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Magnesium in PDB 3hrd: Crystal Structure of Nicotinate Dehydrogenase

Protein crystallography data

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

Other elements in 3hrd:

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

Magnesium Binding Sites:

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 3hrd

Go back to Magnesium Binding Sites List in 3hrd
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 3hrd

Go back to Magnesium Binding Sites List in 3hrd
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

Reference:

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
Page generated: Wed Aug 14 15:19:13 2024

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