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Magnesium in PDB 1kqp: NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution

Enzymatic activity of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution

All present enzymatic activity of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution:
6.3.5.1;

Protein crystallography data

The structure of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution, PDB code: 1kqp was solved by J.Symersky, Y.Devedjiev, K.Moore, C.Brouillette, L.Delucas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.280, 84.790, 59.640, 90.00, 110.50, 90.00
R / Rfree (%) 11.6 / 14.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution (pdb code 1kqp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution, PDB code: 1kqp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1kqp

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Magnesium binding site 1 out of 5 in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5001

b:9.1
occ:1.00
 O4 A:POP4001 2.0 8.6 1.0
O A:HOH6037 2.0 10.8 1.0
OD2 A:ASP50 2.1 9.0 1.0
O2 A:POP4001 2.1 8.4 1.0
O1P A:ADJ3001 2.1 10.1 1.0
OE1 A:GLU162 2.2 9.6 1.0
HB2 A:ASP50 3.1 10.8 1.0
CG A:ASP50 3.2 9.1 1.0
CD A:GLU162 3.2 9.5 1.0
P2 A:POP4001 3.2 8.8 1.0
P1 A:POP4001 3.3 8.3 1.0
O A:POP4001 3.4 8.8 1.0
P1 A:ADJ3001 3.5 12.9 1.0
OE2 A:GLU162 3.5 11.5 1.0
CB A:ASP50 3.6 9.0 1.0
H5S2 A:ADJ3001 3.7 16.0 1.0
O A:HOH6005 3.9 14.8 1.0
O3P A:ADJ3001 3.9 10.5 1.0
HB3 A:ASP50 4.0 10.8 1.0
HOS3 A:ADJ3001 4.0 14.5 1.0
O5S A:ADJ3001 4.0 12.5 1.0
HZ3 A:LYS186 4.0 14.2 1.0
O A:HOH6024 4.0 10.3 1.0
HG1 A:THR157 4.1 13.6 1.0
O A:HOH6002 4.1 18.9 1.0
O3 A:POP4001 4.1 8.6 1.0
O6 A:POP4001 4.2 8.9 1.0
O3S A:ADJ3001 4.2 9.7 1.0
HZ2 A:LYS186 4.2 14.2 1.0
OD1 A:ASP50 4.3 10.0 1.0
NE2 A:HIS159 4.3 9.3 1.0
O5 A:POP4001 4.3 9.3 1.0
HZ1 A:LYS186 4.3 14.2 1.0
C5S A:ADJ3001 4.3 13.3 1.0
NZ A:LYS186 4.4 9.5 1.0
O1 A:POP4001 4.4 8.8 1.0
OG1 A:THR157 4.5 9.1 1.0
H A:ASP50 4.5 10.3 1.0
CG A:GLU162 4.5 9.3 1.0
HD2 A:HIS159 4.6 11.3 1.0
HG3 A:GLU162 4.7 11.2 1.0
H3S A:ADJ3001 4.7 11.7 1.0
HG2 A:GLU162 4.7 11.2 1.0
HB A:THR157 4.7 11.1 1.0
O2P A:ADJ3001 4.8 13.4 1.0
MG A:MG5002 4.8 9.2 1.0
CD2 A:HIS159 4.8 9.4 1.0
HON7 A:ADJ3001 4.9 40.4 1.0
C3S A:ADJ3001 4.9 9.7 1.0
O7N A:ADJ3001 4.9 23.8 1.0
CA A:ASP50 5.0 8.9 1.0

Magnesium binding site 2 out of 5 in 1kqp

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Magnesium binding site 2 out of 5 in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5002

b:9.2
occ:1.00
 O3P A:ADJ3001 2.0 10.5 1.0
O6 A:POP4001 2.0 8.9 1.0
O3 A:POP4001 2.1 8.6 1.0
O A:HOH6075 2.1 10.2 1.0
O A:HOH6234 2.1 10.9 1.0
O A:THR208 2.2 10.1 1.0
P2 A:POP4001 3.2 8.8 1.0
P1 A:POP4001 3.2 8.3 1.0
HG A:SER46 3.3 14.3 1.0
C A:THR208 3.3 9.9 1.0
H A:THR208 3.3 12.0 1.0
O A:POP4001 3.5 8.8 1.0
P1 A:ADJ3001 3.5 12.9 1.0
HA A:ALA209 3.6 13.3 1.0
HA3 A:GLY48 3.8 11.9 1.0
O4 A:POP4001 3.8 8.6 1.0
HG23 A:THR208 3.9 18.6 1.0
O2 A:POP4001 4.0 8.4 1.0
O5S A:ADJ3001 4.0 12.5 1.0
O A:HOH6005 4.0 14.8 1.0
OG A:SER46 4.1 9.5 1.0
N A:THR208 4.1 10.0 1.0
HB2 A:SER46 4.2 10.8 1.0
O A:HOH6060 4.2 11.2 1.0
N A:ALA209 4.2 10.7 1.0
O1P A:ADJ3001 4.3 10.1 1.0
O A:HOH6221 4.3 16.3 1.0
CA A:THR208 4.3 10.6 1.0
CA A:ALA209 4.3 11.1 1.0
HG21 A:THR208 4.4 18.6 1.0
H3S A:ADJ3001 4.4 11.7 1.0
O A:HOH6127 4.4 13.0 1.0
O1 A:POP4001 4.4 8.8 1.0
O5 A:POP4001 4.5 9.3 1.0
O2P A:ADJ3001 4.5 13.4 1.0
CG2 A:THR208 4.5 12.4 1.0
CB A:SER46 4.6 9.0 1.0
CA A:GLY48 4.7 9.9 1.0
HB3 A:SER46 4.8 10.8 1.0
MG A:MG5001 4.8 9.1 1.0
HA A:PRO207 4.8 12.6 1.0
C A:ALA209 4.9 11.1 1.0
H A:GLY48 4.9 11.9 1.0

Magnesium binding site 3 out of 5 in 1kqp

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Magnesium binding site 3 out of 5 in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5003

b:10.7
occ:1.00
 O3 B:POP4002 2.0 9.8 1.0
O3P B:ADJ3002 2.0 12.1 1.0
O6 B:POP4002 2.1 10.7 1.0
O B:HOH6043 2.1 11.8 1.0
O B:HOH6039 2.1 12.5 1.0
O B:THR208 2.1 13.0 1.0
P2 B:POP4002 3.2 10.0 1.0
P1 B:POP4002 3.2 9.3 1.0
HG B:SER46 3.2 14.8 1.0
H B:THR208 3.3 17.1 1.0
C B:THR208 3.3 13.2 1.0
P1 B:ADJ3002 3.5 13.4 1.0
O B:POP4002 3.5 9.7 1.0
HA B:ALA209 3.6 17.5 1.0
O4 B:POP4002 3.8 10.1 1.0
HA3 B:GLY48 3.9 12.0 1.0
HG23 B:THR208 3.9 25.3 1.0
O5S B:ADJ3002 3.9 12.7 1.0
O2 B:POP4002 4.0 9.7 1.0
N B:THR208 4.0 14.2 1.0
OG B:SER46 4.0 9.9 1.0
O B:HOH6006 4.1 20.0 1.0
HB2 B:SER46 4.2 11.4 1.0
O B:HOH6078 4.2 13.2 1.0
N B:ALA209 4.2 13.4 1.0
O1P B:ADJ3002 4.2 11.2 1.0
CA B:THR208 4.2 13.6 1.0
HG21 B:THR208 4.3 25.3 1.0
CA B:ALA209 4.3 14.6 1.0
O B:HOH6225 4.3 20.0 1.0
H3S B:ADJ3002 4.4 12.6 1.0
O1 B:POP4002 4.4 9.4 1.0
O B:HOH6237 4.5 12.8 1.0
CG2 B:THR208 4.5 16.9 1.0
O5 B:POP4002 4.5 10.4 1.0
O2P B:ADJ3002 4.5 14.5 1.0
CB B:SER46 4.5 9.5 1.0
HB3 B:SER46 4.7 11.4 1.0
HA B:PRO207 4.7 16.0 1.0
MG B:MG5004 4.8 10.2 1.0
H B:GLY48 4.8 11.8 1.0
CA B:GLY48 4.8 10.0 1.0
C B:ALA209 4.8 13.8 1.0
CB B:THR208 5.0 15.0 1.0
H B:ALA209 5.0 16.1 1.0

Magnesium binding site 4 out of 5 in 1kqp

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Magnesium binding site 4 out of 5 in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5004

b:10.2
occ:1.00
 O4 B:POP4002 2.0 10.1 1.0
O B:HOH6019 2.1 11.8 1.0
O2 B:POP4002 2.1 9.7 1.0
OD2 B:ASP50 2.1 10.1 1.0
O1P B:ADJ3002 2.1 11.2 1.0
OE2 B:GLU162 2.2 10.7 1.0
HB2 B:ASP50 3.1 11.3 1.0
CG B:ASP50 3.2 9.5 1.0
CD B:GLU162 3.2 10.3 1.0
P2 B:POP4002 3.3 10.0 1.0
P1 B:POP4002 3.3 9.3 1.0
O B:POP4002 3.4 9.7 1.0
P1 B:ADJ3002 3.4 13.4 1.0
OE1 B:GLU162 3.5 14.1 1.0
H5S2 B:ADJ3002 3.6 14.8 1.0
CB B:ASP50 3.6 9.4 1.0
O B:HOH6006 3.8 20.0 1.0
O3P B:ADJ3002 3.9 12.1 1.0
HOS3 B:ADJ3002 4.0 15.6 1.0
O B:HOH6009 4.0 12.0 1.0
HB3 B:ASP50 4.0 11.3 1.0
O5S B:ADJ3002 4.0 12.7 1.0
HZ3 B:LYS186 4.1 16.2 1.0
HG1 B:THR157 4.1 14.6 1.0
O3 B:POP4002 4.1 9.8 1.0
O B:HOH6003 4.1 22.5 1.0
O6 B:POP4002 4.2 10.7 1.0
O3S B:ADJ3002 4.2 10.4 1.0
OD1 B:ASP50 4.2 10.4 1.0
C5S B:ADJ3002 4.3 12.4 1.0
NE2 B:HIS159 4.3 10.2 1.0
HZ1 B:LYS186 4.3 16.2 1.0
O5 B:POP4002 4.3 10.4 1.0
HZ2 B:LYS186 4.3 16.2 1.0
O1 B:POP4002 4.4 9.4 1.0
NZ B:LYS186 4.4 10.8 1.0
OG1 B:THR157 4.5 9.7 1.0
H B:ASP50 4.5 11.3 1.0
CG B:GLU162 4.5 10.0 1.0
O2P B:ADJ3002 4.7 14.5 1.0
HON7 B:ADJ3002 4.7 23.4 1.0
HG3 B:GLU162 4.7 12.1 1.0
H3S B:ADJ3002 4.7 12.6 1.0
HD2 B:HIS159 4.7 12.4 1.0
MG B:MG5003 4.8 10.7 1.0
HG2 B:GLU162 4.8 12.1 1.0
HB B:THR157 4.8 11.3 1.0
C3S B:ADJ3002 4.9 10.5 1.0
CD2 B:HIS159 4.9 10.3 1.0
C7N B:ADJ3002 4.9 29.4 1.0
CA B:ASP50 5.0 9.0 1.0
H5S1 B:ADJ3002 5.0 14.8 1.0

Magnesium binding site 5 out of 5 in 1kqp

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Magnesium binding site 5 out of 5 in the NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5005

b:12.8
occ:1.00
 O B:HOH6061 2.0 15.4 1.0
OD1 B:ASP124 2.0 13.1 1.0
O B:HOH6073 2.1 13.6 1.0
O B:HOH6122 2.1 13.7 1.0
CG B:ASP124 3.2 11.4 1.0
OD2 B:ASP124 3.9 12.2 1.0
O B:HOH6188 4.0 14.8 1.0
O B:GLY123 4.0 12.6 1.0
O B:HOH6104 4.1 14.5 1.0
HA B:ASP124 4.1 14.3 1.0
O B:THR122 4.2 12.4 1.0
C B:GLY123 4.2 11.8 1.0
CB B:ASP124 4.4 12.2 1.0
HA3 B:GLY123 4.4 16.2 1.0
N B:ASP124 4.5 12.7 1.0
CA B:ASP124 4.5 11.9 1.0
HB3 B:ASP124 4.8 14.7 1.0
CA B:GLY123 4.9 13.5 1.0

Reference:

J.Symersky, Y.Devedjiev, K.Moore, C.Brouillette, L.Delucas. NH3-Dependent Nad+ Synthetase From Bacillus Subtilis at 1 A Resolution. Acta Crystallogr.,Sect.D V. 58 1138 2002.
ISSN: ISSN 0907-4449
PubMed: 12077433
DOI: 10.1107/S0907444902006698
Page generated: Sun Aug 10 00:26:00 2025

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