Potassium in PDB 1p7l: S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.

All present enzymatic activity of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.:
2.5.1.6;

The structure of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met., PDB code: 1p7l was solved by F.Takusagawa, J.Komoto, 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 (%)	21.3 / 24.2

The structure of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Potassium atom in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. (pdb code 1p7l). 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 Amppnp and Met., PDB code: 1p7l:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


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 Amppnp and Met. within 5.0Å range: probe atom residue distance (Å) B Occ A:K386 b:2.0 occ:1.00 O2B A:ANP384 3.0 18.2 1.0 OE2 B:GLU42 3.2 22.3 1.0 O A:CYS239 3.2 5.8 1.0 OD1 A:ASP238 3.3 4.0 1.0 CB A:CYS239 3.9 12.3 1.0 CG A:ASP238 3.9 8.9 1.0 N A:CYS239 3.9 8.0 1.0 CG B:GLU42 3.9 6.9 1.0 CD B:GLU42 4.0 13.5 1.0 MG A:MG388 4.0 15.6 1.0 OD2 A:ASP238 4.0 10.4 1.0 C A:CYS239 4.1 5.2 1.0 OE2 B:GLU55 4.1 14.6 1.0 CA A:CYS239 4.1 4.6 1.0 PB A:ANP384 4.1 4.8 1.0 N B:MET385 4.3 12.9 1.0 O1B A:ANP384 4.3 17.3 1.0 C A:ASP238 4.7 12.4 1.0 O3A A:ANP384 4.8 11.9 1.0 NH2 A:ARG244 4.9 2.0 1.0

Potassium binding site 2 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


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 Amppnp and Met. within 5.0Å range: probe atom residue distance (Å) B Occ B:K486 b:2.0 occ:1.00 OD1 B:ASP238 3.1 5.7 1.0 O2B B:ANP484 3.1 19.9 1.0 OE2 A:GLU42 3.2 9.6 1.0 O B:CYS239 3.3 14.2 1.0 CG B:ASP238 3.7 3.1 1.0 CB B:CYS239 3.8 9.2 1.0 N B:CYS239 3.8 2.0 1.0 OD2 B:ASP238 3.9 12.1 1.0 CG A:GLU42 3.9 4.5 1.0 OE2 A:GLU55 4.0 3.6 1.0 CD A:GLU42 4.0 5.1 1.0 CA B:CYS239 4.1 5.6 1.0 C B:CYS239 4.1 6.5 1.0 MG B:MG488 4.1 10.1 1.0 PB B:ANP484 4.2 2.0 1.0 N A:MET485 4.2 8.1 1.0 O1B B:ANP484 4.4 17.3 1.0 C B:ASP238 4.6 4.1 1.0 O3A B:ANP484 4.9 9.2 1.0 CB B:ASP238 4.9 3.7 1.0 CA B:ASP238 5.0 2.0 1.0

Potassium binding site 3 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


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 Amppnp and Met. within 5.0Å range: probe atom residue distance (Å) B Occ C:K686 b:17.8 occ:1.00 OD1 C:ASP238 3.0 9.9 1.0 OE2 D:GLU42 3.0 9.5 1.0 O C:CYS239 3.1 19.2 1.0 O2B C:PPK684 3.3 27.2 1.0 CG C:ASP238 3.7 7.6 1.0 N C:CYS239 3.7 6.9 1.0 CB C:CYS239 3.8 15.2 1.0 OD2 C:ASP238 3.8 5.6 1.0 CG D:GLU42 3.9 7.6 1.0 CD D:GLU42 3.9 9.1 1.0 MG C:MG688 4.0 47.9 1.0 C C:CYS239 4.0 16.5 1.0 O1B C:PPK684 4.0 14.5 1.0 CA C:CYS239 4.0 14.7 1.0 OE2 D:GLU55 4.1 11.9 1.0 PB C:PPK684 4.1 24.8 1.0 C C:ASP238 4.5 7.2 1.0 N C:SAM685 4.7 9.9 1.0 CB C:ASP238 4.8 2.0 1.0 CA C:ASP238 4.9 2.9 1.0

Potassium binding site 4 out of 4 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


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 Amppnp and Met. within 5.0Å range: probe atom residue distance (Å) B Occ D:K886 b:42.0 occ:1.00 OE2 C:GLU42 3.0 10.4 1.0 OD1 D:ASP238 3.1 25.6 1.0 O D:CYS239 3.2 23.1 1.0 O2B D:PPK884 3.3 2.0 1.0 CG D:ASP238 3.7 18.8 1.0 N D:CYS239 3.8 13.2 1.0 CG C:GLU42 3.8 2.0 1.0 CD C:GLU42 3.8 2.0 1.0 OD2 D:ASP238 3.9 14.9 1.0 CB D:CYS239 3.9 12.0 1.0 O1B D:PPK884 4.0 2.0 1.0 C D:CYS239 4.0 21.2 1.0 MG D:MG888 4.0 25.3 1.0 CA D:CYS239 4.1 17.9 1.0 OE2 C:GLU55 4.1 17.4 1.0 PB D:PPK884 4.2 5.8 1.0 C D:ASP238 4.6 17.5 1.0 N C:SAM885 4.7 18.0 1.0 CB D:ASP238 4.9 19.3 1.0 CA D:ASP238 5.0 17.2 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