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 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 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 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 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 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 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 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
Page generated: Fri Sep 25 11:35:12 2020

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