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Magnesium in PDB 2nsy: Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate

Enzymatic activity of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate

All present enzymatic activity of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate:
6.3.5.1;

Protein crystallography data

The structure of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate, PDB code: 2nsy was solved by M.Rizzi, M.Bolognesi, A.Coda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.480, 85.620, 60.120, 90.00, 110.76, 90.00
R / Rfree (%) 15.5 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate (pdb code 2nsy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate, PDB code: 2nsy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2nsy

Go back to Magnesium Binding Sites List in 2nsy
Magnesium binding site 1 out of 4 in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate


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 in Complex with Nad-Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:10.0
occ:1.00
 O A:HOH675 2.0 10.3 1.0
O1P A:AMP300 2.1 9.9 1.0
O1 A:POP863 2.1 9.1 1.0
OD2 A:ASP50 2.1 9.6 1.0
OE2 A:GLU162 2.1 11.7 1.0
O5 A:POP863 2.1 10.4 1.0
CD A:GLU162 3.1 13.8 1.0
CG A:ASP50 3.2 8.9 1.0
P A:AMP300 3.3 10.0 1.0
P2 A:POP863 3.3 9.2 1.0
P1 A:POP863 3.3 8.8 1.0
O A:POP863 3.4 8.6 1.0
OE1 A:GLU162 3.5 17.2 1.0
CB A:ASP50 3.6 9.0 1.0
O A:HOH349 3.7 14.2 1.0
O2P A:AMP300 4.0 10.1 1.0
O5' A:AMP300 4.0 9.0 1.0
O A:HOH395 4.1 11.1 1.0
C5' A:AMP300 4.1 10.1 1.0
O6 A:POP863 4.2 9.2 1.0
O3 A:POP863 4.2 9.5 1.0
O3' A:AMP300 4.2 9.3 1.0
OD1 A:ASP50 4.2 9.8 1.0
CE1 A:HIS159 4.3 6.7 1.0
O2 A:POP863 4.3 9.7 1.0
O A:HOH569 4.3 23.7 1.0
NZ A:LYS186 4.4 10.2 1.0
O4 A:POP863 4.4 10.0 1.0
OG1 A:THR157 4.5 9.1 1.0
CG A:GLU162 4.5 13.7 1.0
O3P A:AMP300 4.5 11.4 1.0
O7N A:NAD301 4.8 20.5 1.0
MG A:MG305 4.8 9.1 1.0
ND1 A:HIS159 4.9 11.9 1.0
C3' A:AMP300 4.9 9.0 1.0
CA A:ASP50 4.9 9.4 1.0
C7N A:NAD301 4.9 17.9 1.0
C4' A:AMP300 5.0 9.1 1.0

Magnesium binding site 2 out of 4 in 2nsy

Go back to Magnesium Binding Sites List in 2nsy
Magnesium binding site 2 out of 4 in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate


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 NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:9.1
occ:1.00
 O2P A:AMP300 2.0 10.1 1.0
O3 A:POP863 2.1 9.5 1.0
O6 A:POP863 2.1 9.2 1.0
O A:HOH676 2.1 10.6 1.0
O A:THR208 2.1 9.8 1.0
O A:HOH677 2.1 10.5 1.0
P1 A:POP863 3.2 8.8 1.0
C A:THR208 3.2 10.2 1.0
P2 A:POP863 3.3 9.2 1.0
P A:AMP300 3.4 10.0 1.0
O A:POP863 3.5 8.6 1.0
O1 A:POP863 3.8 9.1 1.0
O5' A:AMP300 4.0 9.0 1.0
O5 A:POP863 4.0 10.4 1.0
N A:THR208 4.0 9.4 1.0
OG A:SER46 4.1 8.9 1.0
N A:ALA209 4.2 10.4 1.0
O1P A:AMP300 4.2 9.9 1.0
CA A:ALA209 4.2 9.6 1.0
O A:HOH319 4.2 11.0 1.0
CA A:THR208 4.2 11.3 1.0
O A:HOH349 4.3 14.2 1.0
O A:HOH417 4.3 14.8 1.0
O A:HOH357 4.4 11.8 1.0
O4 A:POP863 4.5 10.0 1.0
O2 A:POP863 4.5 9.7 1.0
O3P A:AMP300 4.5 11.4 1.0
CG2 A:THR208 4.6 12.2 1.0
CB A:SER46 4.6 9.0 1.0
CA A:GLY48 4.7 10.4 1.0
C A:ALA209 4.8 10.0 1.0
MG A:MG304 4.8 10.0 1.0

Magnesium binding site 3 out of 4 in 2nsy

Go back to Magnesium Binding Sites List in 2nsy
Magnesium binding site 3 out of 4 in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:11.8
occ:1.00
 O B:THR208 2.0 14.1 1.0
O2P B:AMP302 2.1 13.4 1.0
O B:HOH679 2.1 13.5 1.0
O B:HOH680 2.1 13.6 1.0
O6 B:POP862 2.1 10.5 1.0
O3 B:POP862 2.1 11.8 1.0
C B:THR208 3.2 15.7 1.0
P1 B:POP862 3.2 11.6 1.0
P2 B:POP862 3.3 11.2 1.0
P B:AMP302 3.4 14.7 1.0
O B:POP862 3.6 11.3 1.0
O1 B:POP862 3.8 12.0 1.0
O5' B:AMP302 3.9 12.0 1.0
N B:THR208 4.0 15.8 1.0
O5 B:POP862 4.0 12.7 1.0
OG B:SER46 4.1 11.8 1.0
N B:ALA209 4.1 15.9 1.0
O B:HOH361 4.1 13.8 1.0
CA B:ALA209 4.1 15.7 1.0
O B:HOH486 4.1 19.5 1.0
CA B:THR208 4.2 16.1 1.0
O1P B:AMP302 4.3 12.6 1.0
O B:HOH451 4.3 18.9 1.0
CG2 B:THR208 4.5 17.8 1.0
O B:HOH406 4.5 14.5 1.0
O3P B:AMP302 4.5 16.3 1.0
O4 B:POP862 4.5 13.6 1.0
O2 B:POP862 4.5 13.5 1.0
CB B:SER46 4.6 10.8 1.0
C B:ALA209 4.7 14.2 1.0
CA B:GLY48 4.7 10.5 1.0
MG B:MG307 4.8 11.6 1.0
CB B:THR208 4.9 17.0 1.0
O B:ALA209 5.0 14.6 1.0

Magnesium binding site 4 out of 4 in 2nsy

Go back to Magnesium Binding Sites List in 2nsy
Magnesium binding site 4 out of 4 in the Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis in Complex with Nad-Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:11.6
occ:1.00
 O1 B:POP862 2.0 12.0 1.0
O1P B:AMP302 2.1 12.6 1.0
OE2 B:GLU162 2.1 15.4 1.0
O B:HOH678 2.1 12.4 1.0
O5 B:POP862 2.1 12.7 1.0
OD2 B:ASP50 2.2 11.7 1.0
CD B:GLU162 3.1 16.9 1.0
CG B:ASP50 3.2 11.4 1.0
P B:AMP302 3.2 14.7 1.0
P1 B:POP862 3.3 11.6 1.0
P2 B:POP862 3.3 11.2 1.0
O B:POP862 3.3 11.3 1.0
OE1 B:GLU162 3.5 18.0 1.0
O B:HOH486 3.6 19.5 1.0
CB B:ASP50 3.7 9.7 1.0
O2P B:AMP302 3.9 13.4 1.0
O B:HOH390 3.9 15.3 1.0
O5' B:AMP302 4.0 12.0 1.0
C5' B:AMP302 4.1 12.9 1.0
O3 B:POP862 4.1 11.8 1.0
O6 B:POP862 4.2 10.5 1.0
OD1 B:ASP50 4.3 11.7 1.0
O2 B:POP862 4.3 13.5 1.0
NE2 B:HIS159 4.3 11.0 1.0
O3' B:AMP302 4.4 11.2 1.0
NZ B:LYS186 4.4 12.7 1.0
O B:HOH586 4.4 28.7 1.0
O4 B:POP862 4.5 13.6 1.0
O3P B:AMP302 4.5 16.3 1.0
CG B:GLU162 4.5 15.2 1.0
OG1 B:THR157 4.5 11.5 1.0
O7N B:NAD303 4.8 36.3 1.0
MG B:MG306 4.8 11.8 1.0
C3' B:AMP302 4.9 11.3 1.0
C7N B:NAD303 4.9 36.6 1.0
CD2 B:HIS159 5.0 10.2 1.0

Reference:

M.Rizzi, M.Bolognesi, A.Coda. A Novel Deamido-Nad+-Binding Site Revealed By the Trapped Nad-Adenylate Intermediate in the Nad+ Synthetase Structure. Structure V. 6 1129 1998.
ISSN: ISSN 0969-2126
PubMed: 9753692
DOI: 10.1016/S0969-2126(98)00114-2
Page generated: Mon Dec 14 07:31:02 2020

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