Molybdenum in PDB 3hrd: Crystal Structure of Nicotinate Dehydrogenase

The structure of Crystal Structure of Nicotinate Dehydrogenase, PDB code: 3hrd was solved by N.Wagener, A.J.Pierik, R.Hille, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.069, 71.700, 214.485, 90.00, 90.23, 90.00
R / Rfree (%)	21.3 / 25.1

The structure of Crystal Structure of Nicotinate Dehydrogenase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	8 atoms
Calcium	(Ca)	1 atom

The binding sites of Molybdenum atom in the Crystal Structure of Nicotinate Dehydrogenase (pdb code 3hrd). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Crystal Structure of Nicotinate Dehydrogenase, PDB code: 3hrd:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in the Crystal Structure of Nicotinate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure of Nicotinate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mo920 b:17.3 occ:1.00 MO B:MOS920 0.0 17.3 1.0 O1 B:MOS920 1.7 9.1 1.0 O2 B:MOS920 1.8 14.0 1.0 SE A:SE922 2.3 21.3 0.8 S7' B:MCN921 2.4 14.0 1.0 S8' B:MCN921 2.5 15.0 1.0 OE2 B:GLU289 3.1 15.7 1.0 C7' B:MCN921 3.4 15.6 1.0 C8' B:MCN921 3.5 15.7 1.0 CD B:GLU289 3.6 13.7 1.0 CA B:SER85 3.9 17.2 1.0 CB B:SER85 4.0 18.6 1.0 N B:ALA86 4.1 18.5 1.0 OE1 B:GLU289 4.1 13.0 1.0 CA A:GLY240 4.1 12.3 1.0 CG B:GLU289 4.2 12.4 1.0 N A:GLY240 4.2 14.0 1.0 C A:PHE239 4.4 14.5 1.0 O A:PHE239 4.4 14.8 1.0 CA A:ARG351 4.5 14.1 1.0 N A:ARG351 4.5 13.9 1.0 C B:SER85 4.6 17.2 1.0 C6' B:MCN921 4.8 14.2 1.0 NE2 A:GLN208 4.8 13.0 1.0 O B:THR84 4.8 14.6 1.0 CD1 A:LEU243 4.9 8.5 1.0 C9' B:MCN921 4.9 15.9 1.0

Molybdenum binding site 2 out of 2 in the Crystal Structure of Nicotinate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure of Nicotinate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mo920 b:35.9 occ:1.00 MO F:MOS920 0.0 35.9 1.0 O1 F:MOS920 1.7 37.5 1.0 O2 F:MOS920 1.8 34.8 1.0 SE E:SE922 2.3 38.4 0.8 S7' F:MCN921 2.4 32.2 1.0 S8' F:MCN921 2.5 32.6 1.0 OE2 F:GLU289 2.9 34.5 1.0 CD F:GLU289 3.4 36.2 1.0 C7' F:MCN921 3.4 31.3 1.0 C8' F:MCN921 3.4 31.2 1.0 OE1 F:GLU289 3.9 35.6 1.0 CA F:SER85 4.0 33.7 1.0 CG F:GLU289 4.0 35.4 1.0 CB F:SER85 4.0 35.2 1.0 N F:ALA86 4.1 32.9 1.0 CA E:GLY240 4.2 28.1 1.0 N E:GLY240 4.4 28.6 1.0 CA E:ARG351 4.5 36.9 1.0 N E:ARG351 4.6 36.8 1.0 C E:PHE239 4.6 28.7 1.0 C F:SER85 4.6 32.1 1.0 O E:PHE239 4.6 30.2 1.0 O F:THR84 4.7 32.1 1.0 C6' F:MCN921 4.8 29.1 1.0 CD1 E:LEU243 4.8 35.9 1.0 C9' F:MCN921 4.9 30.9 1.0 NE2 E:GLN208 4.9 26.9 1.0

N.Wagener, A.J.Pierik, A.Ibdah, R.Hille, H.Dobbek. The Mo-Se Active Site of Nicotinate Dehydrogenase Proc.Natl.Acad.Sci.Usa V. 106 11055 2009.
ISSN: ISSN 0027-8424
PubMed: 19549881
DOI: 10.1073/PNAS.0902210106