 26.8 1.0 SG A:CYS231 4.7 23.9 1.0 C A:CYS257 4.8 23.5 1.0 ND1 A:HIS228 4.8 33.0 1.0 CG1 A:ILE252 4.9 20.4 1.0 N A:VAL253 4.9 30.5 1.0 CD A:PRO260 4.9 28.7 1.0 O A:CYS257 5.0 26.1 1.0

Iron binding site 2 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:26.4 occ:1.00 FE2 A:SF4501 0.0 26.4 1.0 ND1 A:HIS228 2.2 33.0 1.0 S4 A:SF4501 2.3 35.0 1.0 S3 A:SF4501 2.3 15.2 1.0 S1 A:SF4501 2.3 21.3 1.0 FE3 A:SF4501 2.5 30.6 1.0 FE1 A:SF4501 2.7 21.7 1.0 FE4 A:SF4501 2.7 19.1 1.0 CE1 A:HIS228 3.1 32.8 1.0 CG A:HIS228 3.2 38.0 1.0 CB A:HIS228 3.6 38.4 1.0 S2 A:SF4501 3.9 14.5 1.0 CA A:HIS228 3.9 29.4 1.0 NE2 A:HIS228 4.2 31.4 1.0 CG A:PRO260 4.3 29.3 1.0 CD2 A:HIS228 4.3 33.2 1.0 CD A:PRO260 4.4 28.7 1.0 CB A:CYS231 4.5 20.3 1.0 SG A:CYS251 4.6 37.0 1.0 CD2 A:TYR237 4.6 55.8 1.0 SG A:CYS231 4.6 23.9 1.0 N A:PRO260 4.8 29.0 1.0 SG A:CYS257 4.9 30.1 1.0 N A:HIS228 4.9 27.2 1.0 CA A:GLY259 4.9 23.0 1.0 O A:HIS228 4.9 32.3 1.0 C A:HIS228 5.0 27.8 1.0

Iron binding site 3 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:30.6 occ:1.00 FE3 A:SF4501 0.0 30.6 1.0 S1 A:SF4501 2.2 21.3 1.0 S4 A:SF4501 2.3 35.0 1.0 S2 A:SF4501 2.3 14.5 1.0 SG A:CYS251 2.3 37.0 1.0 FE2 A:SF4501 2.5 26.4 1.0 FE4 A:SF4501 2.6 19.1 1.0 FE1 A:SF4501 2.7 21.7 1.0 CB A:CYS251 3.5 23.3 1.0 S3 A:SF4501 3.8 15.2 1.0 CA A:CYS251 4.0 33.4 1.0 CD2 A:TYR237 4.0 55.8 1.0 N A:ILE252 4.2 29.9 1.0 ND1 A:HIS228 4.3 33.0 1.0 N A:VAL253 4.5 30.5 1.0 C A:CYS251 4.5 31.8 1.0 CB A:TYR237 4.6 50.2 1.0 CB A:VAL253 4.6 27.4 1.0 CE1 A:HIS228 4.6 32.8 1.0 CB A:ARG233 4.7 23.9 1.0 CG A:TYR237 4.7 53.4 1.0 SG A:CYS231 4.7 23.9 1.0 O A:ARG233 4.8 29.2 1.0 CE2 A:TYR237 4.8 57.3 1.0 SG A:CYS257 4.8 30.1 1.0 C A:ARG233 4.9 30.0 1.0 CA A:VAL253 5.0 32.2 1.0

Iron binding site 4 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.1 occ:1.00 FE4 A:SF4501 0.0 19.1 1.0 SG A:CYS231 2.3 23.9 1.0 S2 A:SF4501 2.3 14.5 1.0 S3 A:SF4501 2.3 15.2 1.0 S1 A:SF4501 2.3 21.3 1.0 FE1 A:SF4501 2.6 21.7 1.0 FE3 A:SF4501 2.6 30.6 1.0 FE2 A:SF4501 2.7 26.4 1.0 CB A:CYS231 3.1 20.3 1.0 S4 A:SF4501 3.9 35.0 1.0 CB A:PRO279 4.0 29.2 1.0 CB A:ARG233 4.1 23.9 1.0 CG A:PRO279 4.4 30.4 1.0 ND1 A:HIS228 4.5 33.0 1.0 CA A:CYS231 4.5 26.0 1.0 SG A:CYS257 4.6 30.1 1.0 N A:ALA234 4.7 30.1 1.0 C A:ARG233 4.7 30.0 1.0 CA A:ARG233 4.8 24.9 1.0 N A:ARG233 4.8 22.2 1.0 SG A:CYS251 4.8 37.0 1.0 CG A:ARG233 4.9 21.9 1.0 C A:CYS231 5.0 32.6 1.0

Iron binding site 5 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:26.0 occ:1.00 FE1 A:SF4502 0.0 26.0 1.0 SG A:CYS285 2.3 36.8 1.0 S3 A:SF4502 2.3 23.9 1.0 S4 A:SF4502 2.3 27.9 1.0 S2 A:SF4502 2.3 31.8 1.0 FE2 A:SF4502 2.6 19.8 1.0 FE3 A:SF4502 2.6 20.3 1.0 FE4 A:SF4502 2.7 17.9 1.0 CB A:CYS285 3.5 29.0 1.0 CA A:CYS285 3.9 29.7 1.0 S1 A:SF4502 3.9 15.1 1.0 N A:GLY287 4.0 17.8 1.0 N A:ILE286 4.1 25.7 1.0 CG2 A:VAL227 4.2 17.6 1.0 C A:CYS285 4.3 31.5 1.0 CA A:GLY287 4.5 26.5 1.0 CG1 A:VAL262 4.6 20.1 1.0 SG A:CYS278 4.6 23.4 1.0 N A:CYS288 4.6 19.2 1.0 SG A:CYS264 4.7 16.5 1.0 SG A:CYS288 4.8 24.2 1.0 CB A:CYS264 4.9 16.7 1.0 CB A:CYS278 4.9 24.4 1.0

Iron binding site 6 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.8 occ:1.00 FE2 A:SF4502 0.0 19.8 1.0 S3 A:SF4502 2.3 23.9 1.0 S1 A:SF4502 2.3 15.1 1.0 S4 A:SF4502 2.3 27.9 1.0 SG A:CYS278 2.3 23.4 1.0 FE3 A:SF4502 2.5 20.3 1.0 FE1 A:SF4502 2.6 26.0 1.0 FE4 A:SF4502 2.7 17.9 1.0 CB A:CYS278 3.4 24.4 1.0 S2 A:SF4502 3.8 31.8 1.0 CZ C:ARG203 4.0 28.8 1.0 NE C:ARG203 4.0 28.6 1.0 NH2 C:ARG203 4.1 30.9 1.0 NH1 C:ARG203 4.5 27.3 1.0 SG A:CYS288 4.6 24.2 1.0 CD C:ARG203 4.6 26.7 1.0 SG A:CYS285 4.6 36.8 1.0 CG1 A:VAL266 4.7 17.2 1.0 CA A:CYS278 4.8 27.7 1.0 CB A:VAL266 4.8 22.2 1.0 SG A:CYS264 4.9 16.5 1.0 CG2 A:VAL266 5.0 16.7 1.0 N A:CYS278 5.0 21.7 1.0

Iron binding site 7 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:20.3 occ:1.00 FE3 A:SF4502 0.0 20.3 1.0 S1 A:SF4502 2.2 15.1 1.0 S2 A:SF4502 2.3 31.8 1.0 S4 A:SF4502 2.3 27.9 1.0 SG A:CYS288 2.3 24.2 1.0 FE2 A:SF4502 2.5 19.8 1.0 FE4 A:SF4502 2.6 17.9 1.0 FE1 A:SF4502 2.6 26.0 1.0 CB A:CYS288 3.7 20.4 1.0 N A:CYS288 3.7 19.2 1.0 S3 A:SF4502 3.8 23.9 1.0 NH2 C:ARG203 3.9 30.9 1.0 CA A:CYS288 4.2 18.3 1.0 CZ C:ARG203 4.2 28.8 1.0 NH1 C:ARG203 4.3 27.3 1.0 CG2 A:THR289 4.3 16.2 1.0 N A:THR289 4.4 17.2 1.0 SG A:CYS264 4.5 16.5 1.0 C A:CYS288 4.6 21.2 1.0 SG A:CYS278 4.7 23.4 1.0 C A:GLY287 4.7 26.2 1.0 SG A:CYS285 4.8 36.8 1.0 N A:GLY287 4.8 17.8 1.0 NE C:ARG203 4.9 28.6 1.0 CA A:GLY287 5.0 26.5 1.0

Iron binding site 8 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:17.9 occ:1.00 FE4 A:SF4502 0.0 17.9 1.0 S1 A:SF4502 2.3 15.1 1.0 SG A:CYS264 2.3 16.5 1.0 S2 A:SF4502 2.3 31.8 1.0 S3 A:SF4502 2.3 23.9 1.0 FE3 A:SF4502 2.6 20.3 1.0 FE2 A:SF4502 2.7 19.8 1.0 FE1 A:SF4502 2.7 26.0 1.0 CB A:CYS264 3.2 16.7 1.0 S4 A:SF4502 4.0 27.9 1.0 CB A:VAL266 4.0 22.2 1.0 CG2 A:VAL266 4.0 16.7 1.0 CG2 A:THR289 4.2 16.2 1.0 CG2 A:VAL227 4.4 17.6 1.0 CA A:CYS264 4.7 17.0 1.0 SG A:CYS288 4.7 24.2 1.0 SG A:CYS285 4.7 36.8 1.0 CG1 A:VAL266 4.7 17.2 1.0 SG A:CYS278 4.7 23.4 1.0 CD A:PRO267 4.9 17.7 1.0 N A:VAL266 4.9 25.5 1.0

Iron binding site 9 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:20.9 occ:1.00 FE1 A:SF4503 0.0 20.9 1.0 SG A:CYS32 2.2 30.1 1.0 S4 A:SF4503 2.3 30.1 1.0 S2 A:SF4503 2.3 15.9 1.0 S3 A:SF4503 2.3 22.1 1.0 FE3 A:SF4503 2.5 19.4 1.0 FE2 A:SF4503 2.6 15.0 1.0 FE4 A:SF4503 2.6 19.9 1.0 CB A:CYS32 3.4 25.1 1.0 N A:CYS32 3.7 23.6 1.0 S1 A:SF4503 3.8 18.8 1.0 CA A:CYS32 4.1 21.0 1.0 NE2 C:HIS206 4.3 22.7 1.0 N A:GLY34 4.3 23.6 1.0 OD2 A:ASP35 4.4 28.7 1.0 SG A:CYS186 4.6 25.4 1.0 C A:CYS32 4.6 25.1 1.0 CA A:GLY34 4.7 17.9 1.0 C A:GLY31 4.7 22.3 1.0 N A:ASP33 4.7 33.1 1.0 SG A:CYS145 4.7 17.5 1.0 O C:ARG79 4.7 31.2 1.0 CA A:GLY31 4.8 21.8 1.0 CE1 A:HIS152 5.0 22.7 1.0

Iron binding site 10 out of 78 in the Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Actinobacterial-Type Nife-Hydrogenase From Ralstonia Eutropha H16 at 2.85 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:15.0 occ:1.00 FE2 A:SF4503 0.0 15.0 1.0 SG A:CYS145 2.3 17.5 1.0 S1 A:SF4503 2.3 18.8 1.0 S3 A:SF4503 2.3 22.1 1.0 S4 A:SF4503 2.3 30.1 1.0 FE3 A:SF4503 2.4 19.4 1.0 FE1 A:SF4503 2.6 20.9 1.0 FE4 A:SF4503 2.7 19.9 1.0 CB A:CYS145 3.2 23.8 1.0 S2 A:SF4503 3.8 15.9 1.0 N A:CYS145 4.2 23.4 1.0 CE1 A:HIS152 4.2 22.7 1.0 CA A:CYS145 4.3 17.4 1.0 SG A:CYS186 4.3 25.4 1.0 OD2 A:ASP35 4.5 28.7 1.0 ND1 A:HIS152 4.5 23.0 1.0 CA A:GLY31 4.7 21.8 1.0 SG A:CYS32 4.8 30.1 1.0 N A:CYS32 4.9 23.6 1.0 O A:LEU30 5.0 25.4 1.0

C.Schafer, M.Bommer, S.E.Hennig, J.Jeoung, H.Dobbek, O.Lenz. Structure of An Actinobacterial-Type [Nife]-Hydrogenase Reveals Insight Into O2-Tolerant H2 Oxidation. Structure V. 24 285 2016.
ISSN: ISSN 0969-2126
PubMed: 26749450
DOI: 10.1016/J.STR.2015.11.010