Magnesium in PDB 9cbu: Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
22;
Binding sites:
The binding sites of Magnesium atom in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
(pdb code 9cbu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 22 binding sites of Magnesium where determined in the
Tetrahymena Ribozyme with Consensus Water and Magnesium Ions, PDB code: 9cbu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 1 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg501
b:15.6
occ:1.00
|
OP1
|
N:G257
|
1.9
|
44.2
|
1.0
|
|
OP2
|
N:U258
|
2.1
|
54.4
|
1.0
|
|
OP2
|
N:U305
|
2.5
|
56.3
|
1.0
|
|
O
|
N:HOH608
|
2.8
|
16.4
|
1.0
|
|
O
|
N:HOH699
|
3.1
|
17.2
|
1.0
|
|
O
|
N:HOH663
|
3.3
|
27.5
|
1.0
|
|
P
|
N:G257
|
3.3
|
8.5
|
1.0
|
|
H5
|
N:U259
|
3.3
|
23.4
|
1.0
|
|
P
|
N:U258
|
3.5
|
16.8
|
1.0
|
|
P
|
N:U305
|
3.7
|
11.0
|
1.0
|
|
H3'
|
N:G257
|
3.8
|
26.7
|
1.0
|
|
O4
|
N:U259
|
3.8
|
19.4
|
1.0
|
|
O2
|
N:C260
|
3.9
|
16.1
|
1.0
|
|
H5''
|
N:G257
|
3.9
|
22.1
|
1.0
|
|
O5'
|
N:U305
|
4.0
|
37.4
|
1.0
|
|
OP2
|
N:G257
|
4.1
|
56.2
|
1.0
|
|
O3'
|
N:G257
|
4.1
|
36.9
|
1.0
|
|
O5'
|
N:G257
|
4.1
|
36.5
|
1.0
|
|
OP1
|
N:U258
|
4.2
|
108.9
|
1.0
|
|
C5
|
N:U259
|
4.2
|
23.4
|
1.0
|
|
O3'
|
N:A304
|
4.2
|
41.4
|
1.0
|
|
O3'
|
N:A256
|
4.3
|
59.3
|
1.0
|
|
O2'
|
N:C260
|
4.4
|
17.0
|
1.0
|
|
C3'
|
N:G257
|
4.4
|
26.7
|
1.0
|
|
C4
|
N:U259
|
4.4
|
15.4
|
1.0
|
|
C5'
|
N:G257
|
4.5
|
22.1
|
1.0
|
|
O5'
|
N:U258
|
4.6
|
32.3
|
1.0
|
|
C2
|
N:C260
|
4.6
|
21.4
|
1.0
|
|
H5
|
N:U258
|
4.7
|
24.9
|
1.0
|
|
O
|
N:HOH691
|
4.7
|
16.8
|
1.0
|
|
HO2'
|
N:A304
|
4.7
|
20.2
|
1.0
|
|
HO2'
|
N:C260
|
4.8
|
17.0
|
1.0
|
|
H6
|
N:U258
|
4.9
|
23.1
|
1.0
|
|
H1'
|
N:C260
|
4.9
|
26.5
|
1.0
|
|
OP1
|
N:U305
|
5.0
|
118.3
|
1.0
|
|
Magnesium binding site 2 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 2 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg502
b:18.1
occ:1.00
|
OP2
|
N:A186
|
2.0
|
54.8
|
1.0
|
|
OP1
|
N:A183
|
2.1
|
32.5
|
1.0
|
|
OP2
|
N:A184
|
2.1
|
45.7
|
1.0
|
|
H3'
|
N:A183
|
3.3
|
33.8
|
1.0
|
|
P
|
N:A186
|
3.4
|
10.5
|
1.0
|
|
H3'
|
N:U185
|
3.4
|
42.4
|
1.0
|
|
P
|
N:A184
|
3.4
|
10.5
|
1.0
|
|
P
|
N:A183
|
3.5
|
13.3
|
1.0
|
|
H8
|
N:A186
|
3.6
|
16.9
|
1.0
|
|
H8
|
N:A184
|
3.9
|
24.2
|
1.0
|
|
O3'
|
N:U185
|
4.0
|
66.9
|
1.0
|
|
O
|
N:HOH617
|
4.0
|
11.7
|
1.0
|
|
O3'
|
N:A183
|
4.1
|
30.3
|
1.0
|
|
N7
|
N:A184
|
4.1
|
28.9
|
1.0
|
|
OP1
|
N:A186
|
4.2
|
37.8
|
1.0
|
|
C3'
|
N:U185
|
4.2
|
42.4
|
1.0
|
|
OP2
|
N:A183
|
4.2
|
87.3
|
1.0
|
|
C3'
|
N:A183
|
4.2
|
33.8
|
1.0
|
|
OP1
|
N:A184
|
4.2
|
52.0
|
1.0
|
|
C8
|
N:A186
|
4.3
|
16.9
|
1.0
|
|
N7
|
N:A186
|
4.3
|
20.6
|
1.0
|
|
O5'
|
N:A183
|
4.4
|
45.6
|
1.0
|
|
C8
|
N:A184
|
4.4
|
24.2
|
1.0
|
|
O3'
|
N:U182
|
4.4
|
67.8
|
1.0
|
|
O5'
|
N:A186
|
4.4
|
38.2
|
1.0
|
|
O5'
|
N:A184
|
4.5
|
65.9
|
1.0
|
|
H5''
|
N:A183
|
4.6
|
15.0
|
1.0
|
|
HO2'
|
N:U185
|
4.7
|
46.8
|
1.0
|
|
MG
|
N:MG503
|
4.8
|
17.6
|
1.0
|
|
C5'
|
N:A183
|
4.9
|
15.0
|
1.0
|
|
N3
|
N:A139
|
4.9
|
29.5
|
1.0
|
|
H2
|
N:A139
|
4.9
|
20.9
|
1.0
|
|
H2'
|
N:A183
|
5.0
|
20.9
|
1.0
|
|
Magnesium binding site 3 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 3 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg503
b:17.6
occ:1.00
|
OP1
|
N:A184
|
2.2
|
52.0
|
1.0
|
|
OP2
|
N:A187
|
2.2
|
55.0
|
1.0
|
|
OP1
|
N:A186
|
2.2
|
37.8
|
1.0
|
|
H3'
|
N:A186
|
3.2
|
27.2
|
1.0
|
|
OP2
|
N:G188
|
3.2
|
77.8
|
1.0
|
|
P
|
N:A184
|
3.3
|
10.5
|
1.0
|
|
H5'
|
N:A187
|
3.4
|
16.0
|
1.0
|
|
P
|
N:A186
|
3.4
|
10.5
|
1.0
|
|
P
|
N:A187
|
3.6
|
13.2
|
1.0
|
|
H4'
|
N:U185
|
3.7
|
36.8
|
1.0
|
|
O3'
|
N:A183
|
3.8
|
30.3
|
1.0
|
|
O
|
N:HOH658
|
3.8
|
11.0
|
1.0
|
|
P
|
N:G188
|
3.9
|
26.7
|
1.0
|
|
H4'
|
N:A187
|
3.9
|
22.9
|
1.0
|
|
OP1
|
N:G188
|
3.9
|
42.0
|
1.0
|
|
OP2
|
N:A186
|
3.9
|
54.8
|
1.0
|
|
OP2
|
N:A184
|
4.0
|
45.7
|
1.0
|
|
O
|
N:HOH641
|
4.1
|
20.9
|
1.0
|
|
C3'
|
N:A186
|
4.1
|
27.2
|
1.0
|
|
C5'
|
N:A187
|
4.2
|
16.0
|
1.0
|
|
H5''
|
N:A186
|
4.2
|
17.2
|
1.0
|
|
H5''
|
N:U185
|
4.2
|
22.9
|
1.0
|
|
O3'
|
N:A187
|
4.2
|
61.2
|
1.0
|
|
O3'
|
N:A186
|
4.2
|
62.2
|
1.0
|
|
H5''
|
N:A183
|
4.3
|
15.0
|
1.0
|
|
O5'
|
N:A187
|
4.3
|
60.1
|
1.0
|
|
O5'
|
N:A186
|
4.4
|
38.2
|
1.0
|
|
C4'
|
N:A187
|
4.4
|
22.9
|
1.0
|
|
O3'
|
N:U185
|
4.6
|
66.9
|
1.0
|
|
C4'
|
N:U185
|
4.6
|
36.8
|
1.0
|
|
H3'
|
N:U185
|
4.6
|
42.4
|
1.0
|
|
O5'
|
N:A184
|
4.6
|
65.9
|
1.0
|
|
OP1
|
N:A187
|
4.7
|
85.2
|
1.0
|
|
H5''
|
N:A184
|
4.7
|
21.5
|
1.0
|
|
C5'
|
N:A186
|
4.7
|
17.2
|
1.0
|
|
C3'
|
N:U185
|
4.8
|
42.4
|
1.0
|
|
HO2'
|
N:U182
|
4.8
|
15.8
|
1.0
|
|
OP1
|
N:A183
|
4.8
|
32.5
|
1.0
|
|
C3'
|
N:A187
|
4.8
|
42.8
|
1.0
|
|
MG
|
N:MG502
|
4.8
|
18.1
|
1.0
|
|
H2'
|
N:A186
|
4.8
|
24.6
|
1.0
|
|
C5'
|
N:U185
|
4.9
|
22.9
|
1.0
|
|
H8
|
N:A186
|
5.0
|
16.9
|
1.0
|
|
Magnesium binding site 4 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 4 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg504
b:18.9
occ:1.00
|
OP2
|
N:A302
|
1.9
|
44.7
|
1.0
|
|
OP1
|
N:A301
|
1.9
|
72.8
|
1.0
|
|
H21
|
N:G303
|
2.9
|
10.1
|
1.0
|
|
H62
|
N:A256
|
3.1
|
10.2
|
1.0
|
|
HO2'
|
N:U300
|
3.2
|
26.1
|
1.0
|
|
P
|
N:A302
|
3.3
|
11.4
|
1.0
|
|
P
|
N:A301
|
3.3
|
15.2
|
1.0
|
|
H1
|
N:G303
|
3.4
|
29.6
|
1.0
|
|
H3'
|
N:A301
|
3.5
|
38.1
|
1.0
|
|
H3'
|
N:U300
|
3.6
|
25.3
|
1.0
|
|
H5''
|
N:A301
|
3.6
|
43.0
|
1.0
|
|
H4'
|
N:U271
|
3.7
|
19.6
|
1.0
|
|
O5'
|
N:A301
|
3.8
|
51.8
|
1.0
|
|
N2
|
N:G303
|
3.9
|
10.1
|
1.0
|
|
O3'
|
N:A301
|
4.0
|
59.3
|
1.0
|
|
OP1
|
N:A302
|
4.0
|
40.6
|
1.0
|
|
O
|
N:HOH700
|
4.1
|
22.1
|
1.0
|
|
N6
|
N:A256
|
4.1
|
10.2
|
1.0
|
|
O2'
|
N:U300
|
4.1
|
26.1
|
1.0
|
|
C3'
|
N:A301
|
4.2
|
38.1
|
1.0
|
|
OP1
|
N:G272
|
4.2
|
78.1
|
1.0
|
|
OP2
|
N:A301
|
4.2
|
39.0
|
1.0
|
|
C5'
|
N:A301
|
4.2
|
43.0
|
1.0
|
|
N1
|
N:A256
|
4.2
|
35.2
|
1.0
|
|
N1
|
N:G303
|
4.3
|
29.6
|
1.0
|
|
C3'
|
N:U300
|
4.3
|
25.3
|
1.0
|
|
O3'
|
N:U300
|
4.3
|
98.5
|
1.0
|
|
O5'
|
N:A302
|
4.4
|
32.3
|
1.0
|
|
H8
|
N:A302
|
4.5
|
12.6
|
1.0
|
|
OP1
|
N:U300
|
4.6
|
82.8
|
1.0
|
|
H22
|
N:G303
|
4.6
|
10.1
|
1.0
|
|
C2
|
N:G303
|
4.6
|
17.0
|
1.0
|
|
O4'
|
N:U271
|
4.6
|
28.3
|
1.0
|
|
O
|
N:HOH659
|
4.6
|
29.4
|
1.0
|
|
C2'
|
N:U300
|
4.7
|
23.3
|
1.0
|
|
C4'
|
N:U271
|
4.7
|
19.6
|
1.0
|
|
C6
|
N:A256
|
4.7
|
16.8
|
1.0
|
|
H2'
|
N:U300
|
4.8
|
23.3
|
1.0
|
|
H61
|
N:A256
|
4.8
|
10.2
|
1.0
|
|
O3'
|
N:U271
|
4.9
|
90.0
|
1.0
|
|
C4'
|
N:A301
|
4.9
|
27.1
|
1.0
|
|
Magnesium binding site 5 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 5 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg505
b:36.9
occ:1.00
|
N7
|
N:G96
|
2.3
|
26.7
|
1.0
|
|
C8
|
N:G96
|
3.1
|
17.7
|
1.0
|
|
H8
|
N:G96
|
3.2
|
17.7
|
1.0
|
|
C6
|
N:U300
|
3.3
|
19.9
|
1.0
|
|
N1
|
N:A299
|
3.3
|
28.4
|
1.0
|
|
C5
|
N:U300
|
3.3
|
18.0
|
1.0
|
|
H5'
|
N:U300
|
3.4
|
25.4
|
1.0
|
|
C5
|
N:G96
|
3.4
|
23.7
|
1.0
|
|
C2
|
N:A299
|
3.4
|
19.5
|
1.0
|
|
N1
|
N:U300
|
3.5
|
24.0
|
1.0
|
|
C6
|
N:A299
|
3.5
|
23.1
|
1.0
|
|
H6
|
N:U300
|
3.6
|
19.9
|
1.0
|
|
C4
|
N:U300
|
3.7
|
12.3
|
1.0
|
|
C2
|
N:U300
|
3.7
|
20.4
|
1.0
|
|
H5
|
N:U300
|
3.8
|
18.0
|
1.0
|
|
H1
|
N:G279
|
3.8
|
27.4
|
1.0
|
|
N3
|
N:A299
|
3.8
|
17.8
|
1.0
|
|
N3
|
N:U300
|
3.8
|
20.0
|
1.0
|
|
H2
|
N:A299
|
3.8
|
19.5
|
1.0
|
|
C5
|
N:A299
|
3.8
|
25.7
|
1.0
|
|
O6
|
N:G96
|
3.8
|
30.9
|
1.0
|
|
O4'
|
N:U300
|
3.9
|
41.4
|
1.0
|
|
C4
|
N:A299
|
3.9
|
19.8
|
1.0
|
|
H5''
|
N:U300
|
3.9
|
25.4
|
1.0
|
|
H2'
|
N:A299
|
4.0
|
15.9
|
1.0
|
|
C6
|
N:G96
|
4.0
|
17.0
|
1.0
|
|
N6
|
N:A299
|
4.0
|
14.7
|
1.0
|
|
C5'
|
N:U300
|
4.1
|
25.4
|
1.0
|
|
H21
|
N:G279
|
4.2
|
17.0
|
1.0
|
|
H61
|
N:A299
|
4.3
|
14.7
|
1.0
|
|
C1'
|
N:U300
|
4.3
|
34.0
|
1.0
|
|
O4
|
N:U300
|
4.4
|
24.7
|
1.0
|
|
N9
|
N:G96
|
4.4
|
28.5
|
1.0
|
|
H3
|
N:U300
|
4.4
|
20.0
|
1.0
|
|
O2
|
N:U300
|
4.5
|
23.2
|
1.0
|
|
N1
|
N:G279
|
4.5
|
27.4
|
1.0
|
|
C4
|
N:G96
|
4.5
|
17.9
|
1.0
|
|
H62
|
N:A299
|
4.6
|
14.7
|
1.0
|
|
N7
|
N:A299
|
4.7
|
17.3
|
1.0
|
|
C4'
|
N:U300
|
4.7
|
29.6
|
1.0
|
|
N9
|
N:A299
|
4.8
|
26.6
|
1.0
|
|
OP2
|
N:G96
|
4.8
|
88.7
|
1.0
|
|
H2'
|
N:U300
|
4.9
|
23.3
|
1.0
|
|
N2
|
N:G279
|
4.9
|
17.0
|
1.0
|
|
OP2
|
N:U300
|
4.9
|
41.1
|
1.0
|
|
H3'
|
N:A299
|
4.9
|
30.6
|
1.0
|
|
Magnesium binding site 6 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 6 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg506
b:19.6
occ:1.00
|
O
|
N:HOH650
|
2.3
|
14.1
|
1.0
|
|
N7
|
N:A308
|
2.4
|
27.8
|
1.0
|
|
H3'
|
N:U307
|
2.5
|
26.1
|
1.0
|
|
H8
|
N:A308
|
3.0
|
17.1
|
1.0
|
|
C8
|
N:A308
|
3.1
|
17.1
|
1.0
|
|
C6
|
N:U307
|
3.2
|
21.6
|
1.0
|
|
N1
|
N:U307
|
3.3
|
27.7
|
1.0
|
|
C5
|
N:U307
|
3.4
|
24.8
|
1.0
|
|
OP2
|
N:A308
|
3.4
|
33.5
|
1.0
|
|
H62
|
N:A308
|
3.5
|
18.0
|
1.0
|
|
H1'
|
N:A306
|
3.5
|
19.5
|
1.0
|
|
O3'
|
N:A306
|
3.5
|
50.5
|
1.0
|
|
C3'
|
N:U307
|
3.5
|
26.1
|
1.0
|
|
H2'
|
N:U307
|
3.6
|
18.4
|
1.0
|
|
C2
|
N:U307
|
3.6
|
14.8
|
1.0
|
|
H6
|
N:U307
|
3.6
|
21.6
|
1.0
|
|
C5
|
N:A308
|
3.6
|
25.4
|
1.0
|
|
OP2
|
N:U307
|
3.7
|
52.4
|
1.0
|
|
C4
|
N:U307
|
3.7
|
16.3
|
1.0
|
|
O5'
|
N:U307
|
3.7
|
35.2
|
1.0
|
|
N3
|
N:U307
|
3.7
|
20.3
|
1.0
|
|
H5
|
N:U307
|
3.9
|
24.8
|
1.0
|
|
P
|
N:U307
|
3.9
|
12.1
|
1.0
|
|
C2'
|
N:U307
|
3.9
|
18.4
|
1.0
|
|
C1'
|
N:U307
|
4.1
|
26.7
|
1.0
|
|
N6
|
N:A308
|
4.3
|
18.0
|
1.0
|
|
O2
|
N:U307
|
4.3
|
26.8
|
1.0
|
|
P
|
N:A308
|
4.4
|
11.8
|
1.0
|
|
C6
|
N:A308
|
4.4
|
16.6
|
1.0
|
|
O3'
|
N:U307
|
4.4
|
72.5
|
1.0
|
|
N9
|
N:A308
|
4.4
|
30.8
|
1.0
|
|
H3
|
N:U307
|
4.4
|
20.3
|
1.0
|
|
C4'
|
N:U307
|
4.4
|
35.6
|
1.0
|
|
C1'
|
N:A306
|
4.5
|
19.5
|
1.0
|
|
O4
|
N:U307
|
4.5
|
22.0
|
1.0
|
|
O4'
|
N:U307
|
4.6
|
44.1
|
1.0
|
|
C5'
|
N:U307
|
4.6
|
26.8
|
1.0
|
|
O5'
|
N:A308
|
4.7
|
41.7
|
1.0
|
|
C4
|
N:A308
|
4.7
|
30.3
|
1.0
|
|
C3'
|
N:A306
|
4.7
|
35.0
|
1.0
|
|
N7
|
N:G309
|
4.7
|
14.3
|
1.0
|
|
O2'
|
N:A306
|
4.8
|
28.4
|
1.0
|
|
N3
|
N:A306
|
4.9
|
14.4
|
1.0
|
|
O4'
|
N:A306
|
4.9
|
44.3
|
1.0
|
|
C2'
|
N:A306
|
4.9
|
19.3
|
1.0
|
|
H4'
|
N:A306
|
4.9
|
25.7
|
1.0
|
|
Magnesium binding site 7 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 7 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg507
b:17.4
occ:1.00
|
OP1
|
N:U273
|
1.8
|
45.3
|
1.0
|
|
OP1
|
N:A256
|
2.3
|
37.9
|
1.0
|
|
P
|
N:U273
|
3.2
|
10.6
|
1.0
|
|
H8
|
N:A256
|
3.5
|
12.3
|
1.0
|
|
P
|
N:A256
|
3.7
|
13.7
|
1.0
|
|
H5''
|
N:U273
|
3.7
|
11.9
|
1.0
|
|
OP2
|
N:U273
|
3.9
|
51.5
|
1.0
|
|
O3'
|
N:C255
|
4.0
|
84.1
|
1.0
|
|
H4'
|
N:C255
|
4.0
|
19.4
|
1.0
|
|
O5'
|
N:U273
|
4.0
|
32.8
|
1.0
|
|
OP2
|
N:C274
|
4.0
|
28.2
|
1.0
|
|
C8
|
N:A256
|
4.2
|
12.3
|
1.0
|
|
N7
|
N:A256
|
4.2
|
22.9
|
1.0
|
|
MG
|
N:MG510
|
4.2
|
25.2
|
1.0
|
|
O3'
|
N:G272
|
4.3
|
52.5
|
1.0
|
|
C5'
|
N:U273
|
4.3
|
11.9
|
1.0
|
|
O
|
N:HOH705
|
4.4
|
25.2
|
1.0
|
|
O5'
|
N:A256
|
4.5
|
54.2
|
1.0
|
|
OP2
|
N:A256
|
4.7
|
63.9
|
1.0
|
|
O
|
N:HOH642
|
4.7
|
16.2
|
1.0
|
|
H5'
|
N:U273
|
4.7
|
11.9
|
1.0
|
|
C4'
|
N:C255
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 8 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 8 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg508
b:13.4
occ:1.00
|
OP1
|
N:A306
|
1.9
|
36.0
|
1.0
|
|
OP1
|
N:A304
|
1.9
|
43.8
|
1.0
|
|
P
|
N:A304
|
3.3
|
7.0
|
1.0
|
|
P
|
N:A306
|
3.3
|
12.3
|
1.0
|
|
H3'
|
N:U305
|
3.5
|
43.1
|
1.0
|
|
H5''
|
N:A304
|
3.6
|
29.2
|
1.0
|
|
OP1
|
N:C208
|
3.7
|
95.4
|
1.0
|
|
O5'
|
N:A304
|
4.0
|
35.3
|
1.0
|
|
O3'
|
N:U305
|
4.1
|
65.7
|
1.0
|
|
OP1
|
N:U307
|
4.1
|
71.0
|
1.0
|
|
OP2
|
N:A304
|
4.1
|
47.9
|
1.0
|
|
OP2
|
N:A306
|
4.2
|
38.2
|
1.0
|
|
O5'
|
N:A306
|
4.2
|
34.1
|
1.0
|
|
C3'
|
N:U305
|
4.3
|
43.1
|
1.0
|
|
C5'
|
N:A304
|
4.3
|
29.2
|
1.0
|
|
O3'
|
N:G303
|
4.3
|
68.2
|
1.0
|
|
O
|
N:HOH681
|
4.4
|
13.1
|
1.0
|
|
O
|
N:HOH665
|
4.4
|
18.9
|
1.0
|
|
HO2'
|
N:U305
|
4.4
|
23.8
|
1.0
|
|
H5'
|
N:A304
|
4.8
|
29.2
|
1.0
|
|
Magnesium binding site 9 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 9 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg509
b:14.0
occ:1.00
|
OP2
|
N:A97
|
2.1
|
34.9
|
1.0
|
|
H1'
|
N:U300
|
2.5
|
34.0
|
1.0
|
|
O2'
|
N:U300
|
2.9
|
26.1
|
1.0
|
|
OP2
|
N:A301
|
3.0
|
39.0
|
1.0
|
|
O3'
|
N:U300
|
3.1
|
98.5
|
1.0
|
|
HO2'
|
N:U300
|
3.1
|
26.1
|
1.0
|
|
O
|
N:HOH669
|
3.4
|
25.1
|
1.0
|
|
C1'
|
N:U300
|
3.4
|
34.0
|
1.0
|
|
P
|
N:A97
|
3.4
|
11.0
|
1.0
|
|
P
|
N:A301
|
3.5
|
15.2
|
1.0
|
|
C2'
|
N:U300
|
3.5
|
23.3
|
1.0
|
|
O
|
N:HOH688
|
3.5
|
12.1
|
1.0
|
|
C3'
|
N:U300
|
3.9
|
25.3
|
1.0
|
|
OP1
|
N:A97
|
3.9
|
66.4
|
1.0
|
|
OP1
|
N:A301
|
4.1
|
72.8
|
1.0
|
|
O
|
N:HOH730
|
4.1
|
23.5
|
1.0
|
|
O2
|
N:U300
|
4.1
|
23.2
|
1.0
|
|
O
|
N:HOH700
|
4.1
|
22.1
|
1.0
|
|
H3'
|
N:G96
|
4.2
|
37.2
|
1.0
|
|
O
|
N:HOH693
|
4.3
|
21.3
|
1.0
|
|
O4'
|
N:U300
|
4.3
|
41.4
|
1.0
|
|
N1
|
N:U300
|
4.3
|
24.0
|
1.0
|
|
O3'
|
N:G96
|
4.4
|
46.0
|
1.0
|
|
O5'
|
N:A97
|
4.4
|
32.1
|
1.0
|
|
C2
|
N:U300
|
4.5
|
20.4
|
1.0
|
|
H2'
|
N:U300
|
4.6
|
23.3
|
1.0
|
|
H3'
|
N:U300
|
4.7
|
25.3
|
1.0
|
|
H5'
|
N:G96
|
4.7
|
25.6
|
1.0
|
|
C4'
|
N:U300
|
4.7
|
29.6
|
1.0
|
|
C3'
|
N:G96
|
4.8
|
37.2
|
1.0
|
|
O5'
|
N:A301
|
5.0
|
51.8
|
1.0
|
|
H5''
|
N:G96
|
5.0
|
25.6
|
1.0
|
|
O
|
N:HOH667
|
5.0
|
17.9
|
1.0
|
|
Magnesium binding site 10 out
of 22 in 9cbu
Go back to
Magnesium Binding Sites List in 9cbu
Magnesium binding site 10 out
of 22 in the Tetrahymena Ribozyme with Consensus Water and Magnesium Ions
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Tetrahymena Ribozyme with Consensus Water and Magnesium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg510
b:25.2
occ:1.00
|
OP2
|
N:C274
|
2.5
|
28.2
|
1.0
|
|
H5
|
N:C274
|
2.6
|
28.3
|
1.0
|
|
OP2
|
N:U273
|
3.3
|
51.5
|
1.0
|
|
H3'
|
N:U273
|
3.3
|
26.3
|
1.0
|
|
C5
|
N:C274
|
3.5
|
28.3
|
1.0
|
|
H6
|
N:C274
|
3.6
|
22.6
|
1.0
|
|
O5'
|
N:U273
|
3.7
|
32.8
|
1.0
|
|
P
|
N:U273
|
3.8
|
10.6
|
1.0
|
|
P
|
N:C274
|
3.8
|
12.4
|
1.0
|
|
OP1
|
N:U273
|
4.0
|
45.3
|
1.0
|
|
C6
|
N:C274
|
4.0
|
22.6
|
1.0
|
|
O5'
|
N:C274
|
4.2
|
24.6
|
1.0
|
|
MG
|
N:MG507
|
4.2
|
17.4
|
1.0
|
|
C3'
|
N:U273
|
4.3
|
26.3
|
1.0
|
|
H42
|
N:C274
|
4.3
|
12.2
|
1.0
|
|
O3'
|
N:U273
|
4.5
|
45.2
|
1.0
|
|
H5''
|
N:U273
|
4.6
|
11.9
|
1.0
|
|
C4
|
N:C274
|
4.7
|
17.9
|
1.0
|
|
C5'
|
N:U273
|
4.7
|
11.9
|
1.0
|
|
H3'
|
N:C274
|
4.8
|
33.5
|
1.0
|
|
H6
|
N:U273
|
4.8
|
17.0
|
1.0
|
|
N4
|
N:C274
|
4.9
|
12.2
|
1.0
|
|
OP1
|
N:C274
|
5.0
|
51.8
|
1.0
|
|
Reference:
R.C.Kretsch,
S.Li,
G.Pintilie,
M.Z.Palo,
D.A.Case,
R.Das,
W.Chiu.
Complex Water Networks Visualized Through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of Rna To Be Published.
Page generated: Fri Aug 15 23:58:44 2025
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