Phosphorus in PDB 111d: Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs

Protein crystallography data

The structure of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs, PDB code: 111d was solved by T.Brown, G.A.Leonard, E.D.Booth, J.Chambers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.230, 41.160, 65.010, 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 Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs (pdb code 111d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs, PDB code: 111d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 111d

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Phosphorus binding site 1 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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 2.6 10.0 1.0
C3' A:DC1 2.6 10.0 1.0
C2' A:DC1 3.3 10.0 1.0
C4' A:DG2 3.8 10.0 1.0
O A:HOH51 3.9 10.0 1.0
C4' A:DC1 3.9 10.0 1.0
C1' A:DC1 4.0 10.0 1.0
C3' A:DG2 4.1 10.0 1.0
C2' A:DG2 4.3 10.0 1.0
O4' A:DG2 4.4 10.0 1.0
C8 A:DG2 4.6 10.0 1.0
O4' A:DC1 4.6 10.0 1.0
C1' A:DG2 4.8 10.0 1.0

Phosphorus binding site 2 out of 22 in 111d

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Phosphorus binding site 2 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
O5' A:DC3 1.6 10.0 1.0
O3' A:DG2 1.6 10.0 1.0
C5' A:DC3 2.7 10.0 1.0
C3' A:DG2 2.7 10.0 1.0
C2' A:DG2 3.3 10.0 1.0
O A:HOH28 3.3 10.0 1.0
C4' A:DC3 3.9 10.0 1.0
O4' A:DC3 4.0 10.0 1.0
C4' A:DG2 4.0 10.0 1.0
C1' A:DG2 4.2 10.0 1.0
C3' A:DC3 4.5 10.0 1.0
O4' A:DG2 4.7 10.0 1.0
C6 A:DC3 4.8 10.0 1.0

Phosphorus binding site 3 out of 22 in 111d

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Phosphorus binding site 3 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:10.0
occ:1.00
P A:DA4 0.0 10.0 1.0
OP2 A:DA4 1.5 10.0 1.0
OP1 A:DA4 1.5 10.0 1.0
O3' A:DC3 1.6 10.0 1.0
O5' A:DA4 1.6 10.0 1.0
C5' A:DA4 2.6 10.0 1.0
C3' A:DC3 2.6 10.0 1.0
C2' A:DC3 3.2 10.0 1.0
C4' A:DA4 3.9 10.0 1.0
C4' A:DC3 4.0 10.0 1.0
C8 A:DA4 4.2 10.0 1.0
O A:HOH44 4.2 10.0 1.0
C2' A:DA4 4.2 10.0 1.0
O4' A:DA4 4.3 10.0 1.0
C3' A:DA4 4.4 10.0 1.0
C1' A:DC3 4.6 10.0 1.0
C5' A:DC3 4.7 10.0 1.0
C1' A:DA4 4.7 10.0 1.0
N9 A:DA4 4.8 10.0 1.0
O4' A:DC3 4.9 10.0 1.0

Phosphorus binding site 4 out of 22 in 111d

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Phosphorus binding site 4 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
O5' A:DA5 1.6 10.0 1.0
O3' A:DA4 1.6 10.0 1.0
C5' A:DA5 2.6 10.0 1.0
C3' A:DA4 2.6 10.0 1.0
C2' A:DA4 3.7 10.0 1.0
C4' A:DA5 3.7 10.0 1.0
C4' A:DA4 3.8 10.0 1.0
O4' A:DA5 3.9 10.0 1.0
C1' A:DA4 4.3 10.0 1.0
O4' A:DA4 4.5 10.0 1.0
C3' A:DA5 4.7 10.0 1.0
C8 A:DA5 4.9 10.0 1.0
C2' A:DA5 4.9 10.0 1.0
C5' A:DA4 5.0 10.0 1.0

Phosphorus binding site 5 out of 22 in 111d

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Phosphorus binding site 5 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
OP1 A:DA6 1.5 10.0 1.0
OP2 A:DA6 1.5 10.0 1.0
O5' A:DA6 1.6 10.0 1.0
O3' A:DA5 1.6 10.0 1.0
C3' A:DA5 2.6 10.0 1.0
C5' A:DA6 2.7 10.0 1.0
C2' A:DA5 3.5 10.0 1.0
C4' A:DA6 3.8 10.0 1.0
C4' A:DA5 3.9 10.0 1.0
O4' A:DA6 4.1 10.0 1.0
C1' A:DA5 4.1 10.0 1.0
C3' A:DA6 4.2 10.0 1.0
C2' A:DA6 4.5 10.0 1.0
O4' A:DA5 4.6 10.0 1.0
C5' A:DA5 4.9 10.0 1.0
C1' A:DA6 5.0 10.0 1.0
C8 A:DA6 5.0 10.0 1.0

Phosphorus binding site 6 out of 22 in 111d

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Phosphorus binding site 6 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
OP2 A:DT7 1.5 10.0 1.0
OP1 A:DT7 1.5 10.0 1.0
O5' A:DT7 1.6 10.0 1.0
O3' A:DA6 1.6 10.0 1.0
C3' A:DA6 2.6 10.0 1.0
C5' A:DT7 2.7 10.0 1.0
C2' A:DA6 3.3 10.0 1.0
C4' A:DT7 3.8 10.0 1.0
C4' A:DA6 3.9 10.0 1.0
O4' A:DT7 4.0 10.0 1.0
C1' A:DA6 4.2 10.0 1.0
C3' A:DT7 4.4 10.0 1.0
O4' A:DA6 4.7 10.0 1.0
C5' A:DA6 5.0 10.0 1.0

Phosphorus binding site 7 out of 22 in 111d

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Phosphorus binding site 7 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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 2.5 10.0 1.0
C3' A:DT7 2.7 10.0 1.0
C2' A:DT7 3.2 10.0 1.0
C4' A:DT8 3.8 10.0 1.0
C4' A:DT7 3.9 10.0 1.0
C3' A:DT8 4.2 10.0 1.0
O A:HOH67 4.3 10.0 1.0
C1' A:DT7 4.4 10.0 1.0
O4' A:DT8 4.4 10.0 1.0
C5' A:DT7 4.7 10.0 1.0
O A:HOH32 4.8 10.0 1.0
O4' A:DT7 4.8 10.0 1.0
C2' A:DT8 4.9 10.0 1.0
C6 A:DT8 4.9 10.0 1.0

Phosphorus binding site 8 out of 22 in 111d

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Phosphorus binding site 8 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:10.0
occ:1.00
P A:DG9 0.0 10.0 1.0
OP2 A:DG9 1.5 10.0 1.0
OP1 A:DG9 1.5 10.0 1.0
O3' A:DT8 1.6 10.0 1.0
O5' A:DG9 1.6 10.0 1.0
C5' A:DG9 2.6 10.0 1.0
C3' A:DT8 2.8 10.0 1.0
C2' A:DT8 3.5 10.0 1.0
C4' A:DG9 3.8 10.0 1.0
C4' A:DT8 3.9 10.0 1.0
C3' A:DG9 4.2 10.0 1.0
C1' A:DT8 4.4 10.0 1.0
O A:HOH32 4.7 10.0 1.0
C2' A:DG9 4.7 10.0 1.0
O4' A:DT8 4.8 10.0 1.0
O4' A:DG9 4.8 10.0 1.0
O A:HOH68 5.0 10.0 1.0
C5' A:DT8 5.0 10.0 1.0

Phosphorus binding site 9 out of 22 in 111d

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Phosphorus binding site 9 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
O5' A:DG10 1.6 10.0 1.0
O3' A:DG9 1.6 10.0 1.0
C5' A:DG10 2.6 10.0 1.0
C3' A:DG9 2.7 10.0 1.0
C2' A:DG9 3.6 10.0 1.0
C4' A:DG10 3.9 10.0 1.0
C4' A:DG9 3.9 10.0 1.0
C1' A:DG9 4.1 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:DG9 4.5 10.0 1.0
O A:HOH81 4.6 10.0 1.0
O5' A:DG9 5.0 10.0 1.0

Phosphorus binding site 10 out of 22 in 111d

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Phosphorus binding site 10 out of 22 in the Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs 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
O5' A:DC11 1.6 10.0 1.0
O3' A:DG10 1.6 10.0 1.0
C5' A:DC11 2.6 10.0 1.0
C3' A:DG10 2.6 10.0 1.0
O A:HOH31 3.4 10.0 1.0
C4' A:DC11 3.6 10.0 1.0
C4' A:DG10 3.7 10.0 1.0
O4' A:DC11 3.7 10.0 1.0
C2' A:DG10 3.8 10.0 1.0
C6 A:DC11 3.9 10.0 1.0
C3' A:DC11 4.2 10.0 1.0
C2' A:DC11 4.2 10.0 1.0
C1' A:DG10 4.3 10.0 1.0
C1' A:DC11 4.5 10.0 1.0
O4' A:DG10 4.5 10.0 1.0
O A:HOH79 4.6 10.0 1.0
N1 A:DC11 4.6 10.0 1.0
C5 A:DC11 4.7 10.0 1.0
C5' A:DG10 4.8 10.0 1.0

Reference:

T.Brown, G.A.Leonard, E.D.Booth, J.Chambers. Crystal Structure and Stability of A Dna Duplex Containing A(Anti).G(Syn) Base-Pairs. J.Mol.Biol. V. 207 455 1989.
ISSN: ISSN 0022-2836
PubMed: 2754734
DOI: 10.1016/0022-2836(89)90268-4
Page generated: Fri Sep 25 11:07:52 2020

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