Molybdenum in PDB 6tg9: Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus

All present enzymatic activity of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus:
1.2.1.2;

The structure of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus also contains other interesting chemical elements:

Iron

(Fe)

48 atoms

The binding sites of Molybdenum atom in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus (pdb code 6tg9). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus, PDB code: 6tg9:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mo1003 b:13.9 occ:1.00 S A:H2S1009 2.2 11.7 1.0 S13 A:MGD1002 2.4 5.1 1.0 S13 A:MGD1001 2.4 7.0 1.0 S12 A:MGD1001 2.5 7.0 1.0 S12 A:MGD1002 2.5 5.1 1.0 SG A:CYS386 2.7 7.5 1.0 CB A:CYS386 2.9 7.5 1.0 C12 A:MGD1002 3.2 5.1 1.0 C13 A:MGD1002 3.3 5.1 1.0 C12 A:MGD1001 3.3 7.0 1.0 C13 A:MGD1001 3.3 7.0 1.0 CA A:GLY588 4.2 4.6 1.0 N A:GLN589 4.2 7.6 1.0 CA A:CYS386 4.4 7.5 1.0 C11 A:MGD1002 4.5 5.1 1.0 OE1 A:GLN589 4.6 7.6 1.0 NH2 A:ARG829 4.6 6.0 1.0 C11 A:MGD1001 4.7 7.0 1.0 C14 A:MGD1002 4.8 5.1 1.0 C14 A:MGD1001 4.8 7.0 1.0 N A:GLY588 4.8 4.6 1.0 C A:GLY588 4.8 4.6 1.0 CG A:GLN589 5.0 7.6 1.0

Molybdenum binding site 2 out of 2 in the Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Cryo-Em Structure of Nadh Reduced Form of Nad+-Dependent Formate Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mo1003 b:12.1 occ:1.00 S E:H2S1009 2.2 11.0 1.0 S13 E:MGD1002 2.4 5.0 1.0 S13 E:MGD1001 2.4 6.8 1.0 S12 E:MGD1001 2.5 6.8 1.0 S12 E:MGD1002 2.5 5.0 1.0 SG E:CYS386 2.7 7.5 1.0 CB E:CYS386 2.9 7.5 1.0 C12 E:MGD1002 3.2 5.0 1.0 C13 E:MGD1002 3.3 5.0 1.0 C12 E:MGD1001 3.3 6.8 1.0 C13 E:MGD1001 3.3 6.8 1.0 CA E:GLY588 4.2 4.5 1.0 N E:GLN589 4.2 7.3 1.0 CA E:CYS386 4.4 7.5 1.0 C11 E:MGD1002 4.5 5.0 1.0 OE1 E:GLN589 4.6 7.3 1.0 NH2 E:ARG829 4.6 5.9 1.0 C11 E:MGD1001 4.7 6.8 1.0 C14 E:MGD1002 4.8 5.0 1.0 C14 E:MGD1001 4.8 6.8 1.0 N E:GLY588 4.8 4.5 1.0 C E:GLY588 4.8 4.5 1.0 CG E:GLN589 5.0 7.3 1.0

P.Wendler, C.Radon, G.Mittelstaedt, B.R.Duffus, J.Buerger, T.Mielke, S.Leimkuehler. Cryo-Em Structures Reveal Intricate Fe-S Cluster Arrangement and Charging in Rhodobacter Capsulatus Formate Dehydrogenase Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-15614-0