Molybdenum in PDB 2vpw: Polysulfide Reductase with Bound Menaquinone

The structure of Polysulfide Reductase with Bound Menaquinone, PDB code: 2vpw was solved by M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.82 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.377, 163.580, 238.891, 90.00, 90.00, 90.00
R / Rfree (%)	27.1 / 27.5

The structure of Polysulfide Reductase with Bound Menaquinone also contains other interesting chemical elements:

Iron

(Fe)

40 atoms

The binding sites of Molybdenum atom in the Polysulfide Reductase with Bound Menaquinone (pdb code 2vpw). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Polysulfide Reductase with Bound Menaquinone, PDB code: 2vpw:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mo1767 b:54.6 occ:1.00 S12 A:MGD1766 2.2 46.6 1.0 S12 A:MGD1765 2.3 51.9 1.0 S13 A:MGD1766 2.3 53.0 1.0 S13 A:MGD1765 2.5 52.1 1.0 SG A:CYS173 2.6 55.9 1.0 C13 A:MGD1766 3.3 48.4 1.0 C12 A:MGD1766 3.3 49.3 1.0 C13 A:MGD1765 3.3 52.1 1.0 C12 A:MGD1765 3.3 53.8 1.0 CB A:CYS173 3.4 57.5 1.0 NE A:ARG332 4.2 63.7 1.0 CD A:ARG332 4.4 61.8 1.0 CZ A:PHE631 4.5 50.2 1.0 CG A:ARG332 4.5 60.1 1.0 NH2 A:ARG625 4.5 57.9 1.0 CE2 A:PHE631 4.5 49.9 1.0 O A:HOH2166 4.5 86.2 1.0 C14 A:MGD1765 4.6 54.1 1.0 C14 A:MGD1766 4.7 44.7 1.0 C11 A:MGD1766 4.7 46.8 1.0 C11 A:MGD1765 4.7 51.5 1.0 CA A:CYS173 4.7 57.6 1.0 CB A:SER169 4.8 59.8 1.0 CA A:SER169 4.9 58.4 1.0

Molybdenum binding site 2 out of 2 in the Polysulfide Reductase with Bound Menaquinone


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Polysulfide Reductase with Bound Menaquinone within 5.0Å range: probe atom residue distance (Å) B Occ E:Mo1767 b:60.5 occ:1.00 SG E:CYS173 2.1 51.9 1.0 O E:HOH2453 2.2 41.7 1.0 S12 E:MGD1765 2.4 52.4 1.0 S13 E:MGD1766 2.4 48.8 1.0 S12 E:MGD1766 2.4 48.6 1.0 S13 E:MGD1765 2.5 51.9 1.0 C13 E:MGD1766 3.4 49.3 1.0 C12 E:MGD1766 3.4 49.0 1.0 C13 E:MGD1765 3.4 55.9 1.0 C12 E:MGD1765 3.4 56.4 1.0 CB E:CYS173 3.4 54.1 1.0 NE E:ARG332 4.2 53.3 1.0 CD E:ARG332 4.3 52.0 1.0 O E:HOH2214 4.3 67.3 1.0 CG E:ARG332 4.5 52.1 1.0 CE2 E:PHE631 4.5 53.2 1.0 NH2 E:ARG625 4.6 55.4 1.0 CZ E:PHE631 4.6 53.4 1.0 C11 E:MGD1766 4.7 46.1 1.0 C14 E:MGD1765 4.7 54.8 1.0 CA E:CYS173 4.8 54.8 1.0 C14 E:MGD1766 4.8 47.1 1.0 C11 E:MGD1765 4.8 54.3 1.0 CA E:SER169 4.9 58.1 1.0 CB E:SER169 5.0 57.8 1.0

M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata. Molecular Mechanism of Energy Conservation in Polysulfide Respiration. Nat.Struct.Mol.Biol. V. 15 730 2008.
ISSN: ISSN 1545-9993
PubMed: 18536726
DOI: 10.1038/NSMB.1434