Potassium in PDB 1rg9: 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;

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

The structure of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp, PDB code: 1rg9:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K386 b:4.2 occ:1.00 O2B A:PPK384 3.1 16.3 1.0 OE2 B:GLU42 3.1 20.3 1.0 O A:CYS239 3.2 3.8 1.0 OD1 A:ASP238 3.3 3.0 1.0 CG A:ASP238 3.8 6.2 1.0 OD2 A:ASP238 3.8 6.8 1.0 CB A:CYS239 3.9 12.0 1.0 N A:CYS239 3.9 7.3 1.0 CG B:GLU42 3.9 7.7 1.0 CD B:GLU42 4.0 12.8 1.0 MG A:MG388 4.0 24.9 1.0 C A:CYS239 4.1 3.5 1.0 OE2 B:GLU55 4.1 15.3 1.0 CA A:CYS239 4.1 3.3 1.0 O1B A:PPK384 4.2 13.1 1.0 PB A:PPK384 4.2 6.8 1.0 N A:SAM385 4.5 17.1 1.0 C A:ASP238 4.7 11.1 1.0 NH2 A:ARG244 4.9 2.0 1.0 O3A A:PPK384 5.0 8.5 1.0 CB A:ASP238 5.0 4.2 1.0

Potassium binding site 2 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:K486 b:2.0 occ:1.00 OD1 B:ASP238 3.1 6.8 1.0 OE2 A:GLU42 3.1 5.5 1.0 O2B B:PPK484 3.2 17.8 1.0 O B:CYS239 3.2 13.8 1.0 CG B:ASP238 3.7 2.0 1.0 CB B:CYS239 3.8 8.2 1.0 N B:CYS239 3.8 2.0 1.0 OD2 B:ASP238 3.8 7.3 1.0 CG A:GLU42 3.9 4.3 1.0 CD A:GLU42 3.9 2.5 1.0 OE2 A:GLU55 4.0 2.1 1.0 CA B:CYS239 4.0 5.7 1.0 C B:CYS239 4.0 6.7 1.0 MG B:MG488 4.1 9.0 1.0 O1B B:PPK484 4.2 10.4 1.0 PB B:PPK484 4.3 2.0 1.0 N B:SAM485 4.3 12.5 1.0 C B:ASP238 4.6 4.9 1.0 CB B:ASP238 4.9 5.2 1.0 O3A B:PPK484 5.0 3.4 1.0 CA B:ASP238 5.0 2.8 1.0

Potassium binding site 3 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:K586 b:18.5 occ:1.00 OD1 C:ASP238 3.0 10.9 1.0 OE2 D:GLU42 3.0 9.1 1.0 O C:CYS239 3.1 17.4 1.0 O2B C:PPK584 3.2 25.9 1.0 CG C:ASP238 3.6 6.8 1.0 N C:CYS239 3.7 7.2 1.0 OD2 C:ASP238 3.7 7.1 1.0 CB C:CYS239 3.8 14.7 1.0 CG D:GLU42 3.9 7.0 1.0 CD D:GLU42 3.9 9.3 1.0 C C:CYS239 3.9 15.6 1.0 MG C:MG588 4.0 40.2 1.0 CA C:CYS239 4.0 14.2 1.0 O1B C:PPK584 4.0 14.1 1.0 OE2 D:GLU55 4.1 12.1 1.0 PB C:PPK584 4.2 21.2 1.0 C C:ASP238 4.5 6.7 1.0 N C:SAM585 4.7 10.4 1.0 CB C:ASP238 4.8 2.6 1.0 CA C:ASP238 4.8 2.6 1.0 O3A C:PPK584 4.9 19.2 1.0

Potassium binding site 4 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of S-Adenosylmethionine Synthetase Complexed with Sam and Ppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:K686 b:41.4 occ:1.00 OE2 C:GLU42 3.0 11.3 1.0 OD1 D:ASP238 3.1 25.4 1.0 O D:CYS239 3.1 22.4 1.0 O2B D:PPK684 3.2 2.4 1.0 CG D:ASP238 3.6 19.1 1.0 N D:CYS239 3.7 13.7 1.0 OD2 D:ASP238 3.7 16.4 1.0 CG C:GLU42 3.8 2.0 1.0 CD C:GLU42 3.8 2.0 1.0 CB D:CYS239 3.9 13.3 1.0 C D:CYS239 3.9 21.2 1.0 CA D:CYS239 4.0 17.7 1.0 O1B D:PPK684 4.0 2.0 1.0 MG D:MG688 4.1 23.4 1.0 OE2 C:GLU55 4.1 18.5 1.0 PB D:PPK684 4.2 2.0 1.0 C D:ASP238 4.6 17.9 1.0 CB D:ASP238 4.8 20.0 1.0 N C:SAM685 4.8 17.2 1.0 CA D:ASP238 4.9 18.1 1.0 O3A D:PPK684 5.0 12.0 1.0

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