Iron in PDB 6gm6: [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q

All present enzymatic activity of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q:
1.18.99.1;

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q, PDB code: 6gm6 was solved by J.Duan, V.Engelbrecht, 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)	48.09 / 1.61
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.790, 70.790, 155.030, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 19.9

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Iron atom in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q (pdb code 6gm6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q, PDB code: 6gm6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:15.9 occ:1.00 FE1 A:SF4601 0.0 15.9 1.0 S4 A:SF4601 2.3 17.6 1.0 S3 A:SF4601 2.3 17.9 1.0 S2 A:SF4601 2.3 14.7 1.0 SG A:CYS170 2.3 14.5 1.0 FE3 A:SF4601 2.7 16.6 1.0 FE4 A:SF4601 2.7 15.9 1.0 FE2 A:SF4601 2.7 17.6 1.0 CB A:CYS170 3.3 15.9 1.0 S1 A:SF4601 3.9 15.6 1.0 CA A:CYS170 3.9 11.2 1.0 N A:ALA416 3.9 14.2 1.0 CB A:ALA416 4.3 17.1 1.0 CD A:PRO171 4.4 16.9 1.0 CE A:MET415 4.4 25.6 1.0 C A:CYS170 4.6 16.6 1.0 CA A:ALA416 4.6 18.3 1.0 N A:PRO171 4.7 16.0 1.0 N A:CYS417 4.7 20.0 1.0 SG A:CYS225 4.7 17.2 1.0 SG A:CYS417 4.8 20.5 1.0 SG A:CYS421 4.8 17.6 1.0 N A:GLY172 4.8 14.2 1.0 C A:MET415 4.9 16.0 1.0 CA A:MET415 4.9 17.7 1.0 CB A:MET415 5.0 19.8 1.0

Iron binding site 2 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:17.6 occ:1.00 FE2 A:SF4601 0.0 17.6 1.0 S4 A:SF4601 2.3 17.6 1.0 SG A:CYS417 2.3 20.5 1.0 S3 A:SF4601 2.3 17.9 1.0 S1 A:SF4601 2.3 15.6 1.0 FE3 A:SF4601 2.7 16.6 1.0 FE1 A:SF4601 2.7 15.9 1.0 FE4 A:SF4601 2.8 15.9 1.0 CB A:CYS417 3.3 20.8 1.0 N A:CYS417 3.8 20.0 1.0 S2 A:SF4601 3.9 14.7 1.0 O A:HOH954 4.0 19.4 1.0 CA A:CYS417 4.2 22.6 1.0 O A:HOH996 4.3 31.1 1.0 CA A:GLY424 4.4 13.0 1.0 SG A:CYS225 4.6 17.2 1.0 CA A:CYS421 4.7 14.6 1.0 CB A:ALA416 4.7 17.1 1.0 C A:ALA416 4.7 22.3 1.0 SG A:CYS170 4.8 14.5 1.0 O A:GLY420 4.8 17.6 1.0 O A:HOH1039 4.8 33.2 1.0 N A:ALA416 4.8 14.2 1.0 C A:GLY420 4.8 21.1 1.0 SG A:CYS421 4.9 17.6 1.0 N A:CYS421 4.9 17.6 1.0

Iron binding site 3 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:16.6 occ:1.00 FE3 A:SF4601 0.0 16.6 1.0 S4 A:SF4601 2.3 17.6 1.0 S1 A:SF4601 2.3 15.6 1.0 SG A:CYS225 2.3 17.2 1.0 S2 A:SF4601 2.3 14.7 1.0 FE1 A:SF4601 2.7 15.9 1.0 FE2 A:SF4601 2.7 17.6 1.0 FE4 A:SF4601 2.7 15.9 1.0 CB A:CYS225 3.1 17.2 1.0 S3 A:SF4601 3.8 17.9 1.0 O A:HOH954 3.9 19.4 1.0 O A:HOH1199 4.1 27.1 1.0 CA A:CYS225 4.1 17.8 1.0 CD A:PRO171 4.5 16.9 1.0 SG A:CYS170 4.7 14.5 1.0 SG A:CYS421 4.7 17.6 1.0 SG A:CYS417 4.8 20.5 1.0 CE A:LYS228 4.9 13.8 1.0 CG A:PRO171 4.9 17.4 1.0 CB A:ARG227 5.0 15.7 1.0

Iron binding site 4 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:15.9 occ:1.00 FE4 A:SF4601 0.0 15.9 1.0 S2 A:SF4601 2.3 14.7 1.0 SG A:CYS421 2.3 17.6 1.0 S3 A:SF4601 2.3 17.9 1.0 S1 A:SF4601 2.3 15.6 1.0 FE3 A:SF4601 2.7 16.6 1.0 FE1 A:SF4601 2.7 15.9 1.0 FE2 A:SF4601 2.8 17.6 1.0 CB A:CYS421 3.4 14.3 1.0 CA A:CYS421 3.5 14.6 1.0 O A:HOH1199 3.8 27.1 1.0 CE A:MET415 3.9 25.6 1.0 N A:CYS421 3.9 17.6 1.0 S4 A:SF4601 3.9 17.6 1.0 O A:HOH1060 4.5 38.8 1.0 C A:GLY420 4.5 21.1 1.0 SG A:CYS225 4.8 17.2 1.0 SG A:CYS417 4.8 20.5 1.0 SG A:CYS170 4.9 14.5 1.0 C A:CYS421 4.9 15.4 1.0 CB A:CYS225 4.9 17.2 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