Phosphorus in PDB 179d: Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
(pdb code 179d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the
Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs, PDB code: 179d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
Phosphorus binding site 1 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 1 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:0.6
occ:1.00
|
P
|
A:DC2
|
0.0
|
0.6
|
1.0
|
OP2
|
A:DC2
|
1.5
|
1.1
|
1.0
|
OP1
|
A:DC2
|
1.5
|
1.1
|
1.0
|
O5'
|
A:DC2
|
1.6
|
0.4
|
1.0
|
O3'
|
A:DT1
|
1.6
|
0.5
|
1.0
|
C3'
|
A:DT1
|
2.6
|
0.5
|
1.0
|
H3'
|
A:DT1
|
2.6
|
0.8
|
1.0
|
C5'
|
A:DC2
|
2.7
|
0.4
|
1.0
|
H5'
|
A:DC2
|
2.7
|
0.5
|
1.0
|
H5''
|
A:DC2
|
3.4
|
0.5
|
1.0
|
O4'
|
A:DC2
|
3.6
|
0.3
|
1.0
|
H4'
|
A:DT1
|
3.6
|
0.6
|
1.0
|
C4'
|
A:DT1
|
3.7
|
0.6
|
1.0
|
C4'
|
A:DC2
|
3.7
|
0.3
|
1.0
|
H2''
|
A:DT1
|
3.8
|
0.5
|
1.0
|
C2'
|
A:DT1
|
3.8
|
0.4
|
1.0
|
H5'
|
A:DT1
|
3.9
|
1.0
|
1.0
|
H6
|
A:DC2
|
4.0
|
0.3
|
1.0
|
H2'
|
A:DC2
|
4.3
|
0.3
|
1.0
|
C5'
|
A:DT1
|
4.3
|
0.9
|
1.0
|
H2'
|
A:DT1
|
4.4
|
0.6
|
1.0
|
H3
|
B:DT5
|
4.5
|
0.2
|
1.0
|
C6
|
A:DC2
|
4.5
|
0.2
|
1.0
|
H3'
|
A:DC2
|
4.5
|
0.3
|
1.0
|
H4'
|
A:DC2
|
4.5
|
0.4
|
1.0
|
C3'
|
A:DC2
|
4.6
|
0.3
|
1.0
|
C1'
|
A:DC2
|
4.6
|
0.2
|
1.0
|
C2'
|
A:DC2
|
4.7
|
0.2
|
1.0
|
H5''
|
A:DT1
|
4.8
|
1.1
|
1.0
|
C1'
|
A:DT1
|
4.8
|
0.2
|
1.0
|
O4'
|
A:DT1
|
4.8
|
0.5
|
1.0
|
N1
|
A:DC2
|
4.9
|
0.2
|
1.0
|
N3
|
B:DT5
|
5.0
|
0.2
|
1.0
|
|
Phosphorus binding site 2 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 2 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:0.3
occ:1.00
|
P
|
A:DG3
|
0.0
|
0.3
|
1.0
|
OP2
|
A:DG3
|
1.5
|
0.4
|
1.0
|
OP1
|
A:DG3
|
1.5
|
0.4
|
1.0
|
O3'
|
A:DC2
|
1.6
|
0.3
|
1.0
|
O5'
|
A:DG3
|
1.6
|
0.2
|
1.0
|
C5'
|
A:DG3
|
2.7
|
0.2
|
1.0
|
C3'
|
A:DC2
|
2.7
|
0.3
|
1.0
|
H5'
|
A:DG3
|
2.8
|
0.2
|
1.0
|
H2''
|
A:DC2
|
3.0
|
0.3
|
1.0
|
H3'
|
A:DC2
|
3.0
|
0.3
|
1.0
|
H5''
|
A:DG3
|
3.0
|
0.3
|
1.0
|
C2'
|
A:DC2
|
3.3
|
0.2
|
1.0
|
H1'
|
A:DC2
|
3.6
|
0.3
|
1.0
|
H4'
|
A:DC2
|
3.8
|
0.4
|
1.0
|
C4'
|
A:DC2
|
3.9
|
0.3
|
1.0
|
C4'
|
A:DG3
|
4.0
|
0.2
|
1.0
|
C1'
|
A:DC2
|
4.1
|
0.2
|
1.0
|
H2'
|
A:DC2
|
4.1
|
0.3
|
1.0
|
H3'
|
A:DG3
|
4.3
|
0.2
|
1.0
|
O4'
|
A:DG3
|
4.4
|
0.2
|
1.0
|
H2'
|
A:DG3
|
4.6
|
0.2
|
1.0
|
C3'
|
A:DG3
|
4.6
|
0.2
|
1.0
|
O4'
|
A:DC2
|
4.6
|
0.3
|
1.0
|
H4'
|
A:DG3
|
4.8
|
0.2
|
1.0
|
|
Phosphorus binding site 3 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 3 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:0.3
occ:1.00
|
P
|
A:DA4
|
0.0
|
0.3
|
1.0
|
OP1
|
A:DA4
|
1.5
|
0.3
|
1.0
|
OP2
|
A:DA4
|
1.5
|
0.4
|
1.0
|
O3'
|
A:DG3
|
1.6
|
0.2
|
1.0
|
O5'
|
A:DA4
|
1.6
|
0.3
|
1.0
|
C5'
|
A:DA4
|
2.6
|
0.2
|
1.0
|
C3'
|
A:DG3
|
2.7
|
0.2
|
1.0
|
H3'
|
A:DG3
|
2.8
|
0.2
|
1.0
|
H5'
|
A:DA4
|
2.8
|
0.3
|
1.0
|
H8
|
A:DA4
|
2.9
|
0.2
|
1.0
|
H5''
|
A:DA4
|
3.1
|
0.3
|
1.0
|
H61
|
B:DA8
|
3.1
|
0.3
|
1.0
|
H2''
|
A:DG3
|
3.1
|
0.2
|
1.0
|
C2'
|
A:DG3
|
3.4
|
0.2
|
1.0
|
H4'
|
A:DG3
|
3.7
|
0.2
|
1.0
|
C4'
|
A:DG3
|
3.9
|
0.2
|
1.0
|
C4'
|
A:DA4
|
3.9
|
0.2
|
1.0
|
N6
|
B:DA8
|
3.9
|
0.2
|
1.0
|
C8
|
A:DA4
|
3.9
|
0.2
|
1.0
|
H1'
|
A:DG3
|
4.0
|
0.2
|
1.0
|
H62
|
B:DA8
|
4.0
|
0.2
|
1.0
|
H2'
|
A:DA4
|
4.1
|
0.3
|
1.0
|
O4'
|
A:DA4
|
4.2
|
0.2
|
1.0
|
H2'
|
A:DG3
|
4.2
|
0.2
|
1.0
|
C1'
|
A:DG3
|
4.2
|
0.2
|
1.0
|
H21
|
B:DG7
|
4.4
|
0.3
|
1.0
|
H3'
|
A:DA4
|
4.5
|
0.4
|
1.0
|
H4'
|
A:DA4
|
4.6
|
0.3
|
1.0
|
C3'
|
A:DA4
|
4.7
|
0.3
|
1.0
|
O4'
|
A:DG3
|
4.7
|
0.2
|
1.0
|
C2'
|
A:DA4
|
4.7
|
0.3
|
1.0
|
N7
|
A:DA4
|
4.7
|
0.2
|
1.0
|
N9
|
A:DA4
|
4.8
|
0.2
|
1.0
|
H5''
|
A:DG3
|
4.8
|
0.3
|
1.0
|
C1'
|
A:DA4
|
4.9
|
0.2
|
1.0
|
C5'
|
A:DG3
|
4.9
|
0.2
|
1.0
|
|
Phosphorus binding site 4 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 4 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P6
b:0.5
occ:1.00
|
P
|
B:DC6
|
0.0
|
0.5
|
1.0
|
OP1
|
B:DC6
|
1.5
|
1.1
|
1.0
|
OP2
|
B:DC6
|
1.5
|
1.2
|
1.0
|
O3'
|
B:DT5
|
1.6
|
0.4
|
1.0
|
O5'
|
B:DC6
|
1.6
|
0.5
|
1.0
|
C3'
|
B:DT5
|
2.7
|
0.4
|
1.0
|
H3'
|
B:DT5
|
2.7
|
0.5
|
1.0
|
C5'
|
B:DC6
|
2.7
|
0.4
|
1.0
|
H5'
|
B:DC6
|
2.8
|
0.4
|
1.0
|
H5''
|
B:DC6
|
3.4
|
0.4
|
1.0
|
H2''
|
B:DT5
|
3.6
|
0.3
|
1.0
|
C2'
|
B:DT5
|
3.7
|
0.3
|
1.0
|
O4'
|
B:DC6
|
3.7
|
0.3
|
1.0
|
C4'
|
B:DC6
|
3.8
|
0.3
|
1.0
|
H6
|
B:DC6
|
3.8
|
0.2
|
1.0
|
H4'
|
B:DT5
|
3.8
|
0.5
|
1.0
|
C4'
|
B:DT5
|
3.8
|
0.4
|
1.0
|
H5'
|
B:DT5
|
4.2
|
0.7
|
1.0
|
H2'
|
B:DT5
|
4.2
|
0.4
|
1.0
|
H3
|
A:DT1
|
4.3
|
0.2
|
1.0
|
H2'
|
B:DC6
|
4.4
|
0.3
|
1.0
|
C6
|
B:DC6
|
4.5
|
0.2
|
1.0
|
H3'
|
B:DC6
|
4.5
|
0.3
|
1.0
|
C5'
|
B:DT5
|
4.6
|
0.6
|
1.0
|
C3'
|
B:DC6
|
4.6
|
0.2
|
1.0
|
H4'
|
B:DC6
|
4.6
|
0.3
|
1.0
|
C1'
|
B:DC6
|
4.7
|
0.2
|
1.0
|
C2'
|
B:DC6
|
4.8
|
0.2
|
1.0
|
C1'
|
B:DT5
|
4.8
|
0.3
|
1.0
|
N3
|
A:DT1
|
4.9
|
0.3
|
1.0
|
O4'
|
B:DT5
|
4.9
|
0.4
|
1.0
|
H1'
|
B:DT5
|
4.9
|
0.3
|
1.0
|
N1
|
B:DC6
|
4.9
|
0.2
|
1.0
|
|
Phosphorus binding site 5 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 5 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P7
b:0.2
occ:1.00
|
P
|
B:DG7
|
0.0
|
0.2
|
1.0
|
OP1
|
B:DG7
|
1.5
|
0.3
|
1.0
|
OP2
|
B:DG7
|
1.5
|
0.3
|
1.0
|
O3'
|
B:DC6
|
1.6
|
0.3
|
1.0
|
O5'
|
B:DG7
|
1.6
|
0.2
|
1.0
|
C5'
|
B:DG7
|
2.7
|
0.2
|
1.0
|
C3'
|
B:DC6
|
2.7
|
0.2
|
1.0
|
H5'
|
B:DG7
|
2.8
|
0.3
|
1.0
|
H2''
|
B:DC6
|
3.0
|
0.3
|
1.0
|
H5''
|
B:DG7
|
3.0
|
0.3
|
1.0
|
H3'
|
B:DC6
|
3.0
|
0.3
|
1.0
|
C2'
|
B:DC6
|
3.3
|
0.2
|
1.0
|
H1'
|
B:DC6
|
3.7
|
0.3
|
1.0
|
H4'
|
B:DC6
|
3.8
|
0.3
|
1.0
|
C4'
|
B:DC6
|
3.9
|
0.3
|
1.0
|
C4'
|
B:DG7
|
4.0
|
0.2
|
1.0
|
C1'
|
B:DC6
|
4.1
|
0.2
|
1.0
|
H2'
|
B:DC6
|
4.2
|
0.3
|
1.0
|
H3'
|
B:DG7
|
4.3
|
0.3
|
1.0
|
O4'
|
B:DG7
|
4.4
|
0.2
|
1.0
|
H2'
|
B:DG7
|
4.6
|
0.2
|
1.0
|
C3'
|
B:DG7
|
4.6
|
0.2
|
1.0
|
O4'
|
B:DC6
|
4.7
|
0.3
|
1.0
|
H4'
|
B:DG7
|
4.8
|
0.2
|
1.0
|
|
Phosphorus binding site 6 out
of 6 in 179d
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Phosphorus Binding Sites List in 179d
Phosphorus binding site 6 out
of 6 in the Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Solution Structure of the D(T-C-G-A) Duplex at Acidic pH: A Parallel-Stranded Helix Containing C+.C, G.G and A.A Pairs within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P8
b:0.3
occ:1.00
|
P
|
B:DA8
|
0.0
|
0.3
|
1.0
|
OP1
|
B:DA8
|
1.5
|
0.3
|
1.0
|
OP2
|
B:DA8
|
1.5
|
0.4
|
1.0
|
O3'
|
B:DG7
|
1.6
|
0.3
|
1.0
|
O5'
|
B:DA8
|
1.6
|
0.3
|
1.0
|
C5'
|
B:DA8
|
2.6
|
0.3
|
1.0
|
C3'
|
B:DG7
|
2.7
|
0.2
|
1.0
|
H5'
|
B:DA8
|
2.8
|
0.3
|
1.0
|
H3'
|
B:DG7
|
2.8
|
0.3
|
1.0
|
H8
|
B:DA8
|
2.9
|
0.3
|
1.0
|
H5''
|
B:DA8
|
3.1
|
0.3
|
1.0
|
H61
|
A:DA4
|
3.1
|
0.3
|
1.0
|
H2''
|
B:DG7
|
3.1
|
0.2
|
1.0
|
C2'
|
B:DG7
|
3.4
|
0.2
|
1.0
|
H4'
|
B:DG7
|
3.7
|
0.2
|
1.0
|
C4'
|
B:DG7
|
3.9
|
0.2
|
1.0
|
N6
|
A:DA4
|
3.9
|
0.2
|
1.0
|
C4'
|
B:DA8
|
3.9
|
0.3
|
1.0
|
C8
|
B:DA8
|
3.9
|
0.2
|
1.0
|
H1'
|
B:DG7
|
4.0
|
0.2
|
1.0
|
H62
|
A:DA4
|
4.0
|
0.2
|
1.0
|
H2'
|
B:DA8
|
4.1
|
0.3
|
1.0
|
O4'
|
B:DA8
|
4.2
|
0.3
|
1.0
|
H2'
|
B:DG7
|
4.2
|
0.2
|
1.0
|
C1'
|
B:DG7
|
4.2
|
0.2
|
1.0
|
H21
|
A:DG3
|
4.4
|
0.3
|
1.0
|
H3'
|
B:DA8
|
4.5
|
0.3
|
1.0
|
H4'
|
B:DA8
|
4.6
|
0.3
|
1.0
|
C3'
|
B:DA8
|
4.7
|
0.3
|
1.0
|
O4'
|
B:DG7
|
4.7
|
0.2
|
1.0
|
C2'
|
B:DA8
|
4.7
|
0.3
|
1.0
|
N7
|
B:DA8
|
4.7
|
0.3
|
1.0
|
N9
|
B:DA8
|
4.8
|
0.2
|
1.0
|
H5''
|
B:DG7
|
4.8
|
0.3
|
1.0
|
C1'
|
B:DA8
|
4.9
|
0.2
|
1.0
|
C5'
|
B:DG7
|
4.9
|
0.2
|
1.0
|
|
Reference:
Y.Wang,
D.J.Patel.
Solution Structure of the D(T-C-G-A) Duplex at Acidic pH. A Parallel-Stranded Helix Containing C+ .C, G.G and A.A Pairs. J.Mol.Biol. V. 242 508 1994.
ISSN: ISSN 0022-2836
PubMed: 7932707
Page generated: Fri Sep 25 11:45:23 2020
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