Phosphorus in PDB 187d: Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition

Protein crystallography data

The structure of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d was solved by M.Eisenstein, Z.Shakked, 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 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.360, 43.360, 24.830, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition (pdb code 187d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7;

Phosphorus binding site 1 out of 7 in 187d

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Phosphorus binding site 1 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:25.4
occ:1.00
P A:DC2 0.0 25.4 1.0
OP1 A:DC2 1.5 27.5 1.0
OP2 A:DC2 1.5 24.9 1.0
O5' A:DC2 1.6 23.4 1.0
O3' A:DC1 1.6 24.8 1.0
C5' A:DC2 2.6 23.5 1.0
C3' A:DC1 2.6 24.4 1.0
C2' A:DC1 3.6 24.3 1.0
C4' A:DC2 3.8 25.1 1.0
C4' A:DC1 3.8 23.5 1.0
O A:HOH23 3.9 18.2 1.0
O4' A:DC2 4.0 25.4 1.0
C6 A:DC2 4.3 24.1 1.0
C5' A:DC1 4.3 23.2 1.0
C3' A:DC2 4.4 25.3 1.0
O A:HOH22 4.9 18.6 1.0
O A:HOH24 4.9 67.5 1.0
O A:HOH29 4.9 52.9 1.0
C1' A:DC1 4.9 23.3 1.0
O5' A:DC1 4.9 23.6 1.0
O4' A:DC1 5.0 22.8 1.0
C5 A:DC2 5.0 23.6 1.0

Phosphorus binding site 2 out of 7 in 187d

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Phosphorus binding site 2 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:26.1
occ:1.00
P A:DC3 0.0 26.1 1.0
OP2 A:DC3 1.5 25.8 1.0
OP1 A:DC3 1.5 26.8 1.0
O3' A:DC2 1.6 26.0 1.0
O5' A:DC3 1.6 25.7 1.0
C5' A:DC3 2.6 24.9 1.0
C3' A:DC2 2.6 25.3 1.0
C2' A:DC2 3.4 24.1 1.0
C4' A:DC3 3.8 23.4 1.0
C4' A:DC2 4.0 25.1 1.0
O A:HOH30 4.0 46.7 1.0
O4' A:DC3 4.1 23.1 1.0
C3' A:DC3 4.4 22.2 1.0
C6 A:DC3 4.4 17.9 1.0
C5' A:DC2 4.6 23.5 1.0
O5' A:DC2 4.7 23.4 1.0
C1' A:DC2 4.7 24.5 1.0
O4' A:DC2 5.0 25.4 1.0

Phosphorus binding site 3 out of 7 in 187d

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Phosphorus binding site 3 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:24.1
occ:1.00
P A:DC4 0.0 24.1 1.0
OP1 A:DC4 1.5 24.9 1.0
OP2 A:DC4 1.5 25.6 1.0
O3' A:DC3 1.6 23.1 1.0
O5' A:DC4 1.6 21.8 1.0
C5' A:DC4 2.6 19.2 1.0
C3' A:DC3 2.7 22.2 1.0
C2' A:DC3 3.4 21.8 1.0
C4' A:DC3 3.9 23.4 1.0
C4' A:DC4 4.0 17.8 1.0
O A:HOH45 4.0 61.1 1.0
O A:HOH46 4.0 98.3 1.0
O A:HOH14 4.2 41.1 1.0
O4' A:DC4 4.4 16.6 1.0
C3' A:DC4 4.6 17.9 1.0
C5' A:DC3 4.6 24.9 1.0
C6 A:DC4 4.7 13.6 1.0
C1' A:DC3 4.8 20.8 1.0
O5' A:DC3 5.0 25.7 1.0

Phosphorus binding site 4 out of 7 in 187d

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Phosphorus binding site 4 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:19.4
occ:1.00
P A:DG5 0.0 19.4 1.0
OP1 A:DG5 1.5 21.1 1.0
OP2 A:DG5 1.5 19.2 1.0
O5' A:DG5 1.6 19.9 1.0
O3' A:DC4 1.6 19.8 1.0
C3' A:DC4 2.5 17.9 1.0
C5' A:DG5 2.6 20.3 1.0
C2' A:DC4 3.3 17.3 1.0
O A:HOH21 3.5 44.1 1.0
O A:HOH32 3.8 81.0 1.0
C4' A:DC4 3.9 17.8 1.0
C4' A:DG5 3.9 20.2 1.0
O4' A:DG5 4.3 20.6 1.0
O A:HOH45 4.4 61.1 1.0
C5' A:DC4 4.4 19.2 1.0
O A:HOH40 4.5 77.7 1.0
C1' A:DC4 4.7 14.8 1.0
O5' A:DC4 4.8 21.8 1.0
O4' A:DC4 4.9 16.6 1.0

Phosphorus binding site 5 out of 7 in 187d

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Phosphorus binding site 5 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:22.6
occ:1.00
P A:DG6 0.0 22.6 1.0
OP2 A:DG6 1.5 21.8 1.0
OP1 A:DG6 1.5 20.9 1.0
O3' A:DG5 1.6 21.4 1.0
O5' A:DG6 1.6 21.7 1.0
C5' A:DG6 2.7 20.0 1.0
C3' A:DG5 2.7 19.9 1.0
C2' A:DG5 3.5 18.2 1.0
O A:HOH42 3.6 68.0 1.0
C4' A:DG6 3.9 20.9 1.0
O A:HOH25 3.9 61.6 1.0
C4' A:DG5 4.0 20.2 1.0
O A:HOH13 4.0 71.7 1.0
O4' A:DG6 4.1 18.4 1.0
O A:HOH16 4.1 51.6 1.0
C8 A:DG6 4.2 13.5 1.0
C3' A:DG6 4.6 23.2 1.0
O A:HOH15 4.6 52.6 1.0
C5' A:DG5 4.7 20.3 1.0
C1' A:DG5 4.8 15.2 1.0
OP2 A:DG7 4.9 29.7 1.0

Phosphorus binding site 6 out of 7 in 187d

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Phosphorus binding site 6 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:29.1
occ:1.00
P A:DG7 0.0 29.1 1.0
OP2 A:DG7 1.5 29.7 1.0
OP1 A:DG7 1.5 31.0 1.0
O3' A:DG6 1.6 27.1 1.0
O5' A:DG7 1.6 27.0 1.0
C3' A:DG6 2.6 23.2 1.0
C5' A:DG7 2.6 21.9 1.0
C2' A:DG6 3.5 20.4 1.0
C4' A:DG6 3.8 20.9 1.0
C4' A:DG7 3.9 19.8 1.0
O4' A:DG7 4.0 17.2 1.0
O A:HOH16 4.3 51.6 1.0
C5' A:DG6 4.3 20.0 1.0
C1' A:DG6 4.7 17.3 1.0
C3' A:DG7 4.7 20.2 1.0
O5' A:DG6 4.8 21.7 1.0
O A:HOH13 4.9 71.7 1.0
O4' A:DG6 4.9 18.4 1.0
C8 A:DG7 4.9 16.2 1.0

Phosphorus binding site 7 out of 7 in 187d

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Phosphorus binding site 7 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:24.9
occ:1.00
P A:DG8 0.0 24.9 1.0
OP1 A:DG8 1.5 24.7 1.0
OP2 A:DG8 1.5 24.3 1.0
O5' A:DG8 1.6 25.7 1.0
O3' A:DG7 1.6 22.7 1.0
C3' A:DG7 2.6 20.2 1.0
C5' A:DG8 2.7 27.6 1.0
C2' A:DG7 3.2 19.0 1.0
C4' A:DG8 3.9 28.7 1.0
C4' A:DG7 3.9 19.8 1.0
O4' A:DG8 4.3 27.7 1.0
C3' A:DG8 4.3 29.4 1.0
C8 A:DG8 4.4 23.3 1.0
C1' A:DG7 4.6 17.0 1.0
C2' A:DG8 4.6 27.5 1.0
C5' A:DG7 4.6 21.9 1.0
O4' A:DG7 4.9 17.2 1.0
C1' A:DG8 5.0 26.1 1.0

Reference:

M.Eisenstein, Z.Shakked. Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition. J.Mol.Biol. V. 248 662 1995.
ISSN: ISSN 0022-2836
PubMed: 7752232
DOI: 10.1006/JMBI.1995.0250
Page generated: Fri Sep 25 11:48:02 2020

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