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Potassium 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 (Mg) 8 atoms

Potassium Binding Sites:

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 1rg9

Go back to Potassium Binding Sites List in 1rg9
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 1rg9

Go back to Potassium Binding Sites List in 1rg9
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 1rg9

Go back to Potassium Binding Sites List in 1rg9
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 1rg9

Go back to Potassium Binding Sites List in 1rg9
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

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 Dec 13 23:01:11 2020

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