Magnesium 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:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	8 atoms
Calcium	(Ca)	1 atom

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Nicotinate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg426 b:21.1 occ:1.00 ND2 A:ASN209 2.6 8.6 1.0 O A:HOH448 2.6 24.6 1.0 OG1 A:THR207 2.7 16.5 1.0 OD1 A:ASP213 2.7 13.8 1.0 O A:LYS242 2.9 15.8 1.0 O A:LEU243 2.9 16.4 1.0 O A:ASP244 3.3 19.5 1.0 C A:LEU243 3.4 15.7 1.0 NE2 A:GLN248 3.5 11.9 1.0 CG A:ASP213 3.5 13.1 1.0 OD2 A:ASP213 3.5 15.0 1.0 CG A:ASN209 3.6 14.2 1.0 C A:LYS242 3.7 14.2 1.0 CA A:LEU243 3.8 15.1 1.0 CB A:THR207 3.8 13.7 1.0 C A:ASP244 3.9 17.2 1.0 OD1 A:ASN209 3.9 15.5 1.0 N A:LEU243 4.1 14.2 1.0 N A:ASP244 4.2 17.4 1.0 N A:GLN208 4.4 11.9 1.0 CA A:THR207 4.5 12.9 1.0 N A:LEU245 4.5 13.5 1.0 N A:ASN209 4.5 13.8 1.0 CD2 A:TYR212 4.6 10.1 1.0 CA A:ASP244 4.6 16.5 1.0 CA A:LEU245 4.6 13.0 1.0 CD A:GLN248 4.6 14.5 1.0 O A:ASN209 4.7 11.2 1.0 CA A:LYS242 4.8 13.2 1.0 CE2 A:TYR212 4.9 10.9 1.0 CB A:ASN209 4.9 12.2 1.0 CB A:ASP213 5.0 13.3 1.0 C A:ASN209 5.0 12.2 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nicotinate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg427 b:23.7 occ:1.00 O A:TYR309 2.3 15.0 1.0 OG1 A:THR306 2.3 8.5 1.0 O A:SER347 2.3 13.7 1.0 O A:THR306 2.4 11.1 1.0 O A:ALA310 2.5 13.0 1.0 C A:ALA310 3.0 11.5 1.0 CB A:THR306 3.2 13.3 1.0 C A:THR306 3.3 11.9 1.0 C A:TYR309 3.4 15.1 1.0 C A:SER347 3.4 14.0 1.0 CA A:ALA310 3.5 12.8 1.0 CG2 A:THR306 3.5 10.3 1.0 CA A:THR306 3.6 10.6 1.0 N A:SER347 3.6 13.2 1.0 NE2 A:HIS279 3.8 12.1 1.0 CA A:SER347 3.9 13.5 1.0 N A:ALA310 3.9 14.3 1.0 N A:SER311 3.9 11.9 1.0 CB A:SER347 3.9 13.8 1.0 CB A:SER311 4.0 12.2 1.0 CE1 A:HIS279 4.1 13.8 1.0 N A:GLY313 4.3 15.3 1.0 CG A:MET346 4.3 15.0 1.0 CA A:GLY313 4.4 15.5 1.0 CA A:SER311 4.4 13.1 1.0 N A:GLY348 4.5 14.0 1.0 N A:GLY307 4.6 14.1 1.0 C A:MET346 4.6 15.3 1.0 CA A:TYR309 4.7 14.9 1.0 C A:SER311 4.7 14.7 1.0 N A:TYR309 4.8 14.8 1.0 CD2 A:HIS279 4.8 12.2 1.0 CA A:GLY348 4.9 15.1 1.0 CB A:ALA310 4.9 9.8 1.0 N A:TYR312 4.9 16.2 1.0 CA A:MET346 5.0 14.4 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