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Magnesium in PDB 5f2v: Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp

Enzymatic activity of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp

All present enzymatic activity of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp:
2.7.6.5;

Protein crystallography data

The structure of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp, PDB code: 5f2v was solved by W.Steinchen, J.S.Schuhmacher, F.Altegoer, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.31 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 116.671, 103.631, 138.290, 90.00, 104.84, 90.00
R / Rfree (%) 19.3 / 26.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp (pdb code 5f2v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp, PDB code: 5f2v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5f2v

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Magnesium binding site 1 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:44.8
occ:1.00
 O V:HOH410 1.9 40.2 1.0
O1G V:APC301 2.1 48.9 1.0
O2B V:APC301 2.3 52.0 1.0
OD2 V:ASP72 2.5 45.7 1.0
O3B V:APC301 2.8 43.6 1.0
PG V:APC301 2.9 52.6 1.0
PB V:APC301 2.9 45.1 1.0
H2 V:APC301 3.0 53.4 1.0
O1B V:APC301 3.4 55.0 1.0
CG V:ASP72 3.7 42.4 1.0
O3G V:APC301 3.9 51.4 1.0
O2G V:APC301 3.9 55.1 1.0
NZ V:LYS48 4.0 45.2 1.0
C2 V:APC301 4.0 44.5 1.0
NZ V:LYS56 4.1 43.0 1.0
CB V:ASP72 4.2 44.2 1.0
OE1 V:GLU139 4.3 38.3 1.0
OE2 V:GLU139 4.6 46.2 1.0
OD1 V:ASP72 4.7 45.9 1.0
C3A V:APC301 4.7 45.9 1.0
NH2 V:ARG46 4.7 42.1 1.0
N3 V:APC301 4.7 34.1 1.0
O V:HOH403 4.8 41.5 1.0
NE2 V:GLN141 4.8 35.5 1.0
N1 V:APC301 4.8 44.9 1.0
H3A2 V:APC301 4.9 55.0 1.0
CD V:GLU139 4.9 43.6 1.0

Magnesium binding site 2 out of 12 in 5f2v

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Magnesium binding site 2 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg302

b:39.7
occ:1.00
 O X:HOH408 2.1 39.5 1.0
O3G X:APC301 2.1 49.6 1.0
O1B X:APC301 2.3 51.0 1.0
OD2 X:ASP72 2.3 48.1 1.0
O2B X:APC301 2.7 47.4 1.0
PB X:APC301 3.0 42.3 1.0
PG X:APC301 3.3 63.6 1.0
CG X:ASP72 3.3 42.0 1.0
OE2 X:GLU139 3.5 36.5 1.0
O3B X:APC301 3.5 51.3 1.0
N7 X:APC301 3.6 37.0 1.0
H8 X:APC301 3.7 46.8 1.0
CB X:ASP72 3.7 39.9 1.0
NZ X:LYS48 3.9 48.9 1.0
O2G X:APC301 4.0 57.5 1.0
C8 X:APC301 4.0 39.0 1.0
NZ X:LYS56 4.2 47.8 1.0
OD1 X:ASP72 4.3 38.6 1.0
CD X:GLU139 4.4 44.9 1.0
O1G X:APC301 4.4 52.0 1.0
OE1 X:GLU139 4.4 51.0 1.0
NH2 X:ARG46 4.4 45.9 1.0
NE2 X:GLN141 4.5 39.7 1.0
O1A X:APC301 4.5 49.1 1.0
C3A X:APC301 4.7 40.5 1.0
HN62 X:APC301 4.9 44.7 1.0
H3A1 X:APC301 4.9 48.6 1.0

Magnesium binding site 3 out of 12 in 5f2v

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Magnesium binding site 3 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg302

b:52.1
occ:1.00
 O1B T:APC301 2.1 52.4 1.0
O2B T:APC301 2.1 43.8 1.0
O T:HOH406 2.2 37.2 1.0
O T:HOH413 2.3 58.1 1.0
OE2 T:GLU139 2.5 38.0 1.0
PB T:APC301 2.5 61.0 1.0
CB T:ASP72 2.9 34.8 1.0
OE1 T:GLU139 3.1 31.9 1.0
OD2 T:ASP72 3.1 45.0 1.0
CD T:GLU139 3.1 33.5 1.0
CG T:ASP72 3.1 39.5 1.0
C3A T:APC301 3.5 44.7 1.0
H3A1 T:APC301 3.5 53.6 1.0
H3A2 T:APC301 3.5 53.6 1.0
O T:HOH402 3.7 57.0 1.0
OD1 T:ASP72 3.9 39.0 1.0
O3B T:APC301 4.0 58.2 1.0
OH T:TYR107 4.1 57.5 1.0
NZ T:LYS56 4.2 33.8 1.0
NE2 T:GLN141 4.3 38.1 1.0
CA T:ASP72 4.4 38.7 1.0
CG T:GLU139 4.5 31.6 1.0
O1G T:APC301 4.5 59.2 1.0
N7 T:APC301 4.6 31.9 1.0
HN62 T:APC301 4.6 35.0 1.0
CE2 T:TYR107 4.7 59.1 1.0
CZ T:TYR107 4.7 60.5 1.0
PG T:APC301 4.8 53.5 1.0
CB T:GLU139 4.9 30.4 1.0
O T:HOH416 5.0 36.1 1.0
O T:HOH405 5.0 50.5 1.0
O T:ASP72 5.0 33.2 1.0

Magnesium binding site 4 out of 12 in 5f2v

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Magnesium binding site 4 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


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 the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg301

b:39.1
occ:1.00
 O3B S:APC302 2.3 42.4 1.0
OD2 S:ASP72 2.4 43.8 1.0
CG S:ASP72 3.2 40.2 1.0
OE1 S:GLU139 3.3 31.8 1.0
O2G S:APC302 3.3 51.7 1.0
PG S:APC302 3.4 50.7 1.0
PB S:APC302 3.4 40.6 1.0
CB S:ASP72 3.5 37.1 1.0
OE2 S:GLU139 3.6 42.3 1.0
H3A1 S:APC302 3.7 56.1 1.0
O2B S:APC302 3.7 54.6 1.0
CD S:GLU139 3.8 37.1 1.0
NZ S:LYS56 3.9 39.3 1.0
C3A S:APC302 4.0 46.8 1.0
H3A2 S:APC302 4.1 56.1 1.0
OD1 S:ASP72 4.3 41.0 1.0
N7 S:APC302 4.3 37.6 1.0
O1G S:APC302 4.4 45.5 1.0
NZ S:LYS48 4.4 42.8 1.0
O3G S:APC302 4.4 42.9 1.0
NE2 S:GLN141 4.6 36.6 1.0
O1B S:APC302 4.7 42.0 1.0
NH2 S:ARG46 4.7 43.2 1.0
H8 S:APC302 4.8 45.8 1.0
HN62 S:APC302 4.8 39.8 1.0
C8 S:APC302 5.0 38.2 1.0

Magnesium binding site 5 out of 12 in 5f2v

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Magnesium binding site 5 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:39.1
occ:1.00
 O Y:HOH404 2.2 38.7 1.0
O Y:HOH402 2.4 52.0 1.0
OD2 Y:ASP72 2.4 39.3 1.0
O1G Y:APC301 2.5 52.9 1.0
O3B Y:APC301 2.6 38.6 1.0
CG Y:ASP72 2.9 38.5 1.0
PG Y:APC301 3.0 50.8 1.0
NZ Y:LYS56 3.1 33.1 1.0
OE2 Y:GLU139 3.5 47.2 1.0
OD1 Y:ASP72 3.6 37.4 1.0
CB Y:ASP72 3.6 36.2 1.0
OE1 Y:GLU139 3.7 37.1 1.0
O2G Y:APC301 3.9 39.2 1.0
NZ Y:LYS48 3.9 39.5 1.0
CD Y:GLU139 4.0 42.3 1.0
PB Y:APC301 4.1 40.6 1.0
O3G Y:APC301 4.2 40.7 1.0
CE Y:LYS56 4.5 32.3 1.0
O1B Y:APC301 4.6 45.6 1.0
H3A1 Y:APC301 4.8 48.8 1.0
NH2 Y:ARG46 4.8 37.5 1.0
CD Y:LYS56 4.9 34.4 1.0
O2B Y:APC301 5.0 32.6 1.0

Magnesium binding site 6 out of 12 in 5f2v

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Magnesium binding site 6 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg302

b:63.1
occ:1.00
 OD2 O:ASP72 2.1 66.2 1.0
O3B O:APC301 2.2 69.0 1.0
CG O:ASP72 3.1 64.2 1.0
PB O:APC301 3.1 63.1 1.0
PG O:APC301 3.4 79.9 1.0
O2B O:APC301 3.4 62.1 1.0
O1G O:APC301 3.4 73.5 1.0
H3A2 O:APC301 3.5 82.0 1.0
OE1 O:GLU139 3.5 55.6 1.0
CB O:ASP72 3.6 65.4 1.0
H3A1 O:APC301 3.6 82.0 1.0
C3A O:APC301 3.7 68.3 1.0
OE2 O:GLU139 3.8 65.9 1.0
NZ O:LYS48 3.8 66.8 1.0
N7 O:APC301 3.8 49.8 1.0
H8 O:APC301 4.0 64.3 1.0
NE2 O:GLN141 4.1 54.2 1.0
CD O:GLU139 4.1 59.3 1.0
OD1 O:ASP72 4.1 62.5 1.0
C8 O:APC301 4.3 53.6 1.0
O2G O:APC301 4.4 56.1 1.0
NZ O:LYS56 4.4 70.1 1.0
O1B O:APC301 4.5 62.6 1.0
O3G O:APC301 4.5 66.2 1.0
HN62 O:APC301 4.9 57.3 1.0
CE O:LYS48 4.9 67.2 1.0
NH2 O:ARG46 5.0 65.3 1.0

Magnesium binding site 7 out of 12 in 5f2v

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Magnesium binding site 7 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg302

b:59.6
occ:1.00
 O2B Z:APC301 2.4 69.8 1.0
OD2 Z:ASP69 2.5 74.5 1.0
CG Z:ASP69 3.0 77.5 1.0
O3G Z:APC301 3.0 79.4 1.0
OE2 Z:GLU136 3.0 56.1 1.0
NZ Z:LYS53 3.1 77.1 1.0
O2G Z:APC301 3.2 86.7 1.0
CB Z:ASP69 3.4 69.1 1.0
PG Z:APC301 3.6 89.9 1.0
OE1 Z:GLU136 3.7 53.6 1.0
CD Z:GLU136 3.7 56.1 1.0
PB Z:APC301 3.8 77.0 1.0
OD1 Z:ASP69 3.8 77.9 1.0
O3B Z:APC301 4.1 70.0 1.0
NZ Z:LYS45 4.2 77.2 1.0
CE Z:LYS53 4.5 77.5 1.0
H3A1 Z:APC301 4.7 84.3 1.0
O1B Z:APC301 4.7 72.3 1.0
NE2 Z:GLN138 4.8 48.6 1.0
C3A Z:APC301 4.9 70.2 1.0
O1G Z:APC301 4.9 83.0 1.0
N7 Z:APC301 4.9 56.3 1.0
CA Z:ASP69 4.9 64.5 1.0

Magnesium binding site 8 out of 12 in 5f2v

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Magnesium binding site 8 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg302

b:45.8
occ:1.00
 O2G W:APC301 1.9 51.6 1.0
O W:HOH405 2.2 40.6 1.0
O2B W:APC301 2.3 47.4 1.0
OD2 W:ASP72 2.6 48.1 1.0
PG W:APC301 3.1 54.9 1.0
PB W:APC301 3.1 41.8 1.0
O1B W:APC301 3.3 44.0 1.0
O3B W:APC301 3.4 48.4 1.0
CG W:ASP72 3.6 42.1 1.0
NZ W:LYS56 3.7 44.0 1.0
O1G W:APC301 3.8 49.5 1.0
NZ W:LYS48 4.0 47.8 1.0
O3G W:APC301 4.2 56.1 1.0
N7 W:APC301 4.2 33.8 1.0
H8 W:APC301 4.2 43.9 1.0
OE2 W:GLU139 4.3 36.1 1.0
O W:HOH402 4.3 37.5 1.0
OE1 W:GLU139 4.3 38.8 1.0
CB W:ASP72 4.3 36.1 1.0
OD1 W:ASP72 4.5 38.6 1.0
C8 W:APC301 4.6 36.6 1.0
NE2 W:GLN141 4.7 35.4 1.0
CD W:GLU139 4.7 42.3 1.0
O2A W:APC301 4.8 46.8 1.0
C3A W:APC301 4.9 43.3 1.0
NH2 W:ARG46 5.0 45.3 1.0

Magnesium binding site 9 out of 12 in 5f2v

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Magnesium binding site 9 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg302

b:75.5
occ:1.00
 O1B U:APC301 1.9 60.0 1.0
O U:HOH401 2.7 59.7 1.0
O2G U:APC301 2.9 68.3 1.0
OD2 U:ASP72 3.1 62.9 1.0
NE2 U:GLN141 3.2 50.6 1.0
OE1 U:GLU139 3.3 48.7 1.0
PB U:APC301 3.4 57.7 1.0
N7 U:APC301 3.8 45.3 1.0
PG U:APC301 3.9 75.5 1.0
O3B U:APC301 4.0 66.4 1.0
H8 U:APC301 4.1 59.7 1.0
CD U:GLU139 4.1 54.3 1.0
OE2 U:GLU139 4.1 57.5 1.0
O2B U:APC301 4.1 54.5 1.0
CG U:ASP72 4.3 60.7 1.0
C8 U:APC301 4.3 49.7 1.0
H3A2 U:APC301 4.4 73.0 1.0
O3G U:APC301 4.4 66.5 1.0
CD U:GLN141 4.5 47.3 1.0
C3A U:APC301 4.6 60.9 1.0
HN62 U:APC301 4.7 52.8 1.0
CB U:ASP72 4.7 54.7 1.0

Magnesium binding site 10 out of 12 in 5f2v

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Magnesium binding site 10 out of 12 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg302

b:39.3
occ:1.00
 O3B P:APC301 2.1 44.7 1.0
O P:HOH404 2.1 26.8 1.0
OD2 P:ASP72 2.3 45.5 1.0
O1G P:APC301 3.0 52.1 1.0
PG P:APC301 3.1 62.3 1.0
PB P:APC301 3.1 40.1 1.0
OE1 P:GLU139 3.3 37.3 1.0
CG P:ASP72 3.3 40.3 1.0
H3A1 P:APC301 3.4 58.8 1.0
H3A2 P:APC301 3.5 58.8 1.0
O1B P:APC301 3.6 49.2 1.0
C3A P:APC301 3.6 49.0 1.0
N7 P:APC301 3.8 40.4 1.0
NZ P:LYS48 4.0 47.6 1.0
H8 P:APC301 4.0 47.0 1.0
CB P:ASP72 4.0 40.2 1.0
OD1 P:ASP72 4.2 35.5 1.0
O3G P:APC301 4.2 54.4 1.0
CD P:GLU139 4.2 41.5 1.0
O2G P:APC301 4.2 54.2 1.0
NZ P:LYS56 4.3 38.1 1.0
OE2 P:GLU139 4.3 42.1 1.0
C8 P:APC301 4.3 39.2 1.0
O2B P:APC301 4.4 44.7 1.0
NH2 P:ARG46 4.4 40.2 1.0
NE2 P:GLN141 4.5 39.9 1.0
HN62 P:APC301 5.0 50.9 1.0

Reference:

W.Steinchen, J.S.Schuhmacher, F.Altegoer, C.D.Fage, V.Srinivasan, U.Linne, M.A.Marahiel, G.Bange. Catalytic Mechanism and Allosteric Regulation of An Oligomeric (P)Ppgpp Synthetase By An Alarmone. Proc.Natl.Acad.Sci.Usa V. 112 13348 2015.
ISSN: ESSN 1091-6490
PubMed: 26460002
DOI: 10.1073/PNAS.1505271112
Page generated: Tue Aug 12 07:57:42 2025

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