Magnesium in PDB 3skt: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
Protein crystallography data
The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak, PDB code: 3skt
was solved by
O.Pikovskaya,
A.Polonskaia,
D.J.Patel,
A.Serganov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
97.031,
34.632,
111.598,
90.00,
92.81,
90.00
|
R / Rfree (%)
|
19.6 /
25.2
|
Other elements in 3skt:
The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
(pdb code 3skt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak, PDB code: 3skt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 1 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:58.2
occ:1.00
|
OP1
|
A:A71
|
2.2
|
57.5
|
1.0
|
P
|
A:A71
|
3.3
|
58.1
|
1.0
|
OP2
|
A:A71
|
3.6
|
59.3
|
1.0
|
O5'
|
A:A71
|
4.3
|
57.3
|
1.0
|
O3'
|
A:U70
|
4.5
|
59.7
|
1.0
|
C2'
|
A:U70
|
4.6
|
63.7
|
1.0
|
C3'
|
A:U70
|
4.6
|
62.2
|
1.0
|
C5'
|
A:A71
|
4.9
|
59.4
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 2 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg308
b:58.2
occ:1.00
|
O2A
|
A:GTP23
|
2.2
|
68.6
|
1.0
|
O1B
|
A:GTP23
|
2.7
|
74.5
|
1.0
|
PA
|
A:GTP23
|
3.4
|
69.4
|
1.0
|
OP2
|
A:U83
|
3.4
|
61.5
|
1.0
|
PB
|
A:GTP23
|
3.5
|
76.2
|
1.0
|
O2B
|
A:GTP23
|
3.5
|
75.7
|
1.0
|
OP1
|
A:U83
|
3.8
|
65.2
|
1.0
|
O1A
|
A:GTP23
|
3.9
|
69.4
|
1.0
|
O3A
|
A:GTP23
|
3.9
|
73.4
|
1.0
|
P
|
A:U83
|
4.1
|
62.9
|
1.0
|
O5'
|
A:GTP23
|
4.7
|
68.5
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 3 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:41.0
occ:1.00
|
N7
|
B:A37
|
4.1
|
49.5
|
1.0
|
O6
|
B:G38
|
4.1
|
58.6
|
1.0
|
N6
|
B:A37
|
4.4
|
48.0
|
1.0
|
N7
|
B:G38
|
4.8
|
60.3
|
1.0
|
C5
|
B:A37
|
4.8
|
49.4
|
1.0
|
C8
|
B:A37
|
5.0
|
50.4
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 4 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:54.5
occ:1.00
|
O6
|
B:G53
|
3.3
|
39.1
|
1.0
|
OP1
|
B:C57
|
3.8
|
61.9
|
1.0
|
O6
|
B:G59
|
4.2
|
45.0
|
1.0
|
C6
|
B:G53
|
4.4
|
39.3
|
1.0
|
OP2
|
B:C57
|
4.7
|
62.2
|
1.0
|
P
|
B:C57
|
4.7
|
61.6
|
1.0
|
N7
|
B:G53
|
4.7
|
40.1
|
1.0
|
N4
|
B:C60
|
4.8
|
46.0
|
1.0
|
OP2
|
B:C58
|
4.9
|
59.9
|
1.0
|
C5
|
B:G53
|
5.0
|
39.8
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 5 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:50.0
occ:1.00
|
O2B
|
B:GTP23
|
2.7
|
92.3
|
1.0
|
PB
|
B:GTP23
|
3.9
|
90.5
|
1.0
|
O1B
|
B:GTP23
|
4.0
|
90.0
|
1.0
|
O1G
|
B:GTP23
|
4.2
|
87.3
|
1.0
|
O3B
|
B:GTP23
|
4.5
|
88.1
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 6 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg305
b:25.0
occ:1.00
|
OP2
|
B:G34
|
2.0
|
52.0
|
1.0
|
OP2
|
B:U73
|
2.8
|
72.6
|
1.0
|
O2'
|
B:G33
|
3.5
|
54.6
|
1.0
|
P
|
B:G34
|
3.5
|
51.8
|
1.0
|
MN
|
B:MN206
|
3.9
|
70.1
|
1.0
|
P
|
B:U73
|
4.1
|
74.7
|
1.0
|
OP1
|
B:G34
|
4.3
|
51.9
|
1.0
|
O3'
|
B:G33
|
4.3
|
51.5
|
1.0
|
O5'
|
B:G34
|
4.4
|
50.4
|
1.0
|
O2'
|
B:U72
|
4.4
|
68.5
|
1.0
|
OP1
|
B:U73
|
4.6
|
74.6
|
1.0
|
C2'
|
B:G33
|
4.7
|
53.6
|
1.0
|
OP2
|
B:G47
|
4.8
|
55.5
|
1.0
|
C3'
|
B:G33
|
4.8
|
53.2
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 7 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg306
b:38.9
occ:1.00
|
N7
|
B:G45
|
2.2
|
75.1
|
1.0
|
C8
|
B:G45
|
3.2
|
75.6
|
1.0
|
C5
|
B:G45
|
3.2
|
72.8
|
1.0
|
O6
|
B:G45
|
3.4
|
71.6
|
1.0
|
C6
|
B:G45
|
3.6
|
71.4
|
1.0
|
OP2
|
B:G45
|
4.2
|
84.5
|
1.0
|
N9
|
B:G45
|
4.4
|
73.7
|
1.0
|
C4
|
B:G45
|
4.4
|
71.8
|
1.0
|
C5'
|
B:U44
|
4.8
|
92.9
|
1.0
|
N7
|
B:G46
|
5.0
|
66.3
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 8 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg307
b:49.0
occ:1.00
|
O6
|
B:G75
|
2.2
|
77.5
|
1.0
|
OP1
|
B:G33
|
3.3
|
59.2
|
1.0
|
C6
|
B:G75
|
3.3
|
79.0
|
1.0
|
O4
|
B:U63
|
4.1
|
75.2
|
1.0
|
C5
|
B:G75
|
4.2
|
78.7
|
1.0
|
O3'
|
B:A32
|
4.2
|
57.4
|
1.0
|
N1
|
B:G75
|
4.3
|
80.9
|
1.0
|
N7
|
B:G75
|
4.4
|
77.1
|
1.0
|
P
|
B:G33
|
4.4
|
57.2
|
1.0
|
O4
|
B:U74
|
4.4
|
76.1
|
1.0
|
N4
|
B:C64
|
4.6
|
65.7
|
1.0
|
O6
|
B:G76
|
5.0
|
80.6
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 3skt
Go back to
Magnesium Binding Sites List in 3skt
Magnesium binding site 9 out
of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg309
b:55.6
occ:1.00
|
OP2
|
B:C48
|
2.2
|
59.7
|
1.0
|
OP2
|
B:C61
|
2.2
|
58.0
|
1.0
|
P
|
B:C48
|
3.1
|
61.0
|
1.0
|
N7
|
B:G33
|
3.2
|
55.9
|
1.0
|
MN
|
B:MN205
|
3.3
|
65.2
|
1.0
|
O5'
|
B:C48
|
3.4
|
61.7
|
1.0
|
C8
|
B:G33
|
3.5
|
55.3
|
1.0
|
OP1
|
B:C48
|
3.7
|
61.4
|
1.0
|
P
|
B:C61
|
3.7
|
61.3
|
1.0
|
C5
|
B:G33
|
4.3
|
54.3
|
1.0
|
O3'
|
B:C60
|
4.3
|
56.5
|
1.0
|
O5'
|
B:C61
|
4.5
|
65.2
|
1.0
|
O3'
|
B:G47
|
4.6
|
62.5
|
1.0
|
OP1
|
B:C61
|
4.6
|
61.3
|
1.0
|
N9
|
B:G33
|
4.7
|
53.8
|
1.0
|
C5'
|
B:C48
|
4.8
|
64.5
|
1.0
|
C6
|
B:C48
|
4.8
|
60.2
|
1.0
|
OP2
|
B:U49
|
4.8
|
56.6
|
1.0
|
|
Reference:
O.Pikovskaya,
A.Polonskaia,
D.J.Patel,
A.Serganov.
Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631
Page generated: Thu Aug 15 11:02:22 2024
|