Phosphorus in PDB 118d: Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Protein crystallography data
The structure of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes, PDB code: 118d
was solved by
C.Bingman,
X.Li,
G.Zon,
M.Sundaralingam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.64
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.220,
42.220,
25.070,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
(pdb code 118d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the
Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes, PDB code: 118d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
Phosphorus binding site 1 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 1 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:25.7
occ:1.00
|
P
|
A:DT2
|
0.0
|
25.7
|
1.0
|
OP2
|
A:DT2
|
1.5
|
25.8
|
1.0
|
OP1
|
A:DT2
|
1.5
|
35.1
|
1.0
|
O5'
|
A:DT2
|
1.6
|
22.3
|
1.0
|
O3'
|
A:DG1
|
1.6
|
26.5
|
1.0
|
C3'
|
A:DG1
|
2.7
|
23.6
|
1.0
|
C5'
|
A:DT2
|
2.7
|
24.8
|
1.0
|
C2'
|
A:DG1
|
3.6
|
23.2
|
1.0
|
O
|
A:HOH20
|
3.9
|
49.0
|
1.0
|
O
|
A:HOH21
|
3.9
|
45.6
|
1.0
|
C4'
|
A:DG1
|
3.9
|
24.1
|
1.0
|
C4'
|
A:DT2
|
4.0
|
29.3
|
1.0
|
O4'
|
A:DT2
|
4.4
|
30.1
|
1.0
|
C6
|
A:DT2
|
4.4
|
20.6
|
1.0
|
C5'
|
A:DG1
|
4.4
|
25.0
|
1.0
|
C3'
|
A:DT2
|
4.5
|
29.9
|
1.0
|
C7
|
A:DT2
|
4.6
|
18.5
|
1.0
|
O5'
|
A:DG1
|
4.7
|
27.7
|
1.0
|
C1'
|
A:DG1
|
4.9
|
23.6
|
1.0
|
|
Phosphorus binding site 2 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 2 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:37.6
occ:1.00
|
P
|
A:DG3
|
0.0
|
37.6
|
1.0
|
OP2
|
A:DG3
|
1.5
|
37.1
|
1.0
|
OP1
|
A:DG3
|
1.5
|
39.8
|
1.0
|
O5'
|
A:DG3
|
1.6
|
32.6
|
1.0
|
O3'
|
A:DT2
|
1.6
|
37.0
|
1.0
|
C5'
|
A:DG3
|
2.6
|
34.1
|
1.0
|
C3'
|
A:DT2
|
2.7
|
29.9
|
1.0
|
C2'
|
A:DT2
|
3.4
|
28.9
|
1.0
|
C4'
|
A:DG3
|
3.9
|
35.0
|
1.0
|
C4'
|
A:DT2
|
4.0
|
29.3
|
1.0
|
O
|
A:HOH44
|
4.1
|
56.5
|
1.0
|
O4'
|
A:DG3
|
4.2
|
36.2
|
1.0
|
C3'
|
A:DG3
|
4.4
|
36.7
|
1.0
|
O
|
A:HOH20
|
4.5
|
49.0
|
1.0
|
O
|
A:HOH37
|
4.5
|
63.3
|
1.0
|
C5'
|
A:DT2
|
4.5
|
24.8
|
1.0
|
C8
|
A:DG3
|
4.5
|
24.6
|
1.0
|
O5'
|
A:DT2
|
4.8
|
22.3
|
1.0
|
C1'
|
A:DT2
|
4.8
|
27.0
|
1.0
|
O4'
|
A:DT2
|
5.0
|
30.1
|
1.0
|
|
Phosphorus binding site 3 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 3 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:37.4
occ:1.00
|
P
|
A:DC4
|
0.0
|
37.4
|
1.0
|
OP2
|
A:DC4
|
1.5
|
32.5
|
1.0
|
OP1
|
A:DC4
|
1.5
|
47.7
|
1.0
|
O5'
|
A:DC4
|
1.6
|
31.0
|
1.0
|
O3'
|
A:DG3
|
1.6
|
36.5
|
1.0
|
C5'
|
A:DC4
|
2.6
|
29.3
|
1.0
|
C3'
|
A:DG3
|
2.7
|
36.7
|
1.0
|
C2'
|
A:DG3
|
3.2
|
32.1
|
1.0
|
O
|
A:HOH47
|
3.3
|
71.6
|
1.0
|
C4'
|
A:DC4
|
3.9
|
34.5
|
1.0
|
O
|
A:HOH16
|
3.9
|
60.3
|
1.0
|
C4'
|
A:DG3
|
4.0
|
35.0
|
1.0
|
O
|
A:HOH45
|
4.1
|
59.2
|
1.0
|
O
|
A:HOH49
|
4.2
|
67.7
|
1.0
|
O4'
|
A:DC4
|
4.3
|
33.4
|
1.0
|
C3'
|
A:DC4
|
4.3
|
32.8
|
1.0
|
C6
|
A:DC4
|
4.5
|
19.2
|
1.0
|
O
|
A:HOH43
|
4.5
|
60.3
|
1.0
|
C1'
|
A:DG3
|
4.6
|
31.6
|
1.0
|
C5'
|
A:DG3
|
4.8
|
34.1
|
1.0
|
O4'
|
A:DG3
|
4.9
|
36.2
|
1.0
|
O3'
|
A:DC4
|
5.0
|
28.1
|
1.0
|
|
Phosphorus binding site 4 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 4 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:27.9
occ:1.00
|
P
|
A:DG5
|
0.0
|
27.9
|
1.0
|
OP2
|
A:DG5
|
1.4
|
26.8
|
1.0
|
OP1
|
A:DG5
|
1.5
|
32.4
|
1.0
|
O5'
|
A:DG5
|
1.6
|
24.4
|
1.0
|
O3'
|
A:DC4
|
1.6
|
28.1
|
1.0
|
C3'
|
A:DC4
|
2.6
|
32.8
|
1.0
|
C5'
|
A:DG5
|
2.6
|
19.6
|
1.0
|
C2'
|
A:DC4
|
3.4
|
30.9
|
1.0
|
O
|
A:HOH31
|
3.4
|
66.0
|
1.0
|
O
|
A:HOH43
|
3.8
|
60.3
|
1.0
|
C4'
|
A:DG5
|
3.9
|
20.2
|
1.0
|
C4'
|
A:DC4
|
4.0
|
34.5
|
1.0
|
O
|
A:HOH49
|
4.1
|
67.7
|
1.0
|
O4'
|
A:DG5
|
4.1
|
23.1
|
1.0
|
C5'
|
A:DC4
|
4.6
|
29.3
|
1.0
|
O5'
|
A:DC4
|
4.7
|
31.0
|
1.0
|
C1'
|
A:DC4
|
4.8
|
27.1
|
1.0
|
O4'
|
A:DC4
|
5.0
|
33.4
|
1.0
|
|
Phosphorus binding site 5 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 5 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:23.6
occ:1.00
|
P
|
A:DC6
|
0.0
|
23.6
|
1.0
|
OP2
|
A:DC6
|
1.5
|
22.2
|
1.0
|
OP1
|
A:DC6
|
1.5
|
30.8
|
1.0
|
O3'
|
A:DG5
|
1.6
|
24.5
|
1.0
|
O5'
|
A:DC6
|
1.6
|
21.6
|
1.0
|
C3'
|
A:DG5
|
2.6
|
21.9
|
1.0
|
C5'
|
A:DC6
|
2.7
|
24.5
|
1.0
|
C2'
|
A:DG5
|
3.6
|
19.0
|
1.0
|
O
|
A:HOH39
|
3.6
|
62.3
|
1.0
|
O
|
A:HOH26
|
3.6
|
44.3
|
1.0
|
O
|
A:HOH34
|
3.7
|
88.4
|
1.0
|
O
|
A:HOH46
|
3.8
|
72.6
|
1.0
|
C4'
|
A:DG5
|
3.8
|
20.2
|
1.0
|
C4'
|
A:DC6
|
3.9
|
25.2
|
1.0
|
C6
|
A:DC6
|
4.2
|
18.2
|
1.0
|
C5'
|
A:DG5
|
4.3
|
19.6
|
1.0
|
O4'
|
A:DC6
|
4.3
|
22.6
|
1.0
|
C3'
|
A:DC6
|
4.4
|
25.1
|
1.0
|
O
|
A:HOH40
|
4.4
|
90.9
|
1.0
|
O
|
A:HOH22
|
4.7
|
30.8
|
1.0
|
C5
|
A:DC6
|
4.9
|
17.6
|
1.0
|
C1'
|
A:DG5
|
4.9
|
18.0
|
1.0
|
O4'
|
A:DG5
|
5.0
|
23.1
|
1.0
|
|
Phosphorus binding site 6 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 6 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:27.4
occ:1.00
|
P
|
A:DA7
|
0.0
|
27.4
|
1.0
|
OP1
|
A:DA7
|
1.5
|
32.3
|
1.0
|
OP2
|
A:DA7
|
1.5
|
26.7
|
1.0
|
O3'
|
A:DC6
|
1.6
|
25.5
|
1.0
|
O5'
|
A:DA7
|
1.6
|
23.6
|
1.0
|
C3'
|
A:DC6
|
2.6
|
25.1
|
1.0
|
C5'
|
A:DA7
|
2.7
|
23.3
|
1.0
|
O
|
A:HOH48
|
3.3
|
67.7
|
1.0
|
C2'
|
A:DC6
|
3.3
|
20.2
|
1.0
|
C4'
|
A:DC6
|
3.9
|
25.2
|
1.0
|
C4'
|
A:DA7
|
3.9
|
21.3
|
1.0
|
O
|
A:HOH41
|
4.0
|
56.2
|
1.0
|
O
|
A:HOH11
|
4.0
|
44.8
|
1.0
|
O
|
A:HOH26
|
4.1
|
44.3
|
1.0
|
O4'
|
A:DA7
|
4.3
|
23.7
|
1.0
|
C8
|
A:DA7
|
4.4
|
17.1
|
1.0
|
C3'
|
A:DA7
|
4.5
|
19.6
|
1.0
|
O5'
|
A:DC6
|
4.5
|
21.6
|
1.0
|
C5'
|
A:DC6
|
4.5
|
24.5
|
1.0
|
C1'
|
A:DC6
|
4.7
|
20.6
|
1.0
|
O4'
|
A:DC6
|
4.9
|
22.6
|
1.0
|
|
Phosphorus binding site 7 out
of 7 in 118d
Go back to
Phosphorus Binding Sites List in 118d
Phosphorus binding site 7 out
of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:33.7
occ:1.00
|
P
|
A:DC8
|
0.0
|
33.7
|
1.0
|
OP2
|
A:DC8
|
1.5
|
40.7
|
1.0
|
OP1
|
A:DC8
|
1.5
|
36.7
|
1.0
|
O5'
|
A:DC8
|
1.6
|
29.9
|
1.0
|
O3'
|
A:DA7
|
1.6
|
27.2
|
1.0
|
C5'
|
A:DC8
|
2.6
|
36.4
|
1.0
|
C3'
|
A:DA7
|
2.6
|
19.6
|
1.0
|
C2'
|
A:DA7
|
3.4
|
20.0
|
1.0
|
O
|
A:HOH42
|
3.8
|
52.6
|
1.0
|
O
|
A:HOH41
|
3.8
|
56.2
|
1.0
|
C4'
|
A:DC8
|
3.9
|
36.8
|
1.0
|
C4'
|
A:DA7
|
3.9
|
21.3
|
1.0
|
O4'
|
A:DC8
|
4.3
|
37.2
|
1.0
|
C3'
|
A:DC8
|
4.3
|
39.7
|
1.0
|
C6
|
A:DC8
|
4.5
|
25.9
|
1.0
|
C5'
|
A:DA7
|
4.5
|
23.3
|
1.0
|
O5'
|
A:DA7
|
4.7
|
23.6
|
1.0
|
C1'
|
A:DA7
|
4.8
|
21.5
|
1.0
|
C2'
|
A:DC8
|
4.9
|
38.1
|
1.0
|
O4'
|
A:DA7
|
5.0
|
23.7
|
1.0
|
|
Reference:
C.Bingman,
X.Li,
G.Zon,
M.Sundaralingam.
Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes. Biochemistry V. 31 12803 1992.
ISSN: ISSN 0006-2960
PubMed: 1463751
DOI: 10.1021/BI00166A014
Page generated: Fri Sep 25 11:12:21 2020
|