Phosphorus in PDB 159d: Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Protein crystallography data
The structure of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex, PDB code: 159d
was solved by
X.Chen,
B.Ramakrishnan,
S.T.Rao,
M.Sundaralingam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
1.80
|
Space group
|
P 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
27.930,
27.930,
57.670,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15 /
n/a
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
(pdb code 159d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the
Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex, PDB code: 159d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
Phosphorus binding site 1 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 1 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:10.9
occ:1.00
|
P
|
A:DC2
|
0.0
|
10.9
|
1.0
|
OP2
|
A:DC2
|
1.5
|
11.2
|
1.0
|
OP1
|
A:DC2
|
1.5
|
11.0
|
1.0
|
O5'
|
A:DC2
|
1.6
|
11.0
|
1.0
|
O3'
|
A:DI1
|
1.6
|
9.9
|
1.0
|
C5'
|
A:DC2
|
2.6
|
11.0
|
1.0
|
C3'
|
A:DI1
|
2.7
|
9.7
|
1.0
|
C2'
|
A:DI1
|
3.4
|
9.2
|
1.0
|
O
|
A:HOH63
|
3.7
|
60.4
|
1.0
|
O
|
A:HOH65
|
3.8
|
84.8
|
1.0
|
C4'
|
A:DI1
|
3.9
|
9.5
|
1.0
|
C4'
|
A:DC2
|
3.9
|
11.0
|
1.0
|
O
|
A:HOH64
|
4.0
|
75.7
|
1.0
|
C1'
|
A:DI1
|
4.2
|
9.0
|
1.0
|
O4'
|
A:DC2
|
4.3
|
10.7
|
1.0
|
C3'
|
A:DC2
|
4.3
|
11.3
|
1.0
|
O4'
|
A:DI1
|
4.5
|
9.3
|
1.0
|
O
|
A:HOH69
|
4.6
|
65.7
|
1.0
|
C2'
|
A:DC2
|
4.8
|
10.8
|
1.0
|
|
Phosphorus binding site 2 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 2 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:12.8
occ:1.00
|
P
|
A:DI3
|
0.0
|
12.8
|
1.0
|
OP2
|
A:DI3
|
1.5
|
12.9
|
1.0
|
OP1
|
A:DI3
|
1.5
|
13.5
|
1.0
|
O3'
|
A:DC2
|
1.6
|
11.9
|
1.0
|
O5'
|
A:DI3
|
1.6
|
12.4
|
1.0
|
C3'
|
A:DC2
|
2.6
|
11.3
|
1.0
|
C5'
|
A:DI3
|
2.7
|
11.8
|
1.0
|
C4'
|
A:DC2
|
3.5
|
11.0
|
1.0
|
C2'
|
A:DC2
|
3.7
|
10.8
|
1.0
|
O
|
A:HOH60
|
3.8
|
91.3
|
1.0
|
C4'
|
A:DI3
|
3.9
|
11.5
|
1.0
|
C8
|
A:DI3
|
4.0
|
10.1
|
1.0
|
O4'
|
A:DI3
|
4.2
|
11.4
|
1.0
|
C5'
|
A:DC2
|
4.3
|
11.0
|
1.0
|
O
|
A:HOH27
|
4.4
|
49.4
|
1.0
|
O
|
A:HOH56
|
4.4
|
64.7
|
1.0
|
C3'
|
A:DI3
|
4.4
|
11.7
|
1.0
|
O
|
A:HOH46
|
4.5
|
70.8
|
1.0
|
C1'
|
A:DC2
|
4.5
|
10.5
|
1.0
|
C2'
|
A:DI3
|
4.5
|
11.3
|
1.0
|
O
|
A:HOH29
|
4.6
|
52.3
|
1.0
|
O4'
|
A:DC2
|
4.7
|
10.7
|
1.0
|
O
|
A:HOH73
|
4.7
|
66.7
|
1.0
|
C1'
|
A:DI3
|
4.8
|
10.8
|
1.0
|
N9
|
A:DI3
|
4.8
|
10.2
|
1.0
|
N7
|
A:DI3
|
4.9
|
9.8
|
1.0
|
O5'
|
A:DC2
|
4.9
|
11.0
|
1.0
|
|
Phosphorus binding site 3 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 3 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:12.6
occ:1.00
|
P
|
A:DC4
|
0.0
|
12.6
|
1.0
|
OP2
|
A:DC4
|
1.5
|
12.7
|
1.0
|
OP1
|
A:DC4
|
1.5
|
12.9
|
1.0
|
O5'
|
A:DC4
|
1.6
|
11.8
|
1.0
|
O3'
|
A:DI3
|
1.6
|
12.2
|
1.0
|
C5'
|
A:DC4
|
2.6
|
11.1
|
1.0
|
C3'
|
A:DI3
|
2.6
|
11.7
|
1.0
|
C2'
|
A:DI3
|
3.3
|
11.3
|
1.0
|
O
|
A:HOH31
|
3.8
|
53.2
|
1.0
|
C4'
|
A:DC4
|
3.9
|
10.6
|
1.0
|
C4'
|
A:DI3
|
3.9
|
11.5
|
1.0
|
O
|
A:HOH58
|
4.0
|
60.9
|
1.0
|
O
|
A:HOH57
|
4.1
|
80.5
|
1.0
|
C1'
|
A:DI3
|
4.2
|
10.8
|
1.0
|
O4'
|
A:DC4
|
4.3
|
10.3
|
1.0
|
C3'
|
A:DC4
|
4.3
|
10.3
|
1.0
|
O
|
A:HOH70
|
4.4
|
73.9
|
1.0
|
O
|
A:HOH18
|
4.6
|
20.3
|
1.0
|
O4'
|
A:DI3
|
4.6
|
11.4
|
1.0
|
C2'
|
A:DC4
|
4.8
|
10.2
|
1.0
|
O
|
A:HOH33
|
4.8
|
21.7
|
1.0
|
O
|
A:HOH46
|
5.0
|
70.8
|
1.0
|
C5'
|
A:DI3
|
5.0
|
11.8
|
1.0
|
|
Phosphorus binding site 4 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 4 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:10.7
occ:1.00
|
P
|
A:DI5
|
0.0
|
10.7
|
1.0
|
OP2
|
A:DI5
|
1.5
|
10.7
|
1.0
|
OP1
|
A:DI5
|
1.5
|
11.0
|
1.0
|
O5'
|
A:DI5
|
1.6
|
10.2
|
1.0
|
O3'
|
A:DC4
|
1.6
|
10.6
|
1.0
|
C3'
|
A:DC4
|
2.6
|
10.3
|
1.0
|
C5'
|
A:DI5
|
2.7
|
9.7
|
1.0
|
C4'
|
A:DC4
|
3.5
|
10.6
|
1.0
|
C2'
|
A:DC4
|
3.8
|
10.2
|
1.0
|
O
|
A:HOH15
|
3.8
|
14.0
|
1.0
|
O
|
A:HOH26
|
3.8
|
38.1
|
1.0
|
O
|
A:HOH18
|
3.8
|
20.3
|
1.0
|
C4'
|
A:DI5
|
3.8
|
9.5
|
1.0
|
C8
|
A:DI5
|
3.9
|
8.6
|
1.0
|
O
|
A:HOH12
|
4.0
|
17.0
|
1.0
|
O4'
|
A:DI5
|
4.0
|
9.3
|
1.0
|
C5'
|
A:DC4
|
4.3
|
11.1
|
1.0
|
C3'
|
A:DI5
|
4.4
|
9.4
|
1.0
|
C1'
|
A:DC4
|
4.5
|
9.8
|
1.0
|
N7
|
A:DI5
|
4.6
|
8.6
|
1.0
|
C2'
|
A:DI5
|
4.6
|
9.2
|
1.0
|
N9
|
A:DI5
|
4.6
|
8.8
|
1.0
|
O4'
|
A:DC4
|
4.6
|
10.3
|
1.0
|
C1'
|
A:DI5
|
4.7
|
9.1
|
1.0
|
O5'
|
A:DC4
|
4.9
|
11.8
|
1.0
|
|
Phosphorus binding site 5 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 5 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:9.5
occ:1.00
|
P
|
A:DC6
|
0.0
|
9.5
|
1.0
|
OP1
|
A:DC6
|
1.5
|
9.6
|
1.0
|
OP2
|
A:DC6
|
1.5
|
9.6
|
1.0
|
O3'
|
A:DI5
|
1.6
|
9.3
|
1.0
|
O5'
|
A:DC6
|
1.6
|
9.4
|
1.0
|
C3'
|
A:DI5
|
2.6
|
9.4
|
1.0
|
C5'
|
A:DC6
|
2.6
|
9.2
|
1.0
|
C2'
|
A:DI5
|
3.2
|
9.2
|
1.0
|
MG
|
A:MG10
|
3.4
|
9.2
|
1.0
|
O
|
A:HOH28
|
3.7
|
26.4
|
1.0
|
O
|
A:HOH44
|
3.8
|
65.5
|
1.0
|
C4'
|
A:DI5
|
3.9
|
9.5
|
1.0
|
C4'
|
A:DC6
|
3.9
|
9.0
|
1.0
|
O
|
A:HOH19
|
3.9
|
8.8
|
1.0
|
O
|
A:HOH20
|
4.0
|
10.9
|
1.0
|
O
|
A:HOH32
|
4.1
|
48.2
|
1.0
|
O
|
A:HOH11
|
4.1
|
8.0
|
1.0
|
O4'
|
A:DC6
|
4.2
|
8.6
|
1.0
|
C1'
|
A:DI5
|
4.3
|
9.1
|
1.0
|
C3'
|
A:DC6
|
4.4
|
9.3
|
1.0
|
O4'
|
A:DI5
|
4.6
|
9.3
|
1.0
|
C5'
|
A:DI5
|
5.0
|
9.7
|
1.0
|
|
Phosphorus binding site 6 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 6 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:11.2
occ:1.00
|
P
|
A:DI7
|
0.0
|
11.2
|
1.0
|
OP2
|
A:DI7
|
1.5
|
12.2
|
1.0
|
OP1
|
A:DI7
|
1.5
|
12.2
|
1.0
|
O5'
|
A:DI7
|
1.6
|
11.1
|
1.0
|
O3'
|
A:DC6
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DI7
|
2.6
|
10.3
|
1.0
|
C3'
|
A:DC6
|
2.7
|
9.3
|
1.0
|
C2'
|
A:DC6
|
3.3
|
9.0
|
1.0
|
O
|
A:HOH74
|
3.5
|
67.1
|
1.0
|
O
|
A:HOH23
|
3.8
|
37.4
|
1.0
|
C4'
|
A:DC6
|
3.9
|
9.0
|
1.0
|
C4'
|
A:DI7
|
3.9
|
10.0
|
1.0
|
O
|
A:HOH35
|
4.0
|
47.1
|
1.0
|
O4'
|
A:DI7
|
4.2
|
9.5
|
1.0
|
C1'
|
A:DC6
|
4.4
|
8.6
|
1.0
|
O
|
A:HOH61
|
4.5
|
75.8
|
1.0
|
C3'
|
A:DI7
|
4.5
|
10.1
|
1.0
|
O
|
A:HOH44
|
4.6
|
65.5
|
1.0
|
O
|
A:HOH30
|
4.6
|
51.6
|
1.0
|
C5'
|
A:DC6
|
4.7
|
9.2
|
1.0
|
O4'
|
A:DC6
|
4.8
|
8.6
|
1.0
|
C2'
|
A:DI7
|
4.9
|
9.7
|
1.0
|
|
Phosphorus binding site 7 out
of 7 in 159d
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Phosphorus Binding Sites List in 159d
Phosphorus binding site 7 out
of 7 in the Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Side By Side Binding of Two Distamycin A Drugs in the Minor Groove of An Alternating B-Dna Duplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:11.4
occ:1.00
|
P
|
A:DC8
|
0.0
|
11.4
|
1.0
|
OP2
|
A:DC8
|
1.5
|
11.7
|
1.0
|
OP1
|
A:DC8
|
1.5
|
11.9
|
1.0
|
O5'
|
A:DC8
|
1.6
|
10.8
|
1.0
|
O3'
|
A:DI7
|
1.6
|
10.7
|
1.0
|
C3'
|
A:DI7
|
2.6
|
10.1
|
1.0
|
C5'
|
A:DC8
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DI7
|
3.2
|
9.7
|
1.0
|
O
|
A:HOH36
|
3.6
|
58.0
|
1.0
|
O
|
A:HOH37
|
3.6
|
27.7
|
1.0
|
C4'
|
A:DI7
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DC8
|
3.9
|
9.5
|
1.0
|
O
|
A:HOH55
|
4.0
|
51.4
|
1.0
|
O
|
A:HOH54
|
4.2
|
47.5
|
1.0
|
C1'
|
A:DI7
|
4.3
|
9.3
|
1.0
|
O4'
|
A:DC8
|
4.3
|
9.0
|
1.0
|
C3'
|
A:DC8
|
4.4
|
9.2
|
1.0
|
O4'
|
A:DI7
|
4.7
|
9.5
|
1.0
|
C5'
|
A:DI7
|
4.8
|
10.3
|
1.0
|
C2'
|
A:DC8
|
4.8
|
8.9
|
1.0
|
|
Reference:
X.Chen,
B.Ramakrishnan,
S.T.Rao,
M.Sundaralingam.
Binding of Two Distamycin A Molecules in the Minor Groove of An Alternating B-Dna Duplex. Nat.Struct.Biol. V. 1 169 1994.
ISSN: ISSN 1072-8368
PubMed: 7656035
DOI: 10.1038/NSB0394-169
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