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Magnesium in PDB 1fyd: Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion

Enzymatic activity of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion

All present enzymatic activity of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion:
6.3.5.1;

Protein crystallography data

The structure of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion, PDB code: 1fyd was solved by Y.Devedjiev, J.Symersky, R.Singh, W.Brouillette, D.Muccio, M.Jedrzejas, C.Brouillette, L.Delucas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.450, 87.200, 61.180, 90.00, 111.15, 90.00
R / Rfree (%) 19.1 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion (pdb code 1fyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion, PDB code: 1fyd:

Magnesium binding site 1 out of 1 in 1fyd

Go back to Magnesium Binding Sites List in 1fyd
Magnesium binding site 1 out of 1 in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion


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 NH3-Dependent Nad+ Synthetase From Bacillus Subtilis Complexed with One Molecule Amp, One Pyrophosphate Ion and One MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2500

b:23.8
occ:0.35
 O A:THR208 1.8 37.6 1.0
O3P A:AMP4000 1.9 35.1 1.0
O A:HOH2186 2.1 35.2 0.5
O A:HOH2187 2.2 37.4 0.5
O5 A:POP5000 2.5 29.4 1.0
O3 A:POP5000 2.5 35.5 1.0
C A:THR208 3.0 36.5 1.0
P A:AMP4000 3.4 30.2 1.0
O A:HOH2185 3.6 39.5 1.0
O A:HOH2181 3.6 28.7 1.0
N A:THR208 3.7 37.6 1.0
P2 A:POP5000 3.7 32.9 1.0
P1 A:POP5000 3.9 43.7 1.0
O5' A:AMP4000 3.9 31.9 1.0
O2P A:AMP4000 4.0 40.2 1.0
CA A:THR208 4.0 38.2 1.0
O A:POP5000 4.0 36.1 1.0
N A:ALA209 4.0 38.1 1.0
O6 A:POP5000 4.2 32.3 1.0
CG2 A:THR208 4.2 37.5 1.0
CA A:ALA209 4.2 38.0 1.0
OG A:SER46 4.4 8.5 1.0
O1P A:AMP4000 4.5 35.1 1.0
O1 A:POP5000 4.5 41.2 1.0
CB A:THR208 4.7 37.5 1.0
C A:ALA209 4.8 39.6 1.0
CA A:GLY48 4.8 6.0 1.0
C A:PRO207 4.9 36.2 1.0
O4 A:POP5000 5.0 36.3 1.0
O A:ALA209 5.0 39.5 1.0

Reference:

Y.Devedjiev, J.Symersky, R.Singh, M.Jedrzejas, C.Brouillette, W.Brouillette, D.Muccio, D.Chattopadhyay, L.Delucas. Stabilization of Active-Site Loops in NH3-Dependent Nad+ Synthetase From Bacillus Subtilis. Acta Crystallogr.,Sect.D V. 57 806 2001.
ISSN: ISSN 0907-4449
PubMed: 11375500
DOI: 10.1107/S0907444901003523
Page generated: Sat Aug 9 21:12:48 2025

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