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 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 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 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 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 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 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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