Atomistry » Magnesium » PDB 1rdd-1rtk » 1rg9
Atomistry »
  Magnesium »
    PDB 1rdd-1rtk »
      1rg9 »

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:

Potassium (K) 4 atoms

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: Sun Aug 10 03:51:13 2025

Last articles

Na in 6KCB
Na in 6K96
Na in 6K8G
Na in 6K89
Na in 6K86
Na in 6K82
Na in 6K17
Na in 6K26
Na in 6JZO
Na in 6K5Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy