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Magnesium in PDB 5k7x: Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin

Enzymatic activity of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin

All present enzymatic activity of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin:
6.3.4.4;

Protein crystallography data

The structure of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin, PDB code: 5k7x was solved by Y.Xie, Z.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.12 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.348, 130.549, 168.673, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin (pdb code 5k7x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin, PDB code: 5k7x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5k7x

Go back to Magnesium Binding Sites List in 5k7x
Magnesium binding site 1 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:49.9
occ:1.00
 O A:GLY42 2.1 53.4 1.0
OD1 A:ASP13 2.1 58.1 1.0
O1G A:GTP400 2.2 0.8 1.0
O3B A:GTP400 2.3 0.8 1.0
O A:HDA402 2.4 90.0 1.0
PG A:GTP400 2.7 0.1 1.0
O2A A:GTP400 2.9 49.5 1.0
C A:GLY42 3.1 40.0 1.0
CG A:ASP13 3.3 44.5 1.0
O2G A:GTP400 3.4 0.4 1.0
N A:GLY42 3.5 49.9 1.0
CA A:GLY42 3.6 30.5 1.0
C A:HDA402 3.6 92.1 1.0
NH2 A:ARG258 3.6 42.1 1.0
PB A:GTP400 3.8 39.5 1.0
PA A:GTP400 3.8 50.0 1.0
OG1 A:THR252 3.9 69.6 1.0
O6 A:IMP401 3.9 0.6 1.0
N1 A:IMP401 4.0 0.1 1.0
O3A A:GTP400 4.0 0.0 1.0
OB A:HDA402 4.0 90.1 1.0
O3G A:GTP400 4.0 0.8 1.0
OD2 A:ASP13 4.2 46.9 1.0
CA A:ASP13 4.2 30.3 1.0
CB A:ASP13 4.2 32.6 1.0
O1A A:GTP400 4.2 66.1 1.0
N A:HIS43 4.2 29.9 1.0
C6 A:IMP401 4.3 0.6 1.0
NA A:HDA402 4.3 91.2 1.0
N A:ASP13 4.5 40.1 1.0
CA A:HIS43 4.6 30.3 1.0
CD2 A:HIS43 4.6 39.1 1.0
O2B A:GTP400 4.7 53.4 1.0
CZ A:ARG258 4.7 47.4 1.0
C A:ALA41 4.7 52.8 1.0
O1B A:GTP400 4.7 34.9 1.0
CB A:THR252 5.0 70.4 1.0

Magnesium binding site 2 out of 6 in 5k7x

Go back to Magnesium Binding Sites List in 5k7x
Magnesium binding site 2 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:45.9
occ:1.00
 OD1 B:ASP13 2.1 53.1 1.0
O B:GLY42 2.2 57.4 1.0
O3B B:GTP400 2.3 0.7 1.0
O1G B:GTP400 2.3 0.0 1.0
O B:HDA402 2.4 0.2 1.0
O2A B:GTP400 2.7 66.2 1.0
PG B:GTP400 2.7 0.2 1.0
C B:GLY42 3.2 34.5 1.0
CG B:ASP13 3.3 47.1 1.0
O2G B:GTP400 3.4 0.2 1.0
C B:HDA402 3.6 0.8 1.0
N B:GLY42 3.7 53.7 1.0
PA B:GTP400 3.7 54.9 1.0
PB B:GTP400 3.7 49.6 1.0
CA B:GLY42 3.7 24.8 1.0
O6 B:IMP401 3.8 93.4 1.0
O3A B:GTP400 3.8 0.2 1.0
OG1 B:THR252 3.9 49.1 1.0
N1 B:IMP401 3.9 0.6 1.0
NH2 B:ARG258 4.1 34.6 1.0
O3G B:GTP400 4.1 0.9 1.0
O1A B:GTP400 4.1 59.0 1.0
CA B:ASP13 4.1 24.1 1.0
CB B:ASP13 4.2 33.3 1.0
OB B:HDA402 4.2 0.2 1.0
C6 B:IMP401 4.2 99.9 1.0
OD2 B:ASP13 4.2 57.9 1.0
N B:HIS43 4.3 27.8 1.0
NA B:HDA402 4.4 100.0 1.0
N B:ASP13 4.4 34.9 1.0
CB B:THR252 4.6 52.3 1.0
O2B B:GTP400 4.6 65.9 1.0
O1B B:GTP400 4.7 45.2 1.0
CA B:HIS43 4.7 34.6 1.0
CD2 B:HIS43 4.8 38.4 1.0
C B:ALA41 4.9 54.3 1.0

Magnesium binding site 3 out of 6 in 5k7x

Go back to Magnesium Binding Sites List in 5k7x
Magnesium binding site 3 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:72.4
occ:1.00
 O C:GLY42 2.1 60.4 1.0
O C:HDA402 2.2 99.3 1.0
O3B C:GTP400 2.2 0.6 1.0
OD1 C:ASP13 2.3 47.9 1.0
O1G C:GTP400 2.3 1.0 1.0
O2A C:GTP400 2.7 79.7 1.0
PG C:GTP400 2.7 0.9 1.0
C C:GLY42 3.2 30.2 1.0
C C:HDA402 3.4 99.2 1.0
O2G C:GTP400 3.4 0.2 1.0
CG C:ASP13 3.5 49.2 1.0
PB C:GTP400 3.7 38.3 1.0
PA C:GTP400 3.7 65.8 1.0
N C:GLY42 3.7 64.3 1.0
CA C:GLY42 3.8 27.4 1.0
O3A C:GTP400 3.8 94.4 1.0
NH2 C:ARG258 3.9 41.0 1.0
O6 C:IMP401 3.9 0.7 1.0
OG1 C:THR252 4.0 51.3 1.0
N1 C:IMP401 4.0 89.1 1.0
O1A C:GTP400 4.0 75.0 1.0
O3G C:GTP400 4.0 0.9 1.0
CA C:ASP13 4.1 27.2 1.0
OB C:HDA402 4.2 92.8 1.0
NA C:HDA402 4.2 94.6 1.0
CB C:ASP13 4.2 26.8 1.0
N C:HIS43 4.3 31.8 1.0
C6 C:IMP401 4.4 0.5 1.0
N C:ASP13 4.4 30.9 1.0
OD2 C:ASP13 4.4 56.8 1.0
O1B C:GTP400 4.6 48.4 1.0
O2B C:GTP400 4.6 55.9 1.0
CB C:THR252 4.6 56.4 1.0
CA C:HIS43 4.7 32.4 1.0
CZ C:ARG258 4.8 42.7 1.0
CD2 C:HIS43 4.8 28.6 1.0
C C:ALA41 4.9 64.3 1.0

Magnesium binding site 4 out of 6 in 5k7x

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Magnesium binding site 4 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:53.9
occ:1.00
 O D:HDA402 2.0 0.9 1.0
O D:GLY42 2.1 71.3 1.0
OD1 D:ASP13 2.2 59.8 1.0
O3B D:GTP400 2.3 0.8 1.0
O1G D:GTP400 2.4 0.1 1.0
O2A D:GTP400 2.7 59.2 1.0
PG D:GTP400 2.7 0.8 1.0
C D:GLY42 3.2 51.7 1.0
C D:HDA402 3.2 0.0 1.0
O2G D:GTP400 3.3 0.1 1.0
CG D:ASP13 3.4 57.6 1.0
N D:GLY42 3.6 55.7 1.0
PA D:GTP400 3.7 59.5 1.0
CA D:GLY42 3.7 37.8 1.0
PB D:GTP400 3.7 68.6 1.0
O6 D:IMP401 3.8 94.6 1.0
N1 D:IMP401 3.9 0.4 1.0
O3A D:GTP400 3.9 0.7 1.0
NH2 D:ARG258 3.9 51.3 1.0
OG1 D:THR252 4.0 83.1 1.0
O1A D:GTP400 4.0 73.4 1.0
NA D:HDA402 4.1 1.0 1.0
CA D:ASP13 4.1 47.4 1.0
OB D:HDA402 4.1 0.2 1.0
O3G D:GTP400 4.1 0.4 1.0
CB D:ASP13 4.2 43.6 1.0
C6 D:IMP401 4.2 0.4 1.0
N D:HIS43 4.3 46.9 1.0
OD2 D:ASP13 4.3 71.9 1.0
N D:ASP13 4.4 60.7 1.0
CB D:THR252 4.6 92.2 1.0
O1B D:GTP400 4.7 71.4 1.0
O2B D:GTP400 4.7 66.8 1.0
CD2 D:HIS43 4.7 46.0 1.0
CA D:HIS43 4.7 51.5 1.0
C D:ALA41 4.9 59.8 1.0

Magnesium binding site 5 out of 6 in 5k7x

Go back to Magnesium Binding Sites List in 5k7x
Magnesium binding site 5 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:69.0
occ:1.00
 O E:GLY42 2.1 75.8 1.0
OD1 E:ASP13 2.2 75.1 1.0
O E:HDA402 2.2 98.9 1.0
O1G E:GTP400 2.3 0.5 1.0
O3B E:GTP400 2.3 0.6 1.0
PG E:GTP400 2.7 0.1 1.0
O2A E:GTP400 2.8 71.8 1.0
C E:GLY42 3.1 64.4 1.0
CG E:ASP13 3.4 62.4 1.0
C E:HDA402 3.4 0.2 1.0
O2G E:GTP400 3.5 0.7 1.0
N E:GLY42 3.6 63.4 1.0
CA E:GLY42 3.7 61.6 1.0
PB E:GTP400 3.7 66.6 1.0
PA E:GTP400 3.7 66.8 1.0
O3A E:GTP400 3.9 0.8 1.0
O6 E:IMP401 3.9 96.0 1.0
OG1 E:THR252 3.9 70.9 1.0
N1 E:IMP401 4.0 93.5 1.0
NH2 E:ARG258 4.0 59.4 1.0
O3G E:GTP400 4.0 0.3 1.0
CA E:ASP13 4.1 62.5 1.0
OB E:HDA402 4.1 0.7 1.0
O1A E:GTP400 4.1 69.5 1.0
CB E:ASP13 4.2 61.8 1.0
N E:HIS43 4.2 45.4 1.0
NA E:HDA402 4.3 0.6 1.0
OD2 E:ASP13 4.3 49.1 1.0
C6 E:IMP401 4.3 95.2 1.0
N E:ASP13 4.4 66.5 1.0
O2B E:GTP400 4.6 59.9 1.0
O1B E:GTP400 4.6 57.0 1.0
CA E:HIS43 4.6 57.0 1.0
CB E:THR252 4.6 75.3 1.0
CD2 E:HIS43 4.7 68.2 1.0
C E:ALA41 4.8 71.6 1.0

Magnesium binding site 6 out of 6 in 5k7x

Go back to Magnesium Binding Sites List in 5k7x
Magnesium binding site 6 out of 6 in the Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fully Ligated Adenylosuccinate Synthetase From Pyrococcus Horikoshii OT3 with Gtp, Imp and Hadacidin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:77.4
occ:1.00
 O F:GLY42 2.2 68.2 1.0
OD1 F:ASP13 2.3 71.7 1.0
O3B F:GTP400 2.3 0.6 1.0
O1G F:GTP400 2.3 0.4 1.0
O F:HDA402 2.4 74.7 1.0
PG F:GTP400 2.8 0.9 1.0
O2A F:GTP400 2.9 62.1 1.0
C F:GLY42 3.2 51.0 1.0
C F:HDA402 3.5 75.7 1.0
CG F:ASP13 3.5 59.0 1.0
O2G F:GTP400 3.5 0.8 1.0
N F:GLY42 3.6 52.3 1.0
CA F:GLY42 3.7 41.0 1.0
PB F:GTP400 3.7 55.9 1.0
PA F:GTP400 3.8 58.5 1.0
OG1 F:THR252 3.9 44.8 1.0
O6 F:IMP401 3.9 84.3 1.0
O3A F:GTP400 3.9 1.0 1.0
N1 F:IMP401 4.0 82.2 1.0
NH2 F:ARG258 4.0 46.4 1.0
OB F:HDA402 4.0 74.0 1.0
O3G F:GTP400 4.1 1.0 1.0
O1A F:GTP400 4.1 67.0 1.0
CA F:ASP13 4.2 41.2 1.0
NA F:HDA402 4.2 76.2 1.0
CB F:ASP13 4.3 50.7 1.0
N F:HIS43 4.3 45.7 1.0
C6 F:IMP401 4.3 82.4 1.0
OD2 F:ASP13 4.4 59.1 1.0
N F:ASP13 4.4 45.5 1.0
O F:HOH502 4.5 32.0 1.0
CB F:THR252 4.5 51.3 1.0
O1B F:GTP400 4.6 57.3 1.0
O2B F:GTP400 4.7 54.3 1.0
CA F:HIS43 4.7 45.5 1.0
CD2 F:HIS43 4.8 52.5 1.0
C F:ALA41 4.8 57.8 1.0

Reference:

Y.Xie, S.Kishisita, K.Murayama, M.Shirouzu, S.Yokoyama. Crystal Structure of Hypothetical Adenylosuccinate Synthetase, PH0438 From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Sun Sep 29 18:52:31 2024

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