Sodium 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:

Iron

(Fe)

1 atom

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstituted with Fe-Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl-Tetrahydrofolate Form B, PDB code: 6huz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na406 b:63.0 occ:1.00 OE1 A:GLU325 3.3 96.2 1.0 CG A:MET322 3.4 47.3 1.0 N A:MET322 3.9 35.6 1.0 CB A:PRO321 4.0 35.8 1.0 C A:PRO321 4.1 40.3 1.0 CA A:MET322 4.1 36.8 1.0 CD A:GLU325 4.3 98.8 1.0 CB A:MET322 4.4 40.5 1.0 CG A:PRO321 4.4 37.6 1.0 O A:PRO321 4.4 41.7 1.0 CA A:PRO321 4.6 34.0 1.0 SD A:MET322 4.8 55.1 1.0 OE2 A:GLU325 4.8 100.0 1.0

Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na binding site number 2 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:Na407 b:30.5 occ:1.00 OG A:SER242 2.8 39.5 1.0 O A:GLN238 2.9 25.5 1.0 OE1 A:GLN238 3.0 23.7 1.0 NE2 A:GLN241 3.2 23.9 1.0 N A:SER242 3.5 20.8 1.0 CA A:GLN238 3.6 23.2 1.0 C A:GLN238 3.7 24.9 1.0 CD A:GLN238 3.7 26.3 1.0 CB A:GLN241 3.8 22.2 1.0 CB A:SER242 3.9 20.1 1.0 CA A:SER242 3.9 21.7 1.0 CB A:GLN238 4.1 21.6 1.0 CD A:GLN241 4.1 29.4 1.0 CG A:GLN241 4.1 21.3 1.0 C A:GLN241 4.2 24.7 1.0 NE2 A:GLN238 4.3 34.7 1.0 CG A:GLN238 4.5 22.8 1.0 CA A:GLN241 4.6 23.4 1.0 N A:GLN238 4.9 24.4 1.0 N A:ILE239 4.9 20.8 1.0 O A:PHE237 5.0 25.6 1.0 N A:GLN241 5.0 24.8 1.0

Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na408 b:47.5 occ:1.00 O A:HOH742 2.7 55.3 1.0 O A:LYS356 2.9 74.7 1.0 OE1 A:GLU256 3.0 34.5 1.0 OE2 A:GLU256 3.7 59.9 1.0 CA A:GLY254 3.7 26.7 1.0 CD A:GLU256 3.7 55.7 1.0 C A:LYS356 4.1 0.8 1.0 N A:LEU255 4.3 28.4 1.0 O A:HOH684 4.3 63.8 1.0 C A:GLY254 4.5 29.9 1.0 N A:GLY254 4.7 29.1 1.0 N A:LYS356 4.8 84.3 1.0 O A:HOH544 4.9 39.2 1.0 O A:TYR253 4.9 31.1 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