Phosphorus in PDB 114d: Inosine-Adenine Base Pairs in A B-Dna Duplex

Protein crystallography data

The structure of Inosine-Adenine Base Pairs in A B-Dna Duplex, PDB code: 114d was solved by P.W.R.Corfield, W.N.Hunter, T.Brown, P.Robinson, O.Kennard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.850, 41.990, 65.100, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Inosine-Adenine Base Pairs in A B-Dna Duplex (pdb code 114d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Inosine-Adenine Base Pairs in A B-Dna Duplex, PDB code: 114d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 114d

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Phosphorus binding site 1 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:10.0
occ:1.00
P A:DG2 0.0 10.0 1.0
OP2 A:DG2 1.5 10.0 1.0
OP1 A:DG2 1.5 10.0 1.0
O5' A:DG2 1.6 10.0 1.0
O3' A:DC1 1.6 10.0 1.0
C5' A:DG2 2.7 10.0 1.0
C3' A:DC1 2.7 10.0 1.0
C2' A:DC1 3.6 10.0 1.0
O A:HOH27 3.8 10.0 1.0
C4' A:DG2 3.9 10.0 1.0
C4' A:DC1 3.9 10.0 1.0
C2' A:DG2 4.3 10.0 1.0
C3' A:DG2 4.3 10.0 1.0
C1' A:DC1 4.4 10.0 1.0
O4' A:DG2 4.5 10.0 1.0
O4' A:DC1 4.8 10.0 1.0
O5' A:DC1 4.9 10.0 1.0
C8 A:DG2 4.9 10.0 1.0
C5' A:DC1 4.9 10.0 1.0
O A:HOH62 4.9 10.0 1.0
C1' A:DG2 5.0 10.0 1.0

Phosphorus binding site 2 out of 22 in 114d

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Phosphorus binding site 2 out of 22 in the Inosine-Adenine Base Pairs in A B-Dna Duplex


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:10.0
occ:1.00
P A:DC3 0.0 10.0 1.0
OP2 A:DC3 1.5 10.0 1.0
OP1 A:DC3 1.5 10.0 1.0
O3' A:DG2 1.6 10.0 1.0
O5' A:DC3 1.6 10.0 1.0
C3' A:DG2 2.6 10.0 1.0
C5' A:DC3 2.6 10.0 1.0
C2' A:DG2 3.3 10.0 1.0
C4' A:DC3 3.8 10.0 1.0
O4' A:DC3 3.8 10.0 1.0
C4' A:DG2 4.0 10.0 1.0
O A:HOH72 4.0 10.0 1.0
C1' A:DG2 4.1 10.0 1.0
O A:HOH74 4.2 10.0 1.0
O4' A:DG2 4.6 10.0 1.0
C6 A:DC3 4.6 10.0 1.0
C3' A:DC3 4.7 10.0 1.0

Phosphorus binding site 3 out of 22 in 114d

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Phosphorus binding site 3 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:10.0
occ:1.00
P A:DI4 0.0 10.0 1.0
OP2 A:DI4 1.5 10.0 1.0
OP1 A:DI4 1.5 10.0 1.0
O5' A:DI4 1.6 10.0 1.0
O3' A:DC3 1.6 10.0 1.0
C3' A:DC3 2.6 10.0 1.0
C5' A:DI4 2.7 10.0 1.0
O4' A:DI4 3.4 10.0 1.0
C2' A:DC3 3.4 10.0 1.0
C4' A:DI4 3.6 10.0 1.0
C8 A:DI4 3.8 10.0 1.0
C4' A:DC3 3.9 10.0 1.0
C2' A:DI4 4.2 10.0 1.0
O A:HOH37 4.3 10.0 1.0
C1' A:DI4 4.3 10.0 1.0
C3' A:DI4 4.3 10.0 1.0
N9 A:DI4 4.4 10.0 1.0
O A:HOH84 4.4 10.0 1.0
C5' A:DC3 4.5 10.0 1.0
N7 A:DI4 4.8 10.0 1.0
C1' A:DC3 4.8 10.0 1.0
O4' A:DC3 5.0 10.0 1.0

Phosphorus binding site 4 out of 22 in 114d

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Phosphorus binding site 4 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:10.0
occ:1.00
P A:DA5 0.0 10.0 1.0
OP2 A:DA5 1.5 10.0 1.0
OP1 A:DA5 1.5 10.0 1.0
O3' A:DI4 1.6 10.0 1.0
O5' A:DA5 1.6 10.0 1.0
C5' A:DA5 2.6 10.0 1.0
C3' A:DI4 2.6 10.0 1.0
C2' A:DI4 3.1 10.0 1.0
C4' A:DA5 3.7 10.0 1.0
O A:HOH64 3.8 10.0 1.0
C3' A:DA5 3.9 10.0 1.0
C1' A:DI4 3.9 10.0 1.0
C4' A:DI4 3.9 10.0 1.0
C2' A:DA5 4.1 10.0 1.0
O A:HOH51 4.2 10.0 1.0
O4' A:DI4 4.6 10.0 1.0
O4' A:DA5 4.6 10.0 1.0
C8 A:DA5 4.7 10.0 1.0
C1' A:DA5 4.9 10.0 1.0

Phosphorus binding site 5 out of 22 in 114d

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Phosphorus binding site 5 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:10.0
occ:1.00
P A:DA6 0.0 10.0 1.0
OP2 A:DA6 1.5 10.0 1.0
OP1 A:DA6 1.5 10.0 1.0
O3' A:DA5 1.6 10.0 1.0
O5' A:DA6 1.6 10.0 1.0
C5' A:DA6 2.6 10.0 1.0
C3' A:DA5 2.7 10.0 1.0
C2' A:DA5 3.1 10.0 1.0
C1' A:DA5 3.8 10.0 1.0
C4' A:DA6 3.9 10.0 1.0
C4' A:DA5 3.9 10.0 1.0
C3' A:DA6 4.3 10.0 1.0
O4' A:DA5 4.3 10.0 1.0
O4' A:DA6 4.4 10.0 1.0
C2' A:DA6 4.6 10.0 1.0

Phosphorus binding site 6 out of 22 in 114d

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Phosphorus binding site 6 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:10.0
occ:1.00
P A:DT7 0.0 10.0 1.0
OP1 A:DT7 1.5 10.0 1.0
OP2 A:DT7 1.5 10.0 1.0
O3' A:DA6 1.6 10.0 1.0
O5' A:DT7 1.6 10.0 1.0
C5' A:DT7 2.6 10.0 1.0
C3' A:DA6 2.7 10.0 1.0
C2' A:DA6 3.2 10.0 1.0
O A:HOH80 3.7 10.0 1.0
C4' A:DT7 3.9 10.0 1.0
C4' A:DA6 3.9 10.0 1.0
C1' A:DA6 4.0 10.0 1.0
C3' A:DT7 4.3 10.0 1.0
O4' A:DT7 4.4 10.0 1.0
O4' A:DA6 4.5 10.0 1.0
O A:HOH25 4.9 10.0 1.0

Phosphorus binding site 7 out of 22 in 114d

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Phosphorus binding site 7 out of 22 in the Inosine-Adenine Base Pairs in A 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 Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:10.0
occ:1.00
P A:DT8 0.0 10.0 1.0
OP2 A:DT8 1.5 10.0 1.0
OP1 A:DT8 1.5 10.0 1.0
O3' A:DT7 1.6 10.0 1.0
O5' A:DT8 1.6 10.0 1.0
C5' A:DT8 2.6 10.0 1.0
C3' A:DT7 2.7 10.0 1.0
C2' A:DT7 3.3 10.0 1.0
C4' A:DT7 3.4 10.0 1.0
O A:HOH61 3.6 10.0 1.0
C4' A:DT8 4.0 10.0 1.0
O A:HOH57 4.0 10.0 1.0
C1' A:DT7 4.3 10.0 1.0
O4' A:DT8 4.4 10.0 1.0
C5' A:DT7 4.5 10.0 1.0
O4' A:DT7 4.5 10.0 1.0
C3' A:DT8 4.6 10.0 1.0

Phosphorus binding site 8 out of 22 in 114d

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Phosphorus binding site 8 out of 22 in the Inosine-Adenine Base Pairs in A B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:10.0
occ:1.00
P A:DA9 0.0 10.0 1.0
OP1 A:DA9 1.5 10.0 1.0
OP2 A:DA9 1.5 10.0 1.0
O3' A:DT8 1.6 10.0 1.0
O5' A:DA9 1.6 10.0 1.0
C5' A:DA9 2.7 10.0 1.0
C3' A:DT8 2.8 10.0 1.0
C2' A:DT8 3.3 10.0 1.0
C4' A:DT8 3.5 10.0 1.0
C4' A:DA9 3.9 10.0 1.0
O A:HOH39 4.1 10.0 1.0
C3' A:DA9 4.3 10.0 1.0
C5' A:DT8 4.4 10.0 1.0
O4' A:DA9 4.4 10.0 1.0
C1' A:DT8 4.5 10.0 1.0
O4' A:DT8 4.6 10.0 1.0
N3 A:DA9 4.6 10.0 1.0
C2' A:DA9 4.9 10.0 1.0

Phosphorus binding site 9 out of 22 in 114d

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Phosphorus binding site 9 out of 22 in the Inosine-Adenine Base Pairs in A B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:10.0
occ:1.00
P A:DG10 0.0 10.0 1.0
OP2 A:DG10 1.5 10.0 1.0
OP1 A:DG10 1.5 10.0 1.0
O3' A:DA9 1.6 10.0 1.0
O5' A:DG10 1.6 10.0 1.0
C3' A:DA9 2.6 10.0 1.0
C5' A:DG10 2.6 10.0 1.0
C2' A:DA9 3.3 10.0 1.0
O A:HOH31 3.9 10.0 1.0
C4' A:DA9 3.9 10.0 1.0
C4' A:DG10 3.9 10.0 1.0
O A:HOH66 4.0 10.0 1.0
O A:HOH78 4.2 10.0 1.0
C1' A:DA9 4.3 10.0 1.0
O4' A:DG10 4.3 10.0 1.0
C2' A:DG10 4.4 10.0 1.0
C3' A:DG10 4.4 10.0 1.0
O4' A:DA9 4.8 10.0 1.0
C5' A:DA9 4.9 10.0 1.0
C1' A:DG10 5.0 10.0 1.0

Phosphorus binding site 10 out of 22 in 114d

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Phosphorus binding site 10 out of 22 in the Inosine-Adenine Base Pairs in A B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Inosine-Adenine Base Pairs in A B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:10.0
occ:1.00
P A:DC11 0.0 10.0 1.0
OP2 A:DC11 1.5 10.0 1.0
OP1 A:DC11 1.5 10.0 1.0
O3' A:DG10 1.6 10.0 1.0
O5' A:DC11 1.6 10.0 1.0
C5' A:DC11 2.6 10.0 1.0
C3' A:DG10 2.7 10.0 1.0
O A:HOH63 3.4 10.0 1.0
C4' A:DG10 3.6 10.0 1.0
O A:HOH77 3.8 10.0 1.0
C4' A:DC11 3.9 10.0 1.0
C2' A:DG10 4.0 10.0 1.0
C6 A:DC11 4.2 10.0 1.0
C1' A:DG10 4.4 10.0 1.0
C3' A:DC11 4.5 10.0 1.0
O4' A:DG10 4.5 10.0 1.0
C5' A:DG10 4.7 10.0 1.0
O4' A:DC11 4.8 10.0 1.0
C5 A:DC11 4.8 10.0 1.0
C2' A:DC11 4.9 10.0 1.0

Reference:

P.W.Corfield, W.N.Hunter, T.Brown, P.Robinson, O.Kennard. Inosine.Adenine Base Pairs in A B-Dna Duplex. Nucleic Acids Res. V. 15 7935 1987.
ISSN: ISSN 0305-1048
PubMed: 3671069
DOI: 10.1093/NAR/15.19.7935
Page generated: Fri Sep 25 11:09:55 2020

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