Iron in PDB 6huz: Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B

The structure of Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B, PDB code: 6huz was solved by T.Watanabe, T.Wagner, G.Huang, J.Kahnt, K.Ataka, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.39 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.200, 132.020, 49.160, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.3

The structure of Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Iron atom in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B (pdb code 6huz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B, PDB code: 6huz:

Iron binding site 1 out of 1 in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:38.8 occ:1.00 FE A:FE9401 0.0 38.8 1.0 C1F A:FE9401 1.8 43.6 1.0 C2F A:FE9401 1.8 42.3 1.0 C8 A:FE9401 1.9 36.8 1.0 N1 A:FE9401 2.0 36.7 1.0 O A:HOH509 2.2 38.0 1.0 SG A:CYS117 2.5 41.4 1.0 O18 A:FE9401 2.8 41.1 1.0 C6 A:FE9401 2.8 33.1 1.0 C7 A:FE9401 2.9 36.6 1.0 O1F A:FE9401 3.0 45.5 1.0 O2F A:FE9401 3.0 38.5 1.0 C2 A:FE9401 3.0 32.6 1.0 O2 A:FE9401 3.2 34.7 1.0 CB A:CYS117 3.5 35.5 1.0 O4 A:GUE402 4.1 25.0 1.0 C5 A:FE9401 4.3 35.8 1.0 C3 A:FE9401 4.4 37.5 1.0 N5 A:GUE402 4.6 39.0 1.0 O A:ALA149 4.7 29.6 1.0 C4 A:GUE402 4.7 21.9 1.0 CA A:CYS117 4.8 33.6 1.0 OH A:TYR14 4.8 40.9 1.0 C1 A:GUE402 4.8 39.5 1.0 N A:CYS117 4.8 33.8 1.0 C4 A:FE9401 4.9 39.1 1.0 C4A A:GUE402 4.9 29.4 1.0 CZ A:PHE88 4.9 37.7 1.0 CG A:PRO147 5.0 27.0 1.0 C6 A:GUE402 5.0 34.1 1.0

T.Watanabe, T.Wagner, G.Huang, J.Kahnt, K.Ataka, U.Ermler, S.Shima. The Bacterial [Fe]-Hydrogenase Paralog Hmdii Uses Tetrahydrofolate Derivatives As Substrates. Angew. Chem. Int. Ed. Engl. V. 58 3506 2019.
ISSN: ESSN 1521-3773
PubMed: 30600878
DOI: 10.1002/ANIE.201813465