Potassium in PDB 7loo: S-Adenosyl Methionine Transferase Cocrystallized with Atp
Enzymatic activity of S-Adenosyl Methionine Transferase Cocrystallized with Atp
All present enzymatic activity of S-Adenosyl Methionine Transferase Cocrystallized with Atp:
2.5.1.6;
Protein crystallography data
The structure of S-Adenosyl Methionine Transferase Cocrystallized with Atp, PDB code: 7loo
was solved by
C.J.Jackson,
L.L.Tan,
P.Laurino,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.99 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.922,
117.78,
113.21,
90,
107.52,
90
|
R / Rfree (%)
|
17 /
20.7
|
Other elements in 7loo:
The structure of S-Adenosyl Methionine Transferase Cocrystallized with Atp also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the S-Adenosyl Methionine Transferase Cocrystallized with Atp
(pdb code 7loo). 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-Adenosyl Methionine Transferase Cocrystallized with Atp, PDB code: 7loo:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7loo
Go back to
Potassium Binding Sites List in 7loo
Potassium binding site 1 out
of 4 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:85.7
occ:1.00
|
O
|
Q:HOH503
|
2.5
|
53.4
|
1.0
|
O6
|
A:POP401
|
2.6
|
24.6
|
1.0
|
OD1
|
A:ASP238
|
2.6
|
33.9
|
1.0
|
O4
|
A:POP401
|
2.7
|
31.6
|
1.0
|
O
|
Q:HOH539
|
2.9
|
38.5
|
1.0
|
P2
|
A:POP401
|
3.2
|
26.4
|
1.0
|
OE2
|
Q:GLU42
|
3.3
|
52.4
|
1.0
|
O
|
A:HOH515
|
3.4
|
20.6
|
1.0
|
CG
|
A:ASP238
|
3.5
|
35.7
|
1.0
|
O
|
Q:HOH643
|
3.6
|
44.3
|
1.0
|
OD2
|
A:ASP238
|
3.7
|
39.2
|
1.0
|
O
|
A:HOH503
|
3.8
|
37.4
|
1.0
|
O
|
A:CYS239
|
3.8
|
26.2
|
0.6
|
MG
|
A:MG403
|
3.8
|
20.8
|
1.0
|
O
|
A:HOH547
|
3.8
|
21.2
|
1.0
|
O
|
A:CYS239
|
3.9
|
25.4
|
0.4
|
N
|
A:SAM408
|
4.0
|
34.8
|
1.0
|
O
|
A:POP401
|
4.0
|
28.1
|
1.0
|
CD
|
Q:GLU42
|
4.4
|
47.0
|
1.0
|
N
|
A:CYS239
|
4.5
|
24.0
|
0.6
|
O5
|
A:POP401
|
4.5
|
27.9
|
1.0
|
NH2
|
A:ARG244
|
4.5
|
24.8
|
1.0
|
N
|
A:CYS239
|
4.5
|
24.1
|
0.4
|
CB
|
A:CYS239
|
4.6
|
26.9
|
0.4
|
OE2
|
Q:GLU55
|
4.7
|
42.1
|
1.0
|
CG
|
Q:GLU42
|
4.7
|
37.7
|
1.0
|
C
|
A:CYS239
|
4.7
|
24.6
|
0.6
|
C
|
A:CYS239
|
4.8
|
24.7
|
0.4
|
O1
|
A:POP401
|
4.8
|
18.1
|
1.0
|
CB
|
A:ASP238
|
4.9
|
33.1
|
1.0
|
CG
|
A:SAM408
|
4.9
|
43.3
|
1.0
|
CB
|
A:CYS239
|
4.9
|
27.3
|
0.6
|
CA
|
A:CYS239
|
4.9
|
24.1
|
0.4
|
CA
|
A:CYS239
|
5.0
|
23.4
|
0.6
|
O2
|
A:PO4402
|
5.0
|
44.9
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7loo
Go back to
Potassium Binding Sites List in 7loo
Potassium binding site 2 out
of 4 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K405
b:109.5
occ:1.00
|
NH1
|
A:ARG293
|
3.1
|
84.6
|
1.0
|
OH
|
A:TYR125
|
3.2
|
41.8
|
1.0
|
O
|
Q:HOH724
|
3.8
|
64.7
|
1.0
|
CE1
|
A:PHE315
|
3.9
|
39.2
|
1.0
|
CZ
|
A:TYR125
|
4.1
|
36.3
|
1.0
|
CZ
|
A:PHE315
|
4.1
|
35.6
|
1.0
|
CD1
|
A:PHE315
|
4.2
|
41.9
|
1.0
|
CE1
|
A:TYR125
|
4.2
|
36.7
|
1.0
|
O
|
A:MET254
|
4.3
|
34.7
|
1.0
|
CZ
|
A:ARG293
|
4.3
|
85.5
|
1.0
|
CE2
|
A:PHE315
|
4.5
|
31.3
|
1.0
|
CD
|
A:ARG293
|
4.5
|
64.3
|
1.0
|
CG
|
A:PHE315
|
4.6
|
40.0
|
1.0
|
CD2
|
A:PHE315
|
4.7
|
36.9
|
1.0
|
SD
|
A:MET254
|
4.7
|
45.3
|
1.0
|
O
|
A:HOH559
|
4.7
|
51.8
|
1.0
|
CG
|
A:MET254
|
4.8
|
37.1
|
1.0
|
NH1
|
Q:ARG256
|
4.8
|
48.7
|
1.0
|
NE
|
A:ARG293
|
4.9
|
78.0
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7loo
Go back to
Potassium Binding Sites List in 7loo
Potassium binding site 3 out
of 4 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:K405
b:76.4
occ:1.00
|
O5
|
Q:POP401
|
2.6
|
23.1
|
1.0
|
OD1
|
Q:ASP238
|
2.7
|
36.7
|
1.0
|
O4
|
Q:POP401
|
3.0
|
31.6
|
1.0
|
O
|
A:HOH512
|
3.0
|
45.5
|
1.0
|
OE2
|
A:GLU42
|
3.1
|
51.7
|
1.0
|
O
|
Q:HOH530
|
3.2
|
21.4
|
1.0
|
P2
|
Q:POP401
|
3.3
|
25.9
|
1.0
|
CG
|
Q:ASP238
|
3.5
|
33.2
|
1.0
|
O
|
A:HOH578
|
3.5
|
48.8
|
1.0
|
O
|
Q:CYS239
|
3.5
|
27.5
|
0.6
|
OD2
|
Q:ASP238
|
3.6
|
38.8
|
1.0
|
O
|
Q:HOH547
|
3.6
|
21.3
|
1.0
|
O
|
Q:CYS239
|
3.7
|
27.5
|
0.4
|
MG
|
Q:MG412
|
3.7
|
22.6
|
1.0
|
O
|
Q:HOH505
|
4.0
|
34.3
|
1.0
|
N
|
Q:SAM410
|
4.1
|
32.3
|
1.0
|
O
|
Q:POP401
|
4.1
|
26.6
|
1.0
|
CD
|
A:GLU42
|
4.2
|
44.4
|
1.0
|
N
|
Q:CYS239
|
4.3
|
28.3
|
0.4
|
N
|
Q:CYS239
|
4.3
|
27.4
|
0.6
|
CB
|
Q:CYS239
|
4.4
|
30.4
|
0.4
|
NH2
|
Q:ARG244
|
4.5
|
26.0
|
1.0
|
C
|
Q:CYS239
|
4.5
|
27.6
|
0.6
|
C
|
Q:CYS239
|
4.5
|
27.7
|
0.4
|
CG
|
A:GLU42
|
4.6
|
36.9
|
1.0
|
CA
|
Q:CYS239
|
4.6
|
28.8
|
0.4
|
O6
|
Q:POP401
|
4.7
|
25.9
|
1.0
|
CB
|
Q:CYS239
|
4.7
|
30.7
|
0.6
|
OE2
|
A:GLU55
|
4.7
|
45.6
|
1.0
|
CA
|
Q:CYS239
|
4.7
|
28.7
|
0.6
|
CG
|
Q:SAM410
|
4.8
|
45.0
|
1.0
|
CB
|
Q:ASP238
|
4.8
|
28.5
|
1.0
|
O1
|
Q:POP401
|
4.8
|
20.4
|
1.0
|
C
|
Q:ASP238
|
4.9
|
30.7
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7loo
Go back to
Potassium Binding Sites List in 7loo
Potassium binding site 4 out
of 4 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:K406
b:116.6
occ:1.00
|
NH1
|
Q:ARG293
|
2.8
|
48.5
|
0.5
|
O
|
Q:HOH624
|
2.8
|
52.6
|
1.0
|
OH
|
Q:TYR125
|
3.4
|
40.9
|
1.0
|
O
|
A:HOH727
|
3.9
|
69.9
|
1.0
|
CD
|
Q:ARG293
|
3.9
|
46.5
|
0.5
|
CZ
|
Q:ARG293
|
4.0
|
51.0
|
0.5
|
CD
|
Q:ARG293
|
4.1
|
46.0
|
0.6
|
CE1
|
Q:PHE315
|
4.2
|
37.9
|
1.0
|
CD1
|
Q:PHE315
|
4.3
|
38.4
|
1.0
|
CZ
|
Q:TYR125
|
4.3
|
36.0
|
1.0
|
CZ
|
Q:PHE315
|
4.3
|
34.6
|
1.0
|
NE
|
Q:ARG293
|
4.4
|
50.8
|
0.5
|
CG
|
Q:PHE315
|
4.5
|
39.4
|
1.0
|
CE1
|
Q:TYR125
|
4.5
|
37.4
|
1.0
|
CE2
|
Q:PHE315
|
4.5
|
35.5
|
1.0
|
O
|
Q:MET254
|
4.6
|
34.8
|
1.0
|
CD2
|
Q:PHE315
|
4.6
|
37.9
|
1.0
|
SD
|
Q:MET254
|
4.7
|
43.6
|
1.0
|
CG
|
Q:ARG293
|
4.7
|
43.0
|
0.5
|
NH1
|
A:ARG256
|
5.0
|
46.4
|
1.0
|
|
Reference:
C.J.Jackson,
P.L.Laurino.
Protein and Substrate Flexibility Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferase To Be Published.
Page generated: Mon Aug 12 19:24:03 2024
|