Iron in PDB 6gm8: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q, PDB code: 6gm8 was solved by J.Duan, J.Esselborn, E.Hofmann, M.Winkler, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.650, 72.340, 103.150, 90.00, 96.73, 90.00
R / Rfree (%)	17.6 / 22.1

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q (pdb code 6gm8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q, PDB code: 6gm8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:18.5 occ:0.69 FE1 A:402601 0.0 18.5 0.7 C3 A:402601 1.7 16.8 1.0 C4 A:402601 1.8 19.6 0.8 C5 A:402601 1.9 23.3 0.5 S2 A:402601 2.3 22.8 0.9 S1 A:402601 2.3 23.1 0.8 SG A:CYS503 2.3 20.8 1.0 FE2 A:402601 2.6 26.2 0.8 O3 A:402601 2.9 23.1 0.7 O5 A:402601 3.0 23.0 1.0 N4 A:402601 3.1 13.1 1.0 CB A:CYS503 3.2 14.9 1.0 C2 A:402601 3.4 19.8 1.0 C1 A:402601 3.4 26.1 1.0 C7 A:402601 3.8 17.7 0.8 N1 A:402601 3.8 22.4 1.0 C6 A:402601 3.9 20.3 0.7 FE4 A:SF4602 4.0 20.0 1.0 S2 A:SF4602 4.2 22.4 1.0 CG A:PRO354 4.7 21.1 1.0 CA A:CYS503 4.7 18.1 1.0 CE A:LYS358 4.8 21.4 1.0 O7 A:402601 4.8 17.9 0.7 N6 A:402601 4.9 13.5 1.0 CD A:PRO231 4.9 21.6 1.0

Iron binding site 2 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:26.2 occ:0.80 FE2 A:402601 0.0 26.2 0.8 C7 A:402601 1.8 17.7 0.8 C6 A:402601 1.9 20.3 0.7 C5 A:402601 2.0 23.3 0.5 S1 A:402601 2.3 23.1 0.8 S2 A:402601 2.3 22.8 0.9 FE1 A:402601 2.6 18.5 0.7 O5 A:402601 2.8 23.0 1.0 O7 A:402601 2.9 17.9 0.7 N6 A:402601 3.1 13.5 1.0 N1 A:402601 3.2 22.4 1.0 C1 A:402601 3.3 26.1 1.0 C4 A:402601 3.6 19.6 0.8 C2 A:402601 3.6 19.8 1.0 C3 A:402601 3.7 16.8 1.0 CG A:PRO324 3.9 18.1 1.0 CB A:PRO324 4.2 15.4 1.0 CD A:PRO324 4.3 16.7 1.0 CD2 A:PHE417 4.3 19.2 1.0 SG A:CYS503 4.6 20.8 1.0 N4 A:402601 4.6 13.1 1.0 CD A:PRO231 4.6 21.6 1.0 O3 A:402601 4.7 23.1 0.7 NZ A:LYS358 4.7 20.5 1.0 CE A:LYS358 4.8 21.4 1.0 CG A:PRO231 4.9 20.9 1.0 CB A:PHE417 4.9 15.5 1.0

Iron binding site 3 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:20.5 occ:1.00 FE1 A:SF4602 0.0 20.5 1.0 S2 A:SF4602 2.2 22.4 1.0 SG A:CYS355 2.3 20.2 1.0 S4 A:SF4602 2.3 20.9 1.0 S3 A:SF4602 2.3 18.1 1.0 FE3 A:SF4602 2.7 19.2 1.0 FE4 A:SF4602 2.7 20.0 1.0 FE2 A:SF4602 2.7 19.7 1.0 CB A:CYS355 3.2 19.1 1.0 S1 A:SF4602 3.9 19.8 1.0 O A:HOH753 3.9 17.9 1.0 O3 A:402601 4.0 23.1 0.7 CA A:CYS355 4.2 21.3 1.0 CB A:SER357 4.5 22.0 1.0 C3 A:402601 4.5 16.8 1.0 CD A:PRO301 4.5 16.6 1.0 SG A:CYS503 4.7 20.8 1.0 SG A:CYS300 4.7 18.2 1.0 SG A:CYS499 4.8 21.3 1.0 CG A:PRO301 4.8 18.4 1.0 CG A:LYS358 4.8 20.2 1.0 CE A:LYS358 5.0 21.4 1.0

Iron binding site 4 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:19.7 occ:1.00 FE2 A:SF4602 0.0 19.7 1.0 S1 A:SF4602 2.3 19.8 1.0 SG A:CYS499 2.3 21.3 1.0 S3 A:SF4602 2.3 18.1 1.0 S4 A:SF4602 2.3 20.9 1.0 FE3 A:SF4602 2.7 19.2 1.0 FE1 A:SF4602 2.7 20.5 1.0 FE4 A:SF4602 2.8 20.0 1.0 CB A:CYS499 3.2 18.7 1.0 N A:CYS499 3.8 19.6 1.0 S2 A:SF4602 3.9 22.4 1.0 CA A:CYS499 4.1 22.0 1.0 O A:HOH753 4.2 17.9 1.0 CA A:GLY506 4.3 17.1 1.0 SG A:CYS355 4.6 20.2 1.0 CA A:CYS503 4.7 18.1 1.0 CB A:ALA498 4.8 18.2 1.0 SG A:CYS300 4.8 18.2 1.0 C A:ALA498 4.8 17.9 1.0 N A:ALA498 4.9 17.8 1.0 SG A:CYS503 4.9 20.8 1.0

Iron binding site 5 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:19.2 occ:1.00 FE3 A:SF4602 0.0 19.2 1.0 S4 A:SF4602 2.2 20.9 1.0 SG A:CYS300 2.3 18.2 1.0 S1 A:SF4602 2.3 19.8 1.0 S2 A:SF4602 2.3 22.4 1.0 FE1 A:SF4602 2.7 20.5 1.0 FE2 A:SF4602 2.7 19.7 1.0 FE4 A:SF4602 2.8 20.0 1.0 CB A:CYS300 3.4 17.4 1.0 S3 A:SF4602 3.9 18.1 1.0 CA A:CYS300 4.0 19.4 1.0 N A:ALA498 4.1 17.8 1.0 CB A:ALA498 4.3 18.2 1.0 N A:GLY302 4.4 23.5 1.0 CD A:PRO301 4.4 16.6 1.0 C A:CYS300 4.4 18.2 1.0 N A:PRO301 4.5 15.7 1.0 C2 A:402601 4.6 19.8 1.0 SG A:CYS499 4.7 21.3 1.0 N A:CYS499 4.7 19.6 1.0 CA A:ALA498 4.7 17.5 1.0 SG A:CYS503 4.8 20.8 1.0 SG A:CYS355 4.8 20.2 1.0 SD A:MET497 4.8 21.6 1.0 CA A:GLY302 4.8 19.4 1.0 CA A:MET497 5.0 25.0 1.0 C A:MET497 5.0 18.7 1.0

Iron binding site 6 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:20.0 occ:1.00 FE4 A:SF4602 0.0 20.0 1.0 S3 A:SF4602 2.3 18.1 1.0 SG A:CYS503 2.3 20.8 1.0 S2 A:SF4602 2.3 22.4 1.0 S1 A:SF4602 2.3 19.8 1.0 FE1 A:SF4602 2.7 20.5 1.0 FE2 A:SF4602 2.8 19.7 1.0 FE3 A:SF4602 2.8 19.2 1.0 CB A:CYS503 3.2 14.9 1.0 CA A:CYS503 3.4 18.1 1.0 C3 A:402601 3.7 16.8 1.0 N A:CYS503 3.8 24.0 1.0 S4 A:SF4602 3.9 20.9 1.0 O3 A:402601 3.9 23.1 0.7 FE1 A:402601 4.0 18.5 0.7 C2 A:402601 4.0 19.8 1.0 S2 A:402601 4.2 22.8 0.9 C A:GLY502 4.6 23.3 1.0 SD A:MET497 4.7 21.6 1.0 C A:CYS503 4.7 21.9 1.0 SG A:CYS355 4.7 20.2 1.0 SG A:CYS300 4.8 18.2 1.0 SG A:CYS499 4.9 21.3 1.0 CB A:CYS355 4.9 19.1 1.0

Iron binding site 7 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:19.3 occ:1.00 FE1 A:SF4603 0.0 19.3 1.0 SG A:CYS193 2.3 17.0 1.0 S4 A:SF4603 2.3 19.3 1.0 S3 A:SF4603 2.3 17.4 1.0 S2 A:SF4603 2.3 21.2 1.0 FE3 A:SF4603 2.8 19.3 1.0 FE2 A:SF4603 2.8 18.7 1.0 FE4 A:SF4603 2.8 21.1 1.0 N A:CYS193 3.6 19.9 1.0 CB A:CYS193 3.6 17.6 1.0 N A:GLY194 3.7 17.2 1.0 S1 A:SF4603 3.9 20.1 1.0 CA A:CYS193 4.0 20.1 1.0 CG2 A:THR161 4.2 19.0 1.0 N A:GLN195 4.2 22.4 1.0 C A:CYS193 4.2 18.5 1.0 N A:LEU192 4.4 20.1 1.0 C A:LEU192 4.6 20.3 1.0 SG A:CYS196 4.7 20.2 1.0 N A:LEU191 4.7 17.5 1.0 CB A:LEU191 4.7 16.4 1.0 CA A:GLY194 4.7 17.9 1.0 SG A:CYS190 4.7 20.4 1.0 CB A:GLN195 4.8 23.2 1.0 CA A:LEU192 4.9 18.5 1.0 SG A:CYS157 4.9 18.1 1.0 N A:CYS196 4.9 16.6 1.0 C A:GLY194 4.9 19.7 1.0 C A:LEU191 5.0 23.1 1.0

Iron binding site 8 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:18.7 occ:1.00 FE2 A:SF4603 0.0 18.7 1.0 S3 A:SF4603 2.3 17.4 1.0 S1 A:SF4603 2.3 20.1 1.0 S4 A:SF4603 2.3 19.3 1.0 SG A:CYS157 2.3 18.1 1.0 FE4 A:SF4603 2.7 21.1 1.0 FE3 A:SF4603 2.8 19.3 1.0 FE1 A:SF4603 2.8 19.3 1.0 CB A:CYS157 3.2 14.9 1.0 S2 A:SF4603 3.9 21.2 1.0 CA A:CYS157 3.9 17.2 1.0 CB A:ALA165 4.1 21.6 1.0 OG1 A:THR163 4.2 20.5 1.0 OG1 A:THR161 4.3 19.0 1.0 N A:MET166 4.4 21.0 1.0 CG2 A:THR161 4.5 19.0 1.0 N A:ALA165 4.7 22.2 1.0 CB A:MET166 4.7 25.3 1.0 SG A:CYS193 4.8 17.0 1.0 CA A:ALA165 4.8 20.0 1.0 C A:CYS157 4.8 20.6 1.0 SG A:CYS196 4.9 20.2 1.0 SG A:CYS190 4.9 20.4 1.0 C A:ALA165 5.0 22.2 1.0 O A:CYS157 5.0 20.0 1.0

Iron binding site 9 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:19.3 occ:1.00 FE3 A:SF4603 0.0 19.3 1.0 S2 A:SF4603 2.3 21.2 1.0 SG A:CYS196 2.3 20.2 1.0 S4 A:SF4603 2.3 19.3 1.0 S1 A:SF4603 2.3 20.1 1.0 FE4 A:SF4603 2.7 21.1 1.0 FE1 A:SF4603 2.8 19.3 1.0 FE2 A:SF4603 2.8 18.7 1.0 CB A:CYS196 3.3 19.6 1.0 N A:CYS196 3.9 16.6 1.0 S3 A:SF4603 3.9 17.4 1.0 CA A:CYS196 4.2 20.2 1.0 N A:GLY194 4.4 17.2 1.0 CE A:MET166 4.4 22.2 1.0 N A:GLN195 4.5 22.4 1.0 CD1 A:LEU140 4.6 33.2 1.0 SG A:CYS190 4.7 20.4 1.0 CA A:GLY194 4.7 17.9 1.0 SG A:CYS193 4.7 17.0 1.0 SG A:CYS157 4.8 18.1 1.0 C A:GLY194 4.8 19.7 1.0 CB A:CYS157 4.9 14.9 1.0 C A:GLN195 5.0 21.0 1.0

Iron binding site 10 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:21.1 occ:1.00 FE4 A:SF4603 0.0 21.1 1.0 S1 A:SF4603 2.3 20.1 1.0 S2 A:SF4603 2.3 21.2 1.0 SG A:CYS190 2.3 20.4 1.0 S3 A:SF4603 2.3 17.4 1.0 FE2 A:SF4603 2.7 18.7 1.0 FE3 A:SF4603 2.7 19.3 1.0 FE1 A:SF4603 2.8 19.3 1.0 CB A:CYS190 3.5 18.9 1.0 N A:LEU191 3.8 17.5 1.0 CA A:CYS190 3.9 18.0 1.0 S4 A:SF4603 3.9 19.3 1.0 N A:LEU192 3.9 20.1 1.0 CB A:ALA165 4.0 21.6 1.0 C A:CYS190 4.3 18.1 1.0 CA A:LEU192 4.5 18.5 1.0 CD1 A:LEU140 4.5 33.2 1.0 N A:CYS193 4.7 19.9 1.0 CD2 A:PHE185 4.7 20.9 1.0 SG A:CYS157 4.8 18.1 1.0 SG A:CYS196 4.8 20.2 1.0 CA A:LEU191 4.8 18.7 1.0 C A:LEU191 4.9 23.1 1.0 SG A:CYS193 5.0 17.0 1.0

J.Duan, M.Senger, J.Esselborn, V.Engelbrecht, F.Wittkamp, U.P.Apfel, E.Hofmann, S.T.Stripp, T.Happe, M.Winkler. Crystallographic and Spectroscopic Assignment of the Proton Transfer Pathway in [Fefe]-Hydrogenases. Nat Commun V. 9 4726 2018.
ISSN: ESSN 2041-1723
PubMed: 30413719
DOI: 10.1038/S41467-018-07140-X