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:
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
Go back to
Potassium Binding Sites List in 6rkc
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 Sites List in 6rkc
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 Sites List in 6rkc
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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