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

Protein crystallography data

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

Other elements in 6huz:

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

Iron Binding Sites:

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 6huz

Go back to Iron Binding Sites List in 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

Reference:

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
Page generated: Sun Dec 13 16:29:14 2020

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