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Potassium in PDB 6rkc: Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum

Enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum

All present enzymatic activity of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum:
2.5.1.6;

Protein crystallography data

The structure of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rkc was solved by A.Shahar, R.Zarivach, S.Bershtein, D.Kleiner, F.Shmulevich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 142.372, 79.467, 143.787, 90.00, 105.11, 90.00
R / Rfree (%) 26 / 28.4

Other elements in 6rkc:

The structure of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum (pdb code 6rkc). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum, PDB code: 6rkc:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 6rkc

Go back to Potassium Binding Sites List in 6rkc
Potassium binding site 1 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:50.5
occ:1.00
O2B A:PPK405 2.6 41.8 1.0
OD1 A:ASP231 2.6 48.2 1.0
MG A:MG402 2.7 66.9 1.0
OE1 B:GLU44 2.9 48.4 1.0
O B:HOH516 3.0 43.2 1.0
O A:THR232 3.2 39.9 1.0
CG A:ASP231 3.5 47.8 1.0
PB A:PPK405 3.6 42.5 1.0
OD2 A:ASP231 3.6 47.6 1.0
CD B:GLU44 3.8 46.9 1.0
O1B A:PPK405 4.0 43.3 1.0
C A:THR232 4.1 39.8 1.0
N A:THR232 4.1 42.7 1.0
N A:SAM404 4.3 53.0 1.0
CG B:GLU44 4.4 45.5 1.0
NH2 A:ARG237 4.4 36.6 1.0
O4A A:PPK405 4.4 41.6 1.0
O3A A:PPK405 4.4 42.8 1.0
CA A:THR232 4.4 41.1 1.0
O3G A:PPK405 4.4 43.5 1.0
CB A:THR232 4.4 40.5 1.0
OE2 B:GLU44 4.6 48.1 1.0
CG A:SAM404 4.8 52.8 1.0
C A:ASP231 4.8 44.5 1.0
N3B A:PPK405 4.9 42.8 1.0
CB A:ASP231 4.9 47.1 1.0

Potassium binding site 2 out of 7 in 6rkc

Go back to Potassium Binding Sites List in 6rkc
Potassium binding site 2 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:57.4
occ:1.00
OD1 B:ASP231 2.6 37.6 1.0
OE1 A:GLU44 2.8 61.0 1.0
O1B A:PPK409 3.1 36.7 1.0
O B:THR232 3.1 35.9 1.0
MG B:MG401 3.5 60.0 1.0
CG B:ASP231 3.5 37.1 1.0
OD2 B:ASP231 3.7 36.7 1.0
CD A:GLU44 3.7 60.0 1.0
PB A:PPK409 3.9 36.8 1.0
N B:THR232 3.9 36.7 1.0
C B:THR232 4.0 35.8 1.0
O2B A:PPK409 4.0 37.1 1.0
CG A:GLU44 4.1 56.0 1.0
CB B:THR232 4.2 36.7 1.0
CA B:THR232 4.2 36.5 1.0
N B:SAM402 4.4 44.6 1.0
NH2 B:ARG237 4.4 36.2 1.0
O3A A:PPK409 4.5 36.7 1.0
OE2 A:GLU44 4.6 64.1 1.0
OE1 A:GLU57 4.7 46.0 1.0
C B:ASP231 4.7 36.9 1.0
O3G A:PPK409 4.8 38.0 1.0
CB B:ASP231 4.8 37.1 1.0
O2A A:PPK409 4.9 36.1 1.0
CA B:ASP231 5.0 37.4 1.0

Potassium binding site 3 out of 7 in 6rkc

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Potassium binding site 3 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K401

b:67.2
occ:1.00
OD1 C:ASP231 2.8 54.6 1.0
OE1 D:GLU44 2.9 60.5 1.0
O1B C:PPK405 3.0 42.4 1.0
O C:THR232 3.0 52.0 1.0
MG C:MG402 3.2 40.0 1.0
O D:HOH504 3.4 48.1 1.0
CG C:ASP231 3.6 54.4 1.0
CD D:GLU44 3.6 57.8 1.0
OD2 C:ASP231 3.8 54.8 1.0
C C:THR232 3.9 51.3 1.0
CG D:GLU44 4.1 56.6 1.0
PB C:PPK405 4.1 43.0 1.0
N C:THR232 4.1 52.9 1.0
NH2 C:ARG237 4.2 49.8 1.0
CB C:THR232 4.3 52.0 1.0
CA C:THR232 4.3 52.1 1.0
OE2 D:GLU44 4.4 57.6 1.0
N C:SAM404 4.5 55.8 1.0
O2B C:PPK405 4.6 43.6 1.0
O2G C:PPK405 4.6 41.5 1.0
O3A C:PPK405 4.7 43.2 1.0
O2A C:PPK405 4.8 42.6 1.0
C C:ASP231 4.8 53.9 1.0
CD1 C:LEU234 4.9 51.8 1.0
OE1 D:GLU57 4.9 54.3 1.0
N C:GLY233 4.9 50.5 1.0
CB C:ASP231 5.0 54.8 1.0

Potassium binding site 4 out of 7 in 6rkc

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Potassium binding site 4 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K401

b:73.1
occ:1.00
OD1 E:ASP231 2.7 73.8 1.0
O E:HOH513 2.8 56.0 1.0
O2B E:PPK405 2.9 60.9 1.0
OE2 F:GLU44 3.1 77.8 1.0
O E:THR232 3.2 59.8 1.0
MG E:MG402 3.5 73.1 1.0
CD F:GLU44 3.6 74.9 1.0
CG E:ASP231 3.7 71.7 1.0
OD2 E:ASP231 3.9 72.9 1.0
PB E:PPK405 4.0 61.3 1.0
CG F:GLU44 4.0 72.7 1.0
C E:THR232 4.1 59.6 1.0
N E:THR232 4.1 62.3 1.0
O1B E:PPK405 4.2 60.9 1.0
CB E:THR232 4.3 59.7 1.0
CA E:THR232 4.4 60.5 1.0
OE1 F:GLU44 4.4 79.8 1.0
NH2 E:ARG237 4.4 67.7 1.0
N E:SAM404 4.7 81.6 1.0
O3A E:PPK405 4.7 60.6 1.0
O3G E:PPK405 4.8 62.2 1.0
C E:ASP231 4.9 65.3 1.0
OE2 F:GLU57 4.9 70.0 1.0
CD1 E:LEU234 4.9 61.1 1.0

Potassium binding site 5 out of 7 in 6rkc

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Potassium binding site 5 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K408

b:75.7
occ:1.00
OD1 F:ASP231 2.6 70.3 1.0
O1B E:PPK409 2.9 63.8 1.0
O F:THR232 3.1 63.8 1.0
MG F:MG401 3.2 78.0 1.0
O2B E:PPK409 3.2 63.2 1.0
OE2 E:GLU44 3.3 81.6 1.0
CG F:ASP231 3.5 70.8 1.0
OD2 F:ASP231 3.6 72.2 1.0
PB E:PPK409 3.7 64.1 1.0
CD E:GLU44 3.8 79.1 1.0
C F:THR232 4.0 62.5 1.0
N F:THR232 4.1 64.7 1.0
N F:SAM402 4.1 68.5 1.0
CG E:GLU44 4.2 77.0 1.0
CB F:THR232 4.3 63.4 1.0
CA F:THR232 4.3 63.7 1.0
OE2 E:GLU57 4.4 91.0 1.0
OE1 E:GLU44 4.5 78.6 1.0
NH2 F:ARG237 4.6 78.7 1.0
CB F:SAM402 4.7 69.5 1.0
O3A E:PPK409 4.7 66.9 1.0
OE1 E:GLU57 4.7 90.0 1.0
C F:ASP231 4.8 66.4 1.0
CB F:ASP231 4.9 69.7 1.0
NH1 F:ARG237 5.0 77.6 1.0
O2G E:PPK409 5.0 60.5 1.0
CD1 F:LEU234 5.0 62.8 1.0

Potassium binding site 6 out of 7 in 6rkc

Go back to Potassium Binding Sites List in 6rkc
Potassium binding site 6 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K401

b:67.7
occ:1.00
OD1 G:ASP231 2.5 92.4 1.0
O1B G:PPK404 2.8 61.4 1.0
MG G:MG402 3.0 72.5 1.0
O G:THR232 3.1 76.3 1.0
CG G:ASP231 3.3 89.2 1.0
OE2 H:GLU44 3.4 85.6 1.0
OD2 G:ASP231 3.4 87.9 1.0
PB G:PPK404 3.7 61.9 1.0
O2B G:PPK404 3.9 62.6 1.0
CD H:GLU44 3.9 82.5 1.0
C G:THR232 4.1 77.2 1.0
N G:THR232 4.1 80.9 1.0
O3A G:PPK404 4.2 62.2 1.0
N G:SAM403 4.2 85.7 1.0
NH2 G:ARG237 4.2 67.2 1.0
CG H:GLU44 4.3 80.8 1.0
CA G:THR232 4.5 77.9 1.0
CB G:THR232 4.5 77.0 1.0
O2A G:PPK404 4.6 62.6 1.0
OE1 H:GLU44 4.7 85.1 1.0
CB G:ASP231 4.7 88.7 1.0
C G:ASP231 4.8 84.5 1.0
O2G G:PPK404 4.8 64.5 1.0
OE1 H:GLU57 4.8 94.4 1.0
CA G:SAM403 5.0 86.2 1.0

Potassium binding site 7 out of 7 in 6rkc

Go back to Potassium Binding Sites List in 6rkc
Potassium binding site 7 out of 7 in the Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Inter-Dimeric Interface Controls Function and Stability of S- Methionine Adenosyltransferase From U. Urealiticum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K408

b:0.5
occ:1.00
O2B G:PPK409 2.4 73.8 1.0
OD1 H:ASP231 2.9 84.6 1.0
OE2 G:GLU44 3.0 87.6 1.0
O H:THR232 3.2 80.8 1.0
MG H:MG401 3.2 60.0 1.0
PB G:PPK409 3.3 73.7 1.0
O1B G:PPK409 3.3 74.4 1.0
OG1 H:THR232 3.4 87.9 1.0
CG H:ASP231 3.7 85.6 1.0
CD G:GLU44 3.7 83.1 1.0
OD2 H:ASP231 3.7 86.1 1.0
NH2 H:ARG237 3.9 74.9 1.0
O2G G:PPK409 4.1 71.2 1.0
O3A G:PPK409 4.2 73.8 1.0
C H:THR232 4.2 81.6 1.0
O2A G:PPK409 4.3 73.5 1.0
CG G:GLU44 4.3 81.4 1.0
N H:THR232 4.4 85.7 1.0
OE1 G:GLU44 4.5 83.4 1.0
N H:SAM402 4.6 93.1 1.0
N3B G:PPK409 4.6 73.6 1.0
CB H:THR232 4.7 85.7 1.0
CA H:THR232 4.7 84.8 1.0
CZ H:ARG237 4.8 73.5 1.0
OD2 H:ASP18 4.9 73.3 1.0
CD1 H:LEU234 5.0 73.3 1.0
OD1 H:ASP18 5.0 72.5 1.0
CB H:SAM402 5.0 94.1 1.0

Reference:

D.Kleiner, F.Shmulevich, R.Zarivach, A.Shahar, M.Sharon, G.Ben-Nissan, S.Bershtein. The Inter-Dimeric Interface Controls Function and Stability of Ureaplasma Urealiticum Methionine S-Adenosyltransferase. J.Mol.Biol. 2019.
ISSN: ESSN 1089-8638
PubMed: 31520601
DOI: 10.1016/J.JMB.2019.09.003
Page generated: Mon Aug 12 17:28:28 2024

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