Phosphorus in PDB 148d: Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Phosphorus atom in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) (pdb code 148d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg), PDB code: 148d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 1 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:DG2 0.0 0.0 1.0
OP2 A:DG2 1.5 0.0 1.0
OP1 A:DG2 1.5 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
O5' A:DG2 1.6 0.0 1.0
C3' A:DG1 2.6 0.0 1.0
C5' A:DG2 2.7 0.0 1.0
H3' A:DG1 2.7 0.0 1.0
H5' A:DG2 2.8 0.0 1.0
H5'' A:DG2 3.0 0.0 1.0
H2'' A:DG1 3.3 0.0 1.0
C2' A:DG1 3.5 0.0 1.0
H4' A:DG1 3.8 0.0 1.0
C4' A:DG1 3.9 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
H1' A:DG1 4.0 0.0 1.0
H3' A:DG2 4.0 0.0 1.0
H2' A:DG1 4.3 0.0 1.0
C1' A:DG1 4.3 0.0 1.0
O4' A:DG2 4.4 0.0 1.0
C3' A:DG2 4.6 0.0 1.0
OP2 A:DT4 4.6 0.0 1.0
O4' A:DG1 4.7 0.0 1.0
H5'' A:DG1 4.7 0.0 1.0
H2' A:DG2 4.7 0.0 1.0
H4' A:DG2 4.8 0.0 1.0
C5' A:DG1 4.9 0.0 1.0

Phosphorus binding site 2 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 2 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DT3 0.0 0.0 1.0
OP1 A:DT3 1.5 0.0 1.0
OP2 A:DT3 1.5 0.0 1.0
O5' A:DT3 1.6 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DT3 2.7 0.0 1.0
C3' A:DG2 2.7 0.0 1.0
H6 A:DT3 2.8 0.0 1.0
H5'' A:DT3 2.8 0.0 1.0
H2'' A:DG2 2.9 0.0 1.0
H5' A:DT3 3.1 0.0 1.0
C2' A:DG2 3.2 0.0 1.0
H3' A:DG2 3.4 0.0 1.0
H71 A:DT3 3.4 0.0 1.0
H1' A:DG2 3.4 0.0 1.0
H73 A:DT3 3.4 0.0 1.0
H4' A:DG2 3.5 0.0 1.0
C4' A:DG2 3.8 0.0 1.0
C6 A:DT3 3.8 0.0 1.0
H3' A:DT3 3.8 0.0 1.0
C7 A:DT3 3.8 0.0 1.0
C1' A:DG2 3.8 0.0 1.0
C4' A:DT3 4.0 0.0 1.0
H2' A:DG2 4.1 0.0 1.0
H2' A:DT3 4.2 0.0 1.0
C5 A:DT3 4.3 0.0 1.0
C3' A:DT3 4.4 0.0 1.0
H72 A:DT4 4.4 0.0 1.0
O4' A:DG2 4.5 0.0 1.0
O4' A:DT3 4.6 0.0 1.0
C2' A:DT3 4.7 0.0 1.0
H4' A:DT3 4.8 0.0 1.0
H72 A:DT3 4.8 0.0 1.0
N1 A:DT3 4.8 0.0 1.0
H5'' A:DG2 4.9 0.0 1.0
C1' A:DT3 5.0 0.0 1.0
C5' A:DG2 5.0 0.0 1.0

Phosphorus binding site 3 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 3 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DT4 0.0 0.0 1.0
OP1 A:DT4 1.5 0.0 1.0
OP2 A:DT4 1.5 0.0 1.0
O3' A:DT3 1.6 0.0 1.0
O5' A:DT4 1.6 0.0 1.0
C3' A:DT3 2.7 0.0 1.0
H3' A:DT3 2.7 0.0 1.0
C5' A:DT4 2.7 0.0 1.0
H5'' A:DT4 2.8 0.0 1.0
H5' A:DT4 3.0 0.0 1.0
H2'' A:DT3 3.1 0.0 1.0
C2' A:DT3 3.4 0.0 1.0
H3' A:DT4 3.9 0.0 1.0
H2' A:DT3 3.9 0.0 1.0
H2' A:DG2 4.0 0.0 1.0
C4' A:DT3 4.0 0.0 1.0
H4' A:DT3 4.0 0.0 1.0
C4' A:DT4 4.0 0.0 1.0
H3' A:DG2 4.3 0.0 1.0
C3' A:DT4 4.5 0.0 1.0
H2'' A:DG2 4.7 0.0 1.0
C1' A:DT3 4.7 0.0 1.0
H8 A:DG2 4.7 0.0 1.0
C2' A:DG2 4.7 0.0 1.0
O4' A:DT4 4.7 0.0 1.0
H5'' A:DT3 4.8 0.0 1.0
H1' A:DT3 4.8 0.0 1.0
H6 A:DT4 4.8 0.0 1.0
H2' A:DT4 4.8 0.0 1.0
O4' A:DT3 4.8 0.0 1.0
H4' A:DT4 4.9 0.0 1.0
C5' A:DT3 4.9 0.0 1.0

Phosphorus binding site 4 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 4 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DG5 0.0 0.0 1.0
OP1 A:DG5 1.5 0.0 1.0
OP2 A:DG5 1.5 0.0 1.0
O3' A:DT4 1.6 0.0 1.0
O5' A:DG5 1.6 0.0 1.0
C3' A:DT4 2.7 0.0 1.0
C5' A:DG5 2.7 0.0 1.0
H5'' A:DG5 2.8 0.0 1.0
H3' A:DT4 3.0 0.0 1.0
H5' A:DG5 3.1 0.0 1.0
H4' A:DT4 3.4 0.0 1.0
C4' A:DT4 3.5 0.0 1.0
H5'' A:DT4 3.6 0.0 1.0
C2' A:DT4 3.9 0.0 1.0
C4' A:DG5 4.0 0.0 1.0
H2'' A:DT4 4.0 0.0 1.0
C5' A:DT4 4.1 0.0 1.0
O4' A:DG5 4.3 0.0 1.0
H4' A:DG5 4.4 0.0 1.0
H1' A:DT4 4.5 0.0 1.0
H2' A:DT4 4.6 0.0 1.0
C1' A:DT4 4.7 0.0 1.0
O4' A:DT4 4.7 0.0 1.0
N3 A:DG5 4.9 0.0 1.0
O5' A:DT4 4.9 0.0 1.0
H5' A:DT4 4.9 0.0 1.0

Phosphorus binding site 5 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 5 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DG6 0.0 0.0 1.0
OP2 A:DG6 1.5 0.0 1.0
OP1 A:DG6 1.5 0.0 1.0
O3' A:DG5 1.6 0.0 1.0
O5' A:DG6 1.6 0.0 1.0
C5' A:DG6 2.7 0.0 1.0
C3' A:DG5 2.7 0.0 1.0
H2'' A:DG5 2.9 0.0 1.0
H3' A:DG5 2.9 0.0 1.0
H5'' A:DG6 2.9 0.0 1.0
H5' A:DG6 3.0 0.0 1.0
H1' A:DG5 3.3 0.0 1.0
C2' A:DG5 3.3 0.0 1.0
C1' A:DG5 3.8 0.0 1.0
H4' A:DG5 3.9 0.0 1.0
C4' A:DG5 3.9 0.0 1.0
C4' A:DG6 4.0 0.0 1.0
H2' A:DG6 4.1 0.0 1.0
H3' A:DG6 4.2 0.0 1.0
H2' A:DG5 4.3 0.0 1.0
O4' A:DG5 4.4 0.0 1.0
C3' A:DG6 4.5 0.0 1.0
O4' A:DG6 4.6 0.0 1.0
H8 A:DG6 4.8 0.0 1.0
H4' A:DG6 4.8 0.0 1.0
C2' A:DG6 5.0 0.0 1.0

Phosphorus binding site 6 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 6 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:DT7 0.0 0.0 1.0
OP1 A:DT7 1.5 0.0 1.0
OP2 A:DT7 1.5 0.0 1.0
O5' A:DT7 1.6 0.0 1.0
O3' A:DG6 1.6 0.0 1.0
C5' A:DT7 2.6 0.0 1.0
C3' A:DG6 2.7 0.0 1.0
H6 A:DT7 2.7 0.0 1.0
H5'' A:DT7 2.7 0.0 1.0
H3' A:DG6 2.8 0.0 1.0
H4' A:DG6 2.9 0.0 1.0
H5' A:DT7 3.1 0.0 1.0
C4' A:DG6 3.3 0.0 1.0
H73 A:DT7 3.4 0.0 1.0
H2' A:DT7 3.5 0.0 1.0
H71 A:DT7 3.7 0.0 1.0
C6 A:DT7 3.7 0.0 1.0
H5'' A:DG6 3.7 0.0 1.0
C4' A:DT7 3.9 0.0 1.0
C7 A:DT7 3.9 0.0 1.0
C2' A:DG6 4.0 0.0 1.0
H3' A:DT7 4.1 0.0 1.0
C5' A:DG6 4.1 0.0 1.0
H1' A:DG6 4.2 0.0 1.0
C5 A:DT7 4.3 0.0 1.0
C2' A:DT7 4.4 0.0 1.0
H2'' A:DG6 4.4 0.0 1.0
O4' A:DT7 4.4 0.0 1.0
C3' A:DT7 4.4 0.0 1.0
O4' A:DG6 4.5 0.0 1.0
C1' A:DG6 4.5 0.0 1.0
H2' A:DG6 4.6 0.0 1.0
N1 A:DT7 4.7 0.0 1.0
H4' A:DT7 4.7 0.0 1.0
C1' A:DT7 4.8 0.0 1.0
H72 A:DT7 4.9 0.0 1.0
H5' A:DG6 4.9 0.0 1.0

Phosphorus binding site 7 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 7 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DG8 0.0 0.0 1.0
OP2 A:DG8 1.5 0.0 1.0
OP1 A:DG8 1.5 0.0 1.0
O3' A:DT7 1.6 0.0 1.0
O5' A:DG8 1.6 0.0 1.0
C3' A:DT7 2.7 0.0 1.0
C5' A:DG8 2.7 0.0 1.0
H3' A:DT7 2.8 0.0 1.0
H5'' A:DG8 2.9 0.0 1.0
H5' A:DG8 3.3 0.0 1.0
H4' A:DT7 3.6 0.0 1.0
H2'' A:DT7 3.7 0.0 1.0
C2' A:DT7 3.7 0.0 1.0
C4' A:DT7 3.8 0.0 1.0
H8 A:DG8 3.9 0.0 1.0
H2' A:DG8 3.9 0.0 1.0
C4' A:DG8 3.9 0.0 1.0
H3' A:DG8 4.1 0.0 1.0
H1' A:DT7 4.4 0.0 1.0
H2' A:DT7 4.4 0.0 1.0
C1' A:DT7 4.5 0.0 1.0
C3' A:DG8 4.5 0.0 1.0
C8 A:DG8 4.5 0.0 1.0
H2'' A:DG6 4.5 0.0 1.0
O4' A:DG8 4.6 0.0 1.0
O4' A:DT7 4.6 0.0 1.0
C2' A:DG8 4.8 0.0 1.0
H4' A:DG8 4.8 0.0 1.0
H5'' A:DT7 4.9 0.0 1.0
C5' A:DT7 5.0 0.0 1.0

Phosphorus binding site 8 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 8 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DT9 0.0 0.0 1.0
OP1 A:DT9 1.5 0.0 1.0
OP2 A:DT9 1.5 0.0 1.0
O5' A:DT9 1.6 0.0 1.0
O3' A:DG8 1.6 0.0 1.0
C3' A:DG8 2.6 0.0 1.0
H3' A:DG8 2.6 0.0 1.0
C5' A:DT9 2.8 0.0 1.0
H4' A:DG8 2.8 0.0 1.0
H5'' A:DT9 3.1 0.0 1.0
H5' A:DT9 3.1 0.0 1.0
H6 A:DT9 3.1 0.0 1.0
C4' A:DG8 3.3 0.0 1.0
H73 A:DT9 3.4 0.0 1.0
H5'' A:DG8 3.5 0.0 1.0
H2' A:DT9 3.8 0.0 1.0
C2' A:DG8 3.9 0.0 1.0
C5' A:DG8 3.9 0.0 1.0
C6 A:DT9 4.0 0.0 1.0
C4' A:DT9 4.0 0.0 1.0
C7 A:DT9 4.2 0.0 1.0
H72 A:DT9 4.3 0.0 1.0
H2'' A:DG8 4.3 0.0 1.0
O4' A:DT9 4.3 0.0 1.0
H5' A:DG8 4.4 0.0 1.0
O4' A:DG8 4.4 0.0 1.0
C5 A:DT9 4.5 0.0 1.0
H2' A:DG8 4.6 0.0 1.0
C1' A:DG8 4.6 0.0 1.0
C2' A:DT9 4.7 0.0 1.0
C3' A:DT9 4.8 0.0 1.0
H3' A:DT9 4.8 0.0 1.0
H1' A:DG8 4.8 0.0 1.0
N1 A:DT9 4.9 0.0 1.0
H4' A:DT9 4.9 0.0 1.0
C1' A:DT9 4.9 0.0 1.0

Phosphorus binding site 9 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 9 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DG10 0.0 0.0 1.0
OP1 A:DG10 1.5 0.0 1.0
OP2 A:DG10 1.5 0.0 1.0
O5' A:DG10 1.6 0.0 1.0
O3' A:DT9 1.6 0.0 1.0
H3' A:DT9 2.5 0.0 1.0
C5' A:DG10 2.7 0.0 1.0
C3' A:DT9 2.7 0.0 1.0
H5' A:DG10 2.8 0.0 1.0
H5'' A:DG10 2.8 0.0 1.0
H4' A:DT9 3.4 0.0 1.0
C4' A:DT9 3.6 0.0 1.0
C2' A:DT9 3.9 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
H2'' A:DT9 4.1 0.0 1.0
H4' A:DG10 4.2 0.0 1.0
O4' A:DG10 4.5 0.0 1.0
O4' A:DT9 4.6 0.0 1.0
H2' A:DT9 4.7 0.0 1.0
C1' A:DT9 4.7 0.0 1.0
H1' A:DT9 4.7 0.0 1.0
C5' A:DT9 4.7 0.0 1.0
H5'' A:DT9 4.7 0.0 1.0

Phosphorus binding site 10 out of 14 in 148d

Go back to Phosphorus Binding Sites List in 148d
Phosphorus binding site 10 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.0
occ:1.00
P A:DG11 0.0 0.0 1.0
OP2 A:DG11 1.5 0.0 1.0
OP1 A:DG11 1.5 0.0 1.0
O5' A:DG11 1.6 0.0 1.0
O3' A:DG10 1.6 0.0 1.0
C5' A:DG11 2.7 0.0 1.0
C3' A:DG10 2.7 0.0 1.0
H2'' A:DG10 2.7 0.0 1.0
H3' A:DG10 2.8 0.0 1.0
H5' A:DG11 2.9 0.0 1.0
H5'' A:DG11 3.0 0.0 1.0
C2' A:DG10 3.2 0.0 1.0
H1' A:DG10 3.8 0.0 1.0
H4' A:DG10 4.0 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
C4' A:DG11 4.1 0.0 1.0
C1' A:DG10 4.1 0.0 1.0
H2' A:DG10 4.1 0.0 1.0
H3' A:DG11 4.3 0.0 1.0
H8 A:DG11 4.5 0.0 1.0
O4' A:DG11 4.5 0.0 1.0
OP2 A:DT13 4.6 0.0 1.0
O4' A:DG10 4.7 0.0 1.0
C3' A:DG11 4.8 0.0 1.0
H2' A:DG11 4.8 0.0 1.0
H4' A:DG11 4.8 0.0 1.0

Reference:

P.Schultze, R.F.Macaya, J.Feigon. Three-Dimensional Solution Structure of the Thrombin-Binding Dna Aptamer D(Ggttggtgtggttgg). J.Mol.Biol. V. 235 1532 1994.
ISSN: ISSN 0022-2836
PubMed: 8107090
DOI: 10.1006/JMBI.1994.1105
Page generated: Fri Sep 25 11:30:05 2020

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy