Phosphorus in PDB 151d: Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Protein crystallography data
The structure of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes, PDB code: 151d
was solved by
L.A.Lipscomb,
M.E.Peek,
F.X.Zhou,
J.A.Bertrand,
D.Vanderveer,
L.D.Williams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
1.40
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
27.920,
27.920,
52.390,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
(pdb code 151d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 5 binding sites of Phosphorus where determined in the
Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes, PDB code: 151d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
Phosphorus binding site 1 out
of 5 in 151d
Go back to
Phosphorus Binding Sites List in 151d
Phosphorus binding site 1 out
of 5 in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:8.0
occ:1.00
|
P
|
A:DG2
|
0.0
|
8.0
|
1.0
|
OP2
|
A:DG2
|
1.4
|
7.3
|
1.0
|
OP1
|
A:DG2
|
1.5
|
8.1
|
1.0
|
O3'
|
A:DC1
|
1.6
|
6.3
|
1.0
|
O5'
|
A:DG2
|
1.7
|
7.3
|
1.0
|
C5'
|
A:DG2
|
2.6
|
7.5
|
1.0
|
C3'
|
A:DC1
|
2.6
|
6.5
|
1.0
|
O
|
A:HOH35
|
3.6
|
22.8
|
1.0
|
O
|
A:HOH23
|
3.6
|
26.6
|
1.0
|
O
|
A:HOH48
|
3.7
|
63.2
|
1.0
|
O
|
A:HOH19
|
3.7
|
26.6
|
1.0
|
C4'
|
A:DC1
|
3.7
|
6.0
|
1.0
|
C2'
|
A:DC1
|
3.8
|
6.3
|
1.0
|
C4'
|
A:DG2
|
3.9
|
7.9
|
1.0
|
O4'
|
A:DG2
|
4.3
|
7.4
|
1.0
|
C3'
|
A:DG2
|
4.4
|
8.6
|
1.0
|
C1'
|
A:DC1
|
4.5
|
5.9
|
1.0
|
O4'
|
A:DC1
|
4.6
|
6.1
|
1.0
|
C5'
|
A:DC1
|
4.7
|
6.2
|
1.0
|
C2'
|
A:DG2
|
4.8
|
7.9
|
1.0
|
|
Phosphorus binding site 2 out
of 5 in 151d
Go back to
Phosphorus Binding Sites List in 151d
Phosphorus binding site 2 out
of 5 in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:12.2
occ:1.00
|
P
|
A:DA3
|
0.0
|
12.2
|
1.0
|
OP1
|
A:DA3
|
1.4
|
11.8
|
1.0
|
OP2
|
A:DA3
|
1.5
|
12.6
|
1.0
|
O3'
|
A:DG2
|
1.6
|
10.9
|
1.0
|
O5'
|
A:DA3
|
1.6
|
10.2
|
1.0
|
C5'
|
A:DA3
|
2.5
|
8.8
|
1.0
|
C3'
|
A:DG2
|
2.7
|
8.6
|
1.0
|
O
|
A:HOH14
|
3.4
|
20.1
|
1.0
|
C2'
|
A:DG2
|
3.6
|
7.9
|
1.0
|
O
|
A:HOH42
|
3.6
|
30.0
|
1.0
|
C4'
|
A:DA3
|
3.7
|
8.0
|
1.0
|
O
|
A:HOH41
|
3.8
|
23.3
|
1.0
|
O
|
A:HOH22
|
3.8
|
38.3
|
1.0
|
C4'
|
A:DG2
|
3.8
|
7.9
|
1.0
|
O4'
|
A:DA3
|
3.9
|
7.2
|
1.0
|
O
|
A:HOH20
|
3.9
|
42.5
|
1.0
|
C8
|
A:DA3
|
4.2
|
5.3
|
1.0
|
C3'
|
A:DA3
|
4.4
|
8.3
|
1.0
|
C1'
|
A:DG2
|
4.4
|
7.2
|
1.0
|
C2'
|
A:DA3
|
4.7
|
7.6
|
1.0
|
O4'
|
A:DG2
|
4.8
|
7.4
|
1.0
|
C1'
|
A:DA3
|
4.8
|
6.8
|
1.0
|
C5'
|
A:DG2
|
4.9
|
7.5
|
1.0
|
N9
|
A:DA3
|
4.9
|
5.8
|
1.0
|
|
Phosphorus binding site 3 out
of 5 in 151d
Go back to
Phosphorus Binding Sites List in 151d
Phosphorus binding site 3 out
of 5 in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:9.5
occ:1.00
|
P
|
A:DT4
|
0.0
|
9.5
|
1.0
|
OP1
|
A:DT4
|
1.4
|
9.4
|
1.0
|
OP2
|
A:DT4
|
1.4
|
10.3
|
1.0
|
O3'
|
A:DA3
|
1.6
|
8.5
|
1.0
|
O5'
|
A:DT4
|
1.7
|
8.2
|
1.0
|
C5'
|
A:DT4
|
2.6
|
7.7
|
1.0
|
C3'
|
A:DA3
|
2.7
|
8.3
|
1.0
|
C2'
|
A:DA3
|
3.3
|
7.6
|
1.0
|
O
|
A:HOH49
|
3.7
|
18.6
|
1.0
|
O
|
A:HOH24
|
3.8
|
12.9
|
1.0
|
C4'
|
A:DT4
|
3.9
|
7.5
|
1.0
|
C4'
|
A:DA3
|
3.9
|
8.0
|
1.0
|
O
|
A:HOH36
|
4.0
|
21.3
|
1.0
|
C1'
|
A:DA3
|
4.3
|
6.8
|
1.0
|
O4'
|
A:DT4
|
4.3
|
8.2
|
1.0
|
C3'
|
A:DT4
|
4.4
|
7.5
|
1.0
|
O4'
|
A:DA3
|
4.7
|
7.2
|
1.0
|
O
|
A:HOH27
|
4.7
|
27.7
|
1.0
|
O
|
A:HOH65
|
5.0
|
10.2
|
1.0
|
C2'
|
A:DT4
|
5.0
|
6.8
|
1.0
|
|
Phosphorus binding site 4 out
of 5 in 151d
Go back to
Phosphorus Binding Sites List in 151d
Phosphorus binding site 4 out
of 5 in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:9.6
occ:1.00
|
P
|
A:DC5
|
0.0
|
9.6
|
1.0
|
OP2
|
A:DC5
|
1.4
|
10.3
|
1.0
|
OP1
|
A:DC5
|
1.4
|
11.1
|
1.0
|
O3'
|
A:DT4
|
1.6
|
8.7
|
1.0
|
O5'
|
A:DC5
|
1.7
|
9.1
|
1.0
|
C5'
|
A:DC5
|
2.6
|
8.4
|
1.0
|
C3'
|
A:DT4
|
2.6
|
7.5
|
1.0
|
C2'
|
A:DT4
|
3.3
|
6.8
|
1.0
|
O
|
A:HOH39
|
3.7
|
28.9
|
1.0
|
O
|
A:HOH37
|
3.7
|
21.4
|
1.0
|
C4'
|
A:DT4
|
3.8
|
7.5
|
1.0
|
C4'
|
A:DC5
|
3.8
|
9.2
|
1.0
|
O
|
A:HOH28
|
4.2
|
23.3
|
1.0
|
O4'
|
A:DC5
|
4.3
|
8.4
|
1.0
|
C3'
|
A:DC5
|
4.3
|
9.3
|
1.0
|
C1'
|
A:DT4
|
4.4
|
6.9
|
1.0
|
C2'
|
A:DC5
|
4.6
|
9.0
|
1.0
|
O4'
|
A:DT4
|
4.8
|
8.2
|
1.0
|
C5'
|
A:DT4
|
4.8
|
7.7
|
1.0
|
|
Phosphorus binding site 5 out
of 5 in 151d
Go back to
Phosphorus Binding Sites List in 151d
Phosphorus binding site 5 out
of 5 in the Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Diversity of Water Ring Size at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:10.9
occ:1.00
|
P
|
A:DG6
|
0.0
|
10.9
|
1.0
|
OP1
|
A:DG6
|
1.4
|
10.2
|
1.0
|
OP2
|
A:DG6
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DG6
|
1.6
|
8.8
|
1.0
|
O3'
|
A:DC5
|
1.6
|
10.7
|
1.0
|
C3'
|
A:DC5
|
2.7
|
9.3
|
1.0
|
C5'
|
A:DG6
|
2.7
|
8.2
|
1.0
|
C4'
|
A:DC5
|
3.5
|
9.2
|
1.0
|
O
|
A:HOH30
|
3.8
|
46.8
|
1.0
|
O
|
A:HOH18
|
3.8
|
29.1
|
1.0
|
C2'
|
A:DC5
|
3.8
|
9.0
|
1.0
|
C4'
|
A:DG6
|
3.9
|
8.2
|
1.0
|
O
|
A:HOH43
|
3.9
|
19.9
|
1.0
|
C8
|
A:DG6
|
4.2
|
6.1
|
1.0
|
O
|
A:HOH32
|
4.3
|
42.4
|
1.0
|
C3'
|
A:DG6
|
4.4
|
7.2
|
1.0
|
O4'
|
A:DG6
|
4.4
|
7.7
|
1.0
|
C2'
|
A:DG6
|
4.5
|
7.1
|
1.0
|
C5'
|
A:DC5
|
4.5
|
8.4
|
1.0
|
O
|
A:HOH67
|
4.5
|
28.8
|
1.0
|
C1'
|
A:DC5
|
4.5
|
8.2
|
1.0
|
O4'
|
A:DC5
|
4.6
|
8.4
|
1.0
|
N9
|
A:DG6
|
4.8
|
6.4
|
1.0
|
O5'
|
A:DC5
|
4.9
|
9.1
|
1.0
|
C1'
|
A:DG6
|
4.9
|
6.6
|
1.0
|
N7
|
A:DG6
|
5.0
|
6.6
|
1.0
|
|
Reference:
L.A.Lipscomb,
M.E.Peek,
F.X.Zhou,
J.A.Bertrand,
D.Vanderveer,
L.D.Williams.
Water Ring Structure at Dna Interfaces: Hydration and Dynamics of Dna-Anthracycline Complexes. Biochemistry V. 33 3649 1994.
ISSN: ISSN 0006-2960
PubMed: 8142363
DOI: 10.1021/BI00178A023
Page generated: Fri Sep 25 11:31:38 2020
|