Iron in PDB 5la3: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A, PDB code: 5la3 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)	48.46 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.480, 73.580, 103.810, 90.00, 96.29, 90.00
R / Rfree (%)	16.6 / 21.3

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A also contains other interesting chemical elements:

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;

Binding sites:

The binding sites of Iron atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A (pdb code 5la3). 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 E279A, PDB code: 5la3:
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 E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:17.9 occ:0.82 FE1 A:402601 0.0 17.9 0.8 C3 A:402601 1.7 15.9 1.0 C4 A:402601 1.8 16.2 0.8 C5 A:402601 1.9 19.7 1.0 S1 A:402601 2.3 19.3 0.9 S2 A:402601 2.3 19.0 1.0 SG A:CYS503 2.3 23.6 1.0 FE2 A:402601 2.5 23.4 1.0 O3 A:402601 3.0 18.5 0.8 N4 A:402601 3.0 13.3 1.0 O5 A:402601 3.1 17.9 0.8 CB A:CYS503 3.2 16.1 1.0 C1 A:402601 3.4 18.1 1.0 C2 A:402601 3.5 19.4 1.0 C7 A:402601 3.8 19.7 0.8 N1 A:402601 3.8 22.9 0.8 C6 A:402601 3.8 18.3 0.8 FE4 A:SF4602 4.1 19.4 1.0 S2 A:SF4602 4.3 18.3 1.0 CA A:CYS503 4.7 20.4 1.0 CG A:PRO354 4.8 19.8 1.0 O7 A:402601 4.8 19.0 0.8 CE A:LYS358 4.8 16.1 1.0 N6 A:402601 4.9 16.8 1.0

Iron binding site 2 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:23.4 occ:0.97 FE2 A:402601 0.0 23.4 1.0 C7 A:402601 1.8 19.7 0.8 C6 A:402601 1.9 18.3 0.8 C5 A:402601 2.0 19.7 1.0 S2 A:402601 2.3 19.0 1.0 S1 A:402601 2.3 19.3 0.9 FE1 A:402601 2.5 17.9 0.8 O5 A:402601 2.7 17.9 0.8 O7 A:402601 2.9 19.0 0.8 N6 A:402601 3.1 16.8 1.0 N1 A:402601 3.2 22.9 0.8 C1 A:402601 3.3 18.1 1.0 C2 A:402601 3.6 19.4 1.0 C4 A:402601 3.7 16.2 0.8 C3 A:402601 3.7 15.9 1.0 CG A:PRO324 4.1 19.5 1.0 CD A:PRO324 4.4 20.9 1.0 CB A:PRO324 4.5 15.7 1.0 CD2 A:PHE417 4.5 20.2 1.0 SG A:CYS503 4.5 23.6 1.0 O3 A:402601 4.6 18.5 0.8 N4 A:402601 4.6 13.3 1.0 NZ A:LYS358 4.7 20.3 1.0 CE A:LYS358 4.7 16.1 1.0 CD A:PRO231 4.9 23.7 1.0

Iron binding site 3 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:21.1 occ:0.82 FE1 A:SF4602 0.0 21.1 0.8 S2 A:SF4602 2.3 18.3 1.0 S4 A:SF4602 2.3 20.5 1.0 S3 A:SF4602 2.3 20.8 1.0 SG A:CYS355 2.3 24.3 1.0 FE2 A:SF4602 2.7 20.8 1.0 FE3 A:SF4602 2.7 22.1 1.0 FE4 A:SF4602 2.7 19.4 1.0 CB A:CYS355 3.0 20.3 1.0 O A:HOH742 3.6 24.2 1.0 O3 A:402601 3.8 18.5 0.8 S1 A:SF4602 3.9 18.4 0.9 CA A:CYS355 4.2 21.9 1.0 C3 A:402601 4.5 15.9 1.0 CB A:SER357 4.6 22.3 1.0 SG A:CYS503 4.7 23.6 1.0 CD A:PRO301 4.7 22.2 1.0 CG A:PRO301 4.8 24.6 1.0 SG A:CYS499 4.8 23.7 1.0 SG A:CYS300 4.8 17.6 1.0 CG A:LYS358 4.8 19.9 1.0 CE A:LYS358 5.0 16.1 1.0 C A:CYS355 5.0 22.7 1.0

Iron binding site 4 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:20.8 occ:1.00 FE2 A:SF4602 0.0 20.8 1.0 S4 A:SF4602 2.3 20.5 1.0 S1 A:SF4602 2.3 18.4 0.9 SG A:CYS499 2.3 23.7 1.0 S3 A:SF4602 2.3 20.8 1.0 FE1 A:SF4602 2.7 21.1 0.8 FE3 A:SF4602 2.7 22.1 1.0 FE4 A:SF4602 2.8 19.4 1.0 CB A:CYS499 3.3 15.4 1.0 O A:HOH742 3.9 24.2 1.0 N A:CYS499 3.9 19.8 1.0 S2 A:SF4602 3.9 18.3 1.0 CA A:CYS499 4.2 16.3 1.0 CA A:GLY506 4.4 22.8 1.0 SG A:CYS355 4.7 24.3 1.0 CB A:ALA498 4.7 19.5 1.0 SG A:CYS300 4.8 17.6 1.0 C A:ALA498 4.8 19.0 1.0 CA A:CYS503 4.9 20.4 1.0 SG A:CYS503 4.9 23.6 1.0 CB A:CYS355 5.0 20.3 1.0 N A:ALA498 5.0 17.7 1.0

Iron binding site 5 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:22.1 occ:1.00 FE3 A:SF4602 0.0 22.1 1.0 SG A:CYS300 2.3 17.6 1.0 S4 A:SF4602 2.3 20.5 1.0 S2 A:SF4602 2.3 18.3 1.0 S1 A:SF4602 2.3 18.4 0.9 FE2 A:SF4602 2.7 20.8 1.0 FE1 A:SF4602 2.7 21.1 0.8 FE4 A:SF4602 2.8 19.4 1.0 CB A:CYS300 3.4 20.7 1.0 S3 A:SF4602 3.9 20.8 1.0 CA A:CYS300 4.0 18.7 1.0 N A:ALA498 4.1 17.7 1.0 CB A:ALA498 4.2 19.5 1.0 N A:GLY302 4.4 24.4 1.0 CD A:PRO301 4.4 22.2 1.0 C A:CYS300 4.5 25.2 1.0 N A:PRO301 4.6 26.6 1.0 CA A:ALA498 4.7 22.2 1.0 SG A:CYS499 4.7 23.7 1.0 C2 A:402601 4.7 19.4 1.0 CA A:GLY302 4.7 21.5 1.0 SG A:CYS503 4.8 23.6 1.0 N A:CYS499 4.8 19.8 1.0 SG A:CYS355 4.9 24.3 1.0 SD A:MET497 4.9 30.4 1.0

Iron binding site 6 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:19.4 occ:1.00 FE4 A:SF4602 0.0 19.4 1.0 S3 A:SF4602 2.3 20.8 1.0 S1 A:SF4602 2.3 18.4 0.9 SG A:CYS503 2.3 23.6 1.0 S2 A:SF4602 2.3 18.3 1.0 FE1 A:SF4602 2.7 21.1 0.8 FE2 A:SF4602 2.8 20.8 1.0 FE3 A:SF4602 2.8 22.1 1.0 CB A:CYS503 3.4 16.1 1.0 CA A:CYS503 3.5 20.4 1.0 C3 A:402601 3.7 15.9 1.0 S4 A:SF4602 3.9 20.5 1.0 O3 A:402601 3.9 18.5 0.8 N A:CYS503 4.0 20.2 1.0 FE1 A:402601 4.1 17.9 0.8 C2 A:402601 4.1 19.4 1.0 S2 A:402601 4.2 19.0 1.0 C A:GLY502 4.6 23.8 1.0 CB A:CYS355 4.7 20.3 1.0 SG A:CYS300 4.8 17.6 1.0 C A:CYS503 4.8 26.2 1.0 SD A:MET497 4.8 30.4 1.0 SG A:CYS355 4.8 24.3 1.0 SG A:CYS499 4.9 23.7 1.0 O A:GLY502 5.0 19.5 1.0

Iron binding site 7 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:20.8 occ:1.00 FE1 A:SF4603 0.0 20.8 1.0 S4 A:SF4603 2.3 15.2 0.9 SG A:CYS193 2.3 18.2 1.0 S2 A:SF4603 2.3 15.6 0.9 S3 A:SF4603 2.3 21.4 1.0 FE3 A:SF4603 2.7 15.7 0.9 FE2 A:SF4603 2.8 15.6 1.0 FE4 A:SF4603 2.8 16.8 1.0 N A:CYS193 3.6 21.1 1.0 CB A:CYS193 3.7 21.4 1.0 N A:GLY194 3.7 17.7 1.0 S1 A:SF4603 3.9 24.6 1.0 CA A:CYS193 4.0 18.3 1.0 CG2 A:THR161 4.2 16.8 1.0 N A:GLN195 4.2 20.9 1.0 C A:CYS193 4.3 20.0 1.0 N A:LEU192 4.3 21.4 1.0 C A:LEU192 4.6 24.4 1.0 CA A:GLY194 4.7 17.9 1.0 SG A:CYS190 4.7 19.2 1.0 SG A:CYS196 4.7 19.4 1.0 N A:LEU191 4.7 20.2 1.0 CA A:LEU192 4.8 23.7 1.0 CB A:LEU191 4.8 17.1 1.0 CB A:GLN195 4.9 21.4 1.0 SG A:CYS157 4.9 18.9 1.0 C A:LEU191 4.9 21.7 1.0 C A:GLY194 5.0 23.5 1.0

Iron binding site 8 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:15.6 occ:0.96 FE2 A:SF4603 0.0 15.6 1.0 S3 A:SF4603 2.3 21.4 1.0 S1 A:SF4603 2.3 24.6 1.0 SG A:CYS157 2.3 18.9 1.0 S4 A:SF4603 2.3 15.2 0.9 FE4 A:SF4603 2.7 16.8 1.0 FE3 A:SF4603 2.8 15.7 0.9 FE1 A:SF4603 2.8 20.8 1.0 CB A:CYS157 3.2 14.3 1.0 S2 A:SF4603 3.9 15.6 0.9 CA A:CYS157 4.0 17.9 1.0 CB A:ALA165 4.2 21.9 1.0 OG1 A:THR163 4.3 22.1 1.0 OG1 A:THR161 4.3 19.6 1.0 N A:MET166 4.5 14.2 1.0 CG2 A:THR161 4.5 16.8 1.0 N A:ALA165 4.6 23.7 1.0 SG A:CYS193 4.8 18.2 1.0 CB A:MET166 4.8 17.3 1.0 CA A:ALA165 4.8 26.6 1.0 C A:CYS157 4.8 21.2 1.0 O A:CYS157 4.9 25.7 1.0 SG A:CYS196 4.9 19.4 1.0 C A:ALA165 4.9 25.2 1.0 SG A:CYS190 5.0 19.2 1.0

Iron binding site 9 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:15.7 occ:0.95 FE3 A:SF4603 0.0 15.7 0.9 S2 A:SF4603 2.3 15.6 0.9 S4 A:SF4603 2.3 15.2 0.9 SG A:CYS196 2.3 19.4 1.0 S1 A:SF4603 2.3 24.6 1.0 FE1 A:SF4603 2.7 20.8 1.0 FE4 A:SF4603 2.7 16.8 1.0 FE2 A:SF4603 2.8 15.6 1.0 CB A:CYS196 3.4 13.9 1.0 S3 A:SF4603 3.9 21.4 1.0 N A:CYS196 3.9 16.4 1.0 CA A:CYS196 4.3 14.7 1.0 N A:GLY194 4.4 17.7 1.0 N A:GLN195 4.5 20.9 1.0 CD1 A:LEU140 4.5 29.9 1.0 CE A:MET166 4.6 13.8 1.0 CA A:GLY194 4.6 17.9 1.0 SG A:CYS190 4.7 19.2 1.0 SG A:CYS193 4.7 18.2 1.0 SG A:CYS157 4.7 18.9 1.0 C A:GLY194 4.8 23.5 1.0 CB A:CYS157 4.9 14.3 1.0

Iron binding site 10 out of 40 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E279A


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 E279A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:16.8 occ:1.00 FE4 A:SF4603 0.0 16.8 1.0 S1 A:SF4603 2.3 24.6 1.0 SG A:CYS190 2.3 19.2 1.0 S3 A:SF4603 2.3 21.4 1.0 S2 A:SF4603 2.3 15.6 0.9 FE2 A:SF4603 2.7 15.6 1.0 FE3 A:SF4603 2.7 15.7 0.9 FE1 A:SF4603 2.8 20.8 1.0 CB A:CYS190 3.5 20.8 1.0 N A:LEU191 3.8 20.2 1.0 CA A:CYS190 3.9 24.4 1.0 N A:LEU192 3.9 21.4 1.0 S4 A:SF4603 3.9 15.2 0.9 CB A:ALA165 4.1 21.9 1.0 C A:CYS190 4.3 22.5 1.0 CA A:LEU192 4.5 23.7 1.0 CD1 A:LEU140 4.6 29.9 1.0 N A:CYS193 4.8 21.1 1.0 SG A:CYS157 4.8 18.9 1.0 CA A:LEU191 4.8 19.3 1.0 C A:LEU191 4.9 21.7 1.0 SG A:CYS196 4.9 19.4 1.0 CD2 A:PHE185 4.9 21.0 1.0 SG A:CYS193 5.0 18.2 1.0

M.Winkler, M.Senger, J.Duan, J.Esselborn, F.Wittkamp, E.Hofmann, U.P.Apfel, S.T.Stripp, T.Happe. Accumulating the Hydride State in the Catalytic Cycle of [Fefe]-Hydrogenases. Nat Commun V. 8 16115 2017.
ISSN: ESSN 2041-1723
PubMed: 28722011
DOI: 10.1038/NCOMMS16115