Potassium in PDB 7r3b: S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam

Enzymatic activity of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam

All present enzymatic activity of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam:
2.5.1.6;

Protein crystallography data

The structure of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam, PDB code: 7r3b was solved by A.Shahar, D.Kleiner, S.Bershtein, R.Zarivach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 2.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.426, 110.927, 112.661, 93.82, 104.03, 99.59
R / Rfree (%) 15.6 / 27.5

Other elements in 7r3b:

The structure of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam (pdb code 7r3b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam, PDB code: 7r3b:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 7r3b

Go back to Potassium Binding Sites List in 7r3b
Potassium binding site 1 out of 5 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:110.2
occ:1.00
 O1B A:PPK502 2.1 111.3 1.0
MG A:MG503 2.9 98.0 1.0
PB A:PPK502 3.0 150.9 1.0
OE2 B:GLU44 3.2 84.5 1.0
OD2 A:ASP18 3.2 61.3 1.0
OD1 A:ASP18 3.3 66.8 1.0
O A:ALA251 3.4 70.0 1.0
O2B A:PPK502 3.5 159.2 1.0
N3B A:PPK502 3.6 149.2 1.0
CG A:ASP18 3.7 53.9 1.0
C A:ALA251 4.1 66.3 1.0
CD B:GLU44 4.2 71.5 1.0
NE A:ARG256 4.3 69.7 1.0
CD1 A:LEU253 4.3 63.7 1.0
CZ A:ARG256 4.4 72.3 1.0
O3A A:PPK502 4.4 152.6 1.0
CA A:GLY252 4.5 61.4 1.0
CD A:ARG256 4.5 59.8 1.0
O1G A:PPK502 4.5 106.4 1.0
PG A:PPK502 4.6 142.2 1.0
N A:GLY252 4.6 61.6 1.0
OD1 A:ASP250 4.7 85.1 1.0
NH1 A:ARG256 4.7 75.1 1.0
NH2 A:ARG256 4.7 76.0 1.0
CG B:GLU44 4.9 72.2 1.0
N A:LEU253 4.9 64.2 1.0

Potassium binding site 2 out of 5 in 7r3b

Go back to Potassium Binding Sites List in 7r3b
Potassium binding site 2 out of 5 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:121.2
occ:1.00
 O1B C:ANP501 2.5 152.4 1.0
OD1 C:ASP250 3.2 110.8 1.0
OD2 C:ASP250 3.5 99.4 1.0
CG C:ASP250 3.5 100.5 1.0
MG C:MG502 3.6 86.0 1.0
PB C:ANP501 3.8 146.7 1.0
O C:ALA251 3.8 75.9 1.0
N C:ALA251 3.9 80.6 1.0
OE2 D:GLU44 3.9 122.3 1.0
N3B C:ANP501 4.2 164.8 1.0
O3A C:ANP501 4.3 152.2 1.0
CB C:ALA251 4.4 73.8 1.0
CA C:ALA251 4.5 75.6 1.0
C C:ALA251 4.6 74.5 1.0
CB C:ASP250 4.6 92.6 1.0
C C:ASP250 4.7 83.7 1.0
CA C:ASP250 4.7 84.6 1.0
CD D:GLU44 4.9 91.0 1.0

Potassium binding site 3 out of 5 in 7r3b

Go back to Potassium Binding Sites List in 7r3b
Potassium binding site 3 out of 5 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K504

b:92.6
occ:1.00
 O2B D:ANP501 2.4 144.5 1.0
O1B D:ANP501 3.0 185.4 1.0
O D:ALA251 3.1 74.4 1.0
PB D:ANP501 3.1 156.4 1.0
MG D:MG503 3.2 80.1 1.0
OD1 D:ASP250 3.2 88.7 1.0
OE2 C:GLU44 3.4 91.6 1.0
CG D:ASP250 3.9 91.6 1.0
C D:ALA251 4.0 63.8 1.0
N D:ALA251 4.1 71.0 1.0
OD2 D:ASP250 4.2 109.2 1.0
O3A D:ANP501 4.2 122.8 1.0
N3B D:ANP501 4.2 154.7 1.0
CB D:ALA251 4.3 53.2 1.0
CA D:ALA251 4.4 59.9 1.0
CD C:GLU44 4.6 77.1 1.0
OD2 D:ASP18 4.7 66.3 1.0

Potassium binding site 4 out of 5 in 7r3b

Go back to Potassium Binding Sites List in 7r3b
Potassium binding site 4 out of 5 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K505

b:121.2
occ:1.00
 O1B F:ANP501 2.1 125.5 1.0
MG F:MG503 2.6 82.2 1.0
O F:ALA251 3.1 73.8 1.0
OD1 F:ASP250 3.2 85.2 1.0
PB F:ANP501 3.3 135.2 1.0
OE2 E:GLU44 3.5 82.3 1.0
N3B F:ANP501 3.7 143.6 1.0
O3A F:ANP501 3.8 142.6 1.0
CG F:ASP250 3.9 91.2 1.0
C F:ALA251 4.0 69.7 1.0
N F:ALA251 4.1 67.0 1.0
OD2 F:ASP250 4.2 101.4 1.0
CB F:ALA251 4.3 66.4 1.0
CA F:ALA251 4.4 64.8 1.0
O2B F:ANP501 4.6 141.9 1.0
OD2 F:ASP18 4.7 67.9 1.0
CD E:GLU44 4.7 74.3 1.0
CB F:ASP250 5.0 80.7 1.0

Potassium binding site 5 out of 5 in 7r3b

Go back to Potassium Binding Sites List in 7r3b
Potassium binding site 5 out of 5 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K506

b:113.1
occ:1.00
 O2B H:PPK503 2.4 151.8 1.0
OE2 G:GLU44 3.0 65.7 1.0
OD2 H:ASP18 3.2 62.0 1.0
MG H:MG505 3.3 95.7 1.0
OD1 H:ASP18 3.3 52.9 1.0
PB H:PPK503 3.4 167.7 1.0
N3B H:PPK503 3.6 172.6 1.0
CG H:ASP18 3.6 55.5 1.0
O H:ALA251 3.8 73.3 1.0
NE H:ARG256 3.9 63.5 1.0
CZ H:ARG256 3.9 74.6 1.0
O3G H:PPK503 3.9 132.7 1.0
CD G:GLU44 4.1 71.9 1.0
NH2 H:ARG256 4.1 77.2 1.0
CD1 H:LEU253 4.2 60.4 1.0
PG H:PPK503 4.3 154.8 1.0
O1B H:PPK503 4.3 183.5 1.0
NH1 H:ARG256 4.4 73.9 1.0
CD H:ARG256 4.4 52.2 1.0
C H:ALA251 4.4 71.9 1.0
CA H:GLY252 4.6 60.1 1.0
CB H:ARG256 4.6 59.0 1.0
O2G H:PPK503 4.7 115.5 1.0
O3A H:PPK503 4.7 156.8 1.0
N H:LEU253 4.8 57.4 1.0
N H:GLY252 4.8 64.8 1.0
OE1 G:GLU44 4.9 62.9 1.0
CG H:ARG256 4.9 51.7 1.0
CG G:GLU44 5.0 72.8 1.0

Reference:

D.Kleiner, Z.Shapiro Tuchman, F.Shmulevich, A.Shahar, R.Zarivach, M.Kosloff, S.Bershtein. Evolution of Homo-Oligomerization of Methionine S-Adenosyltransferases Is Replete with Structure-Function Constrains. Protein Sci. V. 31 E4352 2022.
ISSN: ESSN 1469-896X
PubMed: 35762725
DOI: 10.1002/PRO.4352
Page generated: Wed Apr 5 10:09:14 2023

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