Magnesium in PDB 1rg9: S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Enzymatic activity of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
All present enzymatic activity of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp:
2.5.1.6;
Protein crystallography data
The structure of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp, PDB code: 1rg9
was solved by
J.Komoto,
T.Yamada,
Y.Takata,
G.D.Markham,
F.Takusagawa,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
225.820,
69.130,
118.230,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
24.1
|
Other elements in 1rg9:
The structure of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
(pdb code 1rg9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp, PDB code: 1rg9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 1 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg387
b:23.0
occ:1.00
|
O1A
|
A:PPK384
|
2.4
|
13.6
|
1.0
|
O1G
|
A:PPK384
|
2.5
|
19.7
|
1.0
|
NZ
|
A:LYS165
|
3.5
|
2.0
|
1.0
|
OE2
|
A:GLU8
|
3.6
|
4.2
|
1.0
|
PG
|
A:PPK384
|
3.7
|
12.0
|
1.0
|
PA
|
A:PPK384
|
3.8
|
7.5
|
1.0
|
OE1
|
A:GLU8
|
4.0
|
2.0
|
1.0
|
O
|
B:GLN119
|
4.1
|
15.0
|
1.0
|
CD
|
A:GLU8
|
4.3
|
2.0
|
1.0
|
NZ
|
A:LYS245
|
4.3
|
2.0
|
1.0
|
N3B
|
A:PPK384
|
4.3
|
7.6
|
1.0
|
OD2
|
B:ASP118
|
4.3
|
32.9
|
1.0
|
OD2
|
B:ASP271
|
4.3
|
13.6
|
1.0
|
O4A
|
A:PPK384
|
4.3
|
7.2
|
1.0
|
O3A
|
A:PPK384
|
4.4
|
8.5
|
1.0
|
OD1
|
B:ASP271
|
4.4
|
8.5
|
1.0
|
O2G
|
A:PPK384
|
4.6
|
13.5
|
1.0
|
CE
|
A:LYS245
|
4.7
|
2.0
|
1.0
|
CE
|
A:LYS165
|
4.8
|
7.0
|
1.0
|
CG
|
B:ASP271
|
4.8
|
12.7
|
1.0
|
O2A
|
A:PPK384
|
4.9
|
18.0
|
1.0
|
O3G
|
A:PPK384
|
4.9
|
15.2
|
1.0
|
O
|
B:GLY259
|
5.0
|
12.2
|
1.0
|
PB
|
A:PPK384
|
5.0
|
6.8
|
1.0
|
CA
|
B:GLY120
|
5.0
|
17.1
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 2 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg388
b:24.9
occ:1.00
|
O2B
|
A:PPK384
|
2.2
|
16.3
|
1.0
|
OD2
|
A:ASP16
|
2.2
|
21.9
|
1.0
|
O2G
|
A:PPK384
|
2.4
|
13.5
|
1.0
|
O2A
|
A:PPK384
|
2.5
|
18.0
|
1.0
|
CG
|
A:ASP16
|
2.9
|
16.4
|
1.0
|
OD1
|
A:ASP16
|
3.0
|
23.7
|
1.0
|
PB
|
A:PPK384
|
3.4
|
6.8
|
1.0
|
PG
|
A:PPK384
|
3.6
|
12.0
|
1.0
|
PA
|
A:PPK384
|
3.6
|
7.5
|
1.0
|
O3A
|
A:PPK384
|
3.8
|
8.5
|
1.0
|
N3B
|
A:PPK384
|
3.8
|
7.6
|
1.0
|
NZ
|
A:LYS245
|
3.8
|
2.0
|
1.0
|
NH2
|
A:ARG244
|
4.0
|
2.0
|
1.0
|
K
|
A:K386
|
4.0
|
4.2
|
1.0
|
O1A
|
A:PPK384
|
4.2
|
13.6
|
1.0
|
O3G
|
A:PPK384
|
4.3
|
15.2
|
1.0
|
CB
|
A:ARG244
|
4.3
|
5.9
|
1.0
|
O
|
A:CYS239
|
4.3
|
3.8
|
1.0
|
CZ
|
A:ARG244
|
4.3
|
7.9
|
1.0
|
CB
|
A:ASP16
|
4.4
|
16.7
|
1.0
|
OD2
|
A:ASP238
|
4.4
|
6.8
|
1.0
|
CE1
|
A:HIS14
|
4.4
|
4.3
|
1.0
|
NE
|
A:ARG244
|
4.5
|
14.1
|
1.0
|
O1B
|
A:PPK384
|
4.7
|
13.1
|
1.0
|
OE2
|
B:GLU42
|
4.8
|
20.3
|
1.0
|
O1G
|
A:PPK384
|
4.9
|
19.7
|
1.0
|
O
|
A:ARG244
|
4.9
|
2.7
|
1.0
|
CG
|
A:ARG244
|
4.9
|
13.8
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 3 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg487
b:27.6
occ:1.00
|
O1A
|
B:PPK484
|
2.3
|
2.0
|
1.0
|
O1G
|
B:PPK484
|
2.4
|
11.6
|
1.0
|
NZ
|
B:LYS165
|
3.6
|
2.0
|
1.0
|
PG
|
B:PPK484
|
3.6
|
10.5
|
1.0
|
OE2
|
B:GLU8
|
3.7
|
13.0
|
1.0
|
PA
|
B:PPK484
|
3.8
|
2.0
|
1.0
|
NZ
|
B:LYS245
|
4.1
|
15.2
|
1.0
|
N3B
|
B:PPK484
|
4.2
|
7.8
|
1.0
|
OE1
|
B:GLU8
|
4.3
|
2.0
|
1.0
|
OD2
|
A:ASP271
|
4.3
|
15.9
|
1.0
|
O
|
A:GLN119
|
4.3
|
17.0
|
1.0
|
OD1
|
A:ASP271
|
4.3
|
9.7
|
1.0
|
O4A
|
B:PPK484
|
4.4
|
8.3
|
1.0
|
CD
|
B:GLU8
|
4.4
|
5.8
|
1.0
|
O3A
|
B:PPK484
|
4.4
|
3.4
|
1.0
|
OD2
|
A:ASP118
|
4.4
|
4.8
|
1.0
|
O2G
|
B:PPK484
|
4.5
|
15.1
|
1.0
|
CE
|
B:LYS245
|
4.6
|
3.3
|
1.0
|
CG
|
A:ASP271
|
4.8
|
16.1
|
1.0
|
O
|
A:GLY259
|
4.8
|
22.2
|
1.0
|
O2A
|
B:PPK484
|
4.8
|
12.2
|
1.0
|
O3G
|
B:PPK484
|
4.8
|
8.1
|
1.0
|
PB
|
B:PPK484
|
4.9
|
2.0
|
1.0
|
CE
|
B:LYS165
|
5.0
|
3.2
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 4 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg488
b:9.0
occ:1.00
|
O2B
|
B:PPK484
|
2.2
|
17.8
|
1.0
|
OD2
|
B:ASP16
|
2.2
|
12.5
|
1.0
|
O2G
|
B:PPK484
|
2.4
|
15.1
|
1.0
|
O2A
|
B:PPK484
|
2.5
|
12.2
|
1.0
|
CG
|
B:ASP16
|
2.9
|
9.3
|
1.0
|
OD1
|
B:ASP16
|
3.0
|
14.9
|
1.0
|
PB
|
B:PPK484
|
3.4
|
2.0
|
1.0
|
PG
|
B:PPK484
|
3.6
|
10.5
|
1.0
|
PA
|
B:PPK484
|
3.7
|
2.0
|
1.0
|
N3B
|
B:PPK484
|
3.8
|
7.8
|
1.0
|
O3A
|
B:PPK484
|
3.8
|
3.4
|
1.0
|
NH2
|
B:ARG244
|
3.9
|
5.5
|
1.0
|
NZ
|
B:LYS245
|
3.9
|
15.2
|
1.0
|
K
|
B:K486
|
4.1
|
2.0
|
1.0
|
O3G
|
B:PPK484
|
4.2
|
8.1
|
1.0
|
CZ
|
B:ARG244
|
4.2
|
6.3
|
1.0
|
CB
|
B:ARG244
|
4.2
|
7.7
|
1.0
|
O
|
B:CYS239
|
4.2
|
13.8
|
1.0
|
O1A
|
B:PPK484
|
4.2
|
2.0
|
1.0
|
CB
|
B:ASP16
|
4.3
|
10.4
|
1.0
|
NE
|
B:ARG244
|
4.4
|
12.2
|
1.0
|
OD2
|
B:ASP238
|
4.5
|
7.3
|
1.0
|
CE1
|
B:HIS14
|
4.5
|
6.5
|
1.0
|
OE2
|
A:GLU42
|
4.7
|
5.5
|
1.0
|
O1B
|
B:PPK484
|
4.7
|
10.4
|
1.0
|
CG
|
B:ARG244
|
4.8
|
12.6
|
1.0
|
O1G
|
B:PPK484
|
4.9
|
11.6
|
1.0
|
O
|
B:ARG244
|
4.9
|
10.4
|
1.0
|
NH1
|
B:ARG244
|
4.9
|
5.5
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 5 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg588
b:40.2
occ:1.00
|
OD2
|
C:ASP16
|
2.1
|
2.9
|
1.0
|
O2B
|
C:PPK584
|
2.2
|
25.9
|
1.0
|
O2A
|
C:PPK584
|
2.6
|
22.6
|
1.0
|
CG
|
C:ASP16
|
2.8
|
2.7
|
1.0
|
OD1
|
C:ASP16
|
2.8
|
5.2
|
1.0
|
O2G
|
C:PPK584
|
2.9
|
11.4
|
1.0
|
PB
|
C:PPK584
|
3.5
|
21.2
|
1.0
|
PA
|
C:PPK584
|
3.8
|
15.7
|
1.0
|
O3A
|
C:PPK584
|
3.9
|
19.2
|
1.0
|
K
|
C:K586
|
4.0
|
18.5
|
1.0
|
O
|
C:CYS239
|
4.0
|
17.4
|
1.0
|
PG
|
C:PPK584
|
4.0
|
20.1
|
1.0
|
NZ
|
C:LYS245
|
4.0
|
32.4
|
1.0
|
NH2
|
C:ARG244
|
4.1
|
21.2
|
1.0
|
N3B
|
C:PPK584
|
4.1
|
18.8
|
1.0
|
CB
|
C:ASP16
|
4.2
|
7.7
|
1.0
|
OD2
|
C:ASP238
|
4.3
|
7.1
|
1.0
|
CB
|
C:ARG244
|
4.3
|
18.6
|
1.0
|
CZ
|
C:ARG244
|
4.4
|
17.6
|
1.0
|
CE1
|
C:HIS14
|
4.4
|
2.0
|
1.0
|
O1A
|
C:PPK584
|
4.5
|
29.9
|
1.0
|
NE
|
C:ARG244
|
4.5
|
18.7
|
1.0
|
OE2
|
D:GLU42
|
4.6
|
9.1
|
1.0
|
O3G
|
C:PPK584
|
4.6
|
4.0
|
1.0
|
O1B
|
C:PPK584
|
4.8
|
14.1
|
1.0
|
CG
|
C:ARG244
|
4.9
|
17.8
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 6 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg687
b:41.8
occ:1.00
|
O1G
|
D:PPK684
|
2.4
|
24.2
|
1.0
|
O1A
|
D:PPK684
|
2.5
|
19.5
|
1.0
|
OD1
|
C:ASP271
|
3.1
|
10.0
|
1.0
|
OD2
|
C:ASP271
|
3.3
|
23.0
|
1.0
|
PG
|
D:PPK684
|
3.4
|
10.7
|
1.0
|
N3B
|
D:PPK684
|
3.6
|
7.6
|
1.0
|
CG
|
C:ASP271
|
3.6
|
24.9
|
1.0
|
NZ
|
D:LYS165
|
3.7
|
17.1
|
1.0
|
PA
|
D:PPK684
|
3.7
|
16.3
|
1.0
|
OD2
|
C:ASP118
|
3.7
|
15.8
|
1.0
|
O3A
|
D:PPK684
|
3.9
|
12.0
|
1.0
|
O
|
C:GLN119
|
3.9
|
18.6
|
1.0
|
PB
|
D:PPK684
|
4.3
|
2.0
|
1.0
|
O4A
|
D:PPK684
|
4.4
|
13.9
|
1.0
|
CG
|
C:ASP118
|
4.6
|
17.8
|
1.0
|
O2G
|
D:PPK684
|
4.6
|
2.0
|
1.0
|
O3G
|
D:PPK684
|
4.6
|
9.6
|
1.0
|
OE2
|
D:GLU8
|
4.7
|
23.1
|
1.0
|
CA
|
C:GLY260
|
4.9
|
18.1
|
1.0
|
OE1
|
D:GLU8
|
4.9
|
20.7
|
1.0
|
O2A
|
D:PPK684
|
5.0
|
24.1
|
1.0
|
CB
|
C:ASP118
|
5.0
|
11.7
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 7 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg587
b:17.9
occ:1.00
|
O1A
|
C:PPK584
|
2.4
|
29.9
|
1.0
|
O1G
|
C:PPK584
|
2.5
|
19.7
|
1.0
|
OD1
|
D:ASP271
|
3.3
|
17.8
|
1.0
|
OD2
|
D:ASP271
|
3.5
|
16.5
|
1.0
|
PG
|
C:PPK584
|
3.5
|
20.1
|
1.0
|
NZ
|
C:LYS165
|
3.5
|
27.9
|
1.0
|
OD2
|
D:ASP118
|
3.6
|
20.7
|
1.0
|
PA
|
C:PPK584
|
3.7
|
15.7
|
1.0
|
CG
|
D:ASP271
|
3.8
|
21.5
|
1.0
|
N3B
|
C:PPK584
|
3.8
|
18.8
|
1.0
|
O
|
D:GLN119
|
3.8
|
9.0
|
1.0
|
O3A
|
C:PPK584
|
3.9
|
19.2
|
1.0
|
O4A
|
C:PPK584
|
4.2
|
20.0
|
1.0
|
PB
|
C:PPK584
|
4.5
|
21.2
|
1.0
|
CG
|
D:ASP118
|
4.5
|
20.5
|
1.0
|
O2G
|
C:PPK584
|
4.6
|
11.4
|
1.0
|
OE2
|
C:GLU8
|
4.7
|
11.3
|
1.0
|
O3G
|
C:PPK584
|
4.8
|
4.0
|
1.0
|
OE1
|
C:GLU8
|
4.8
|
10.1
|
1.0
|
O2A
|
C:PPK584
|
4.9
|
22.6
|
1.0
|
CA
|
D:GLY260
|
4.9
|
2.7
|
1.0
|
NZ
|
C:LYS245
|
4.9
|
32.4
|
1.0
|
CB
|
D:ASP118
|
5.0
|
13.6
|
1.0
|
C
|
D:GLN119
|
5.0
|
2.9
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 1rg9
Go back to
Magnesium Binding Sites List in 1rg9
Magnesium binding site 8 out
of 8 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg688
b:23.4
occ:1.00
|
OD2
|
D:ASP16
|
2.1
|
6.7
|
1.0
|
O2B
|
D:PPK684
|
2.2
|
2.4
|
1.0
|
O2G
|
D:PPK684
|
2.7
|
2.0
|
1.0
|
O2A
|
D:PPK684
|
2.7
|
24.1
|
1.0
|
CG
|
D:ASP16
|
2.8
|
6.8
|
1.0
|
OD1
|
D:ASP16
|
2.9
|
10.1
|
1.0
|
PB
|
D:PPK684
|
3.5
|
2.0
|
1.0
|
PG
|
D:PPK684
|
3.8
|
10.7
|
1.0
|
PA
|
D:PPK684
|
3.8
|
16.3
|
1.0
|
O3A
|
D:PPK684
|
3.8
|
12.0
|
1.0
|
NZ
|
D:LYS245
|
3.9
|
23.7
|
1.0
|
N3B
|
D:PPK684
|
4.0
|
7.6
|
1.0
|
K
|
D:K686
|
4.1
|
41.4
|
1.0
|
NH2
|
D:ARG244
|
4.1
|
28.0
|
1.0
|
O
|
D:CYS239
|
4.2
|
22.4
|
1.0
|
CB
|
D:ARG244
|
4.2
|
31.4
|
1.0
|
CB
|
D:ASP16
|
4.3
|
7.7
|
1.0
|
CZ
|
D:ARG244
|
4.3
|
27.0
|
1.0
|
O3G
|
D:PPK684
|
4.4
|
9.6
|
1.0
|
CE1
|
D:HIS14
|
4.4
|
15.5
|
1.0
|
NE
|
D:ARG244
|
4.5
|
26.0
|
1.0
|
O1A
|
D:PPK684
|
4.5
|
19.5
|
1.0
|
OD2
|
D:ASP238
|
4.5
|
16.4
|
1.0
|
OE2
|
C:GLU42
|
4.6
|
11.3
|
1.0
|
O1B
|
D:PPK684
|
4.7
|
2.0
|
1.0
|
CG
|
D:ARG244
|
4.8
|
28.5
|
1.0
|
|
Reference:
J.Komoto,
T.Yamada,
Y.Takata,
G.D.Markham,
F.Takusagawa.
Crystal Structure of the S-Adenosylmethionine Synthetase Ternary Complex: A Novel Catalytic Mechanism of S-Adenosylmethionine Synthesis From Atp and Met. Biochemistry V. 43 1821 2004.
ISSN: ISSN 0006-2960
PubMed: 14967023
DOI: 10.1021/BI035611T
Page generated: Tue Aug 13 12:59:52 2024
|