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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

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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

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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

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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

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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

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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

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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

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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

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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

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