Phosphorus in PDB 152d: 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: 152d 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 (°) 27.850, 27.850, 52.330, 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 152d). 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: 152d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5;

Phosphorus binding site 1 out of 5 in 152d

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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:6.7
occ:1.00
P A:DG2 0.0 6.7 1.0
OP2 A:DG2 1.4 7.2 1.0
OP1 A:DG2 1.5 7.0 1.0
O3' A:DC1 1.6 5.2 1.0
O5' A:DG2 1.6 6.8 1.0
C3' A:DC1 2.6 5.7 1.0
C5' A:DG2 2.6 6.9 1.0
C4' A:DC1 3.7 5.8 1.0
C2' A:DC1 3.7 5.8 1.0
O A:HOH31 3.8 24.1 1.0
O A:HOH34 3.9 28.3 1.0
O A:HOH9 3.9 8.6 1.0
C4' A:DG2 3.9 7.3 1.0
O4' A:DG2 4.3 6.6 1.0
C3' A:DG2 4.3 8.1 1.0
C1' A:DC1 4.5 5.3 1.0
O A:HOH50 4.6 27.5 1.0
O4' A:DC1 4.7 5.8 1.0
C5' A:DC1 4.7 6.0 1.0
C2' A:DG2 4.7 7.0 1.0
O A:HOH8 5.0 8.2 1.0

Phosphorus binding site 2 out of 5 in 152d

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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:13.4
occ:1.00
P A:DA3 0.0 13.4 1.0
OP1 A:DA3 1.4 12.1 1.0
OP2 A:DA3 1.5 13.2 1.0
O3' A:DG2 1.6 10.4 1.0
O5' A:DA3 1.6 10.6 1.0
C5' A:DA3 2.5 8.7 1.0
C3' A:DG2 2.7 8.1 1.0
O A:HOH30 3.4 27.4 1.0
O A:HOH24 3.4 20.0 1.0
C2' A:DG2 3.6 7.0 1.0
C4' A:DA3 3.7 6.9 1.0
C4' A:DG2 3.8 7.3 1.0
O4' A:DA3 3.8 5.2 1.0
O A:HOH35 3.9 21.0 1.0
O A:HOH29 4.0 32.7 1.0
C8 A:DA3 4.2 4.2 1.0
C3' A:DA3 4.3 7.6 1.0
C1' A:DG2 4.4 6.6 1.0
C2' A:DA3 4.6 6.9 1.0
O A:HOH60 4.6 45.8 1.0
O4' A:DG2 4.7 6.6 1.0
C1' A:DA3 4.8 6.0 1.0
N9 A:DA3 4.9 5.0 1.0
C5' A:DG2 4.9 6.9 1.0

Phosphorus binding site 3 out of 5 in 152d

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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:10.7
occ:1.00
P A:DT4 0.0 10.7 1.0
OP2 A:DT4 1.4 11.2 1.0
OP1 A:DT4 1.4 11.2 1.0
O3' A:DA3 1.6 8.4 1.0
O5' A:DT4 1.7 9.0 1.0
C5' A:DT4 2.6 8.2 1.0
C3' A:DA3 2.7 7.6 1.0
O A:HOH38 3.3 18.7 1.0
C2' A:DA3 3.3 6.9 1.0
C4' A:DT4 3.9 6.9 1.0
C4' A:DA3 3.9 6.9 1.0
O A:HOH14 4.0 19.9 1.0
C1' A:DA3 4.3 6.0 1.0
C3' A:DT4 4.3 7.4 1.0
O4' A:DT4 4.4 6.4 1.0
O4' A:DA3 4.8 5.2 1.0
O A:HOH26 4.9 19.7 1.0
C2' A:DT4 5.0 6.4 1.0

Phosphorus binding site 4 out of 5 in 152d

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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:9.2
occ:1.00
P A:DC5 0.0 9.2 1.0
OP2 A:DC5 1.4 9.2 1.0
OP1 A:DC5 1.4 9.9 1.0
O3' A:DT4 1.6 8.0 1.0
O5' A:DC5 1.7 8.8 1.0
C3' A:DT4 2.6 7.4 1.0
C5' A:DC5 2.6 7.4 1.0
C2' A:DT4 3.3 6.4 1.0
O A:HOH16 3.9 17.0 1.0
C4' A:DC5 3.9 7.7 1.0
C4' A:DT4 3.9 6.9 1.0
O A:HOH26 4.0 19.7 1.0
O4' A:DC5 4.3 7.2 1.0
C3' A:DC5 4.4 8.0 1.0
C1' A:DT4 4.4 6.4 1.0
C2' A:DC5 4.7 7.6 1.0
O A:HOH43 4.8 20.9 1.0
O A:HOH51 4.8 38.7 1.0
O A:HOH36 4.8 40.3 1.0
O4' A:DT4 4.8 6.4 1.0
C5' A:DT4 5.0 8.2 1.0

Phosphorus binding site 5 out of 5 in 152d

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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:9.8
occ:1.00
P A:DG6 0.0 9.8 1.0
OP1 A:DG6 1.4 10.7 1.0
OP2 A:DG6 1.5 9.4 1.0
O3' A:DC5 1.6 8.7 1.0
O5' A:DG6 1.6 8.2 1.0
C5' A:DG6 2.6 7.3 1.0
C3' A:DC5 2.6 8.0 1.0
C4' A:DC5 3.5 7.7 1.0
O A:HOH18 3.7 14.9 1.0
C2' A:DC5 3.8 7.6 1.0
O A:HOH36 3.9 40.3 1.0
O A:HOH33 3.9 35.4 1.0
C4' A:DG6 3.9 6.7 1.0
C8 A:DG6 4.1 5.9 1.0
O A:HOH28 4.2 38.9 1.0
O4' A:DG6 4.4 5.8 1.0
C2' A:DG6 4.4 5.5 1.0
C5' A:DC5 4.4 7.4 1.0
C3' A:DG6 4.5 5.9 1.0
C1' A:DC5 4.6 7.4 1.0
O4' A:DC5 4.7 7.2 1.0
N9 A:DG6 4.8 5.6 1.0
C1' A:DG6 4.8 5.4 1.0
O5' A:DC5 4.8 8.8 1.0
N7 A:DG6 4.9 6.5 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 11:32:23 2020

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