Phosphorus in PDB 115d: Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution

Protein crystallography data

The structure of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution, PDB code: 115d was solved by O.Kennard, W.B.T.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 45.084, 45.084, 41.720, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Phosphorus atom in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution (pdb code 115d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution, PDB code: 115d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 115d

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Phosphorus binding site 1 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:17.8
occ:1.00
 P A:DG2 0.0 17.8 1.0
OP2 A:DG2 1.4 17.8 1.0
OP1 A:DG2 1.4 17.8 1.0
O3' A:DG1 1.6 16.2 1.0
O5' A:DG2 1.6 16.2 1.0
C3' A:DG1 2.6 16.2 1.0
C5' A:DG2 2.7 16.2 1.0
C2' A:DG1 3.5 16.2 1.0
O A:HOH70 3.8 33.4 1.0
C4' A:DG1 3.8 16.2 1.0
C4' A:DG2 3.9 16.2 1.0
O A:HOH35 4.0 33.4 1.0
O A:HOH39 4.1 33.4 1.0
O4' A:DG2 4.3 16.2 1.0
O5' A:DG1 4.4 16.2 1.0
C8 A:DG2 4.4 14.6 1.0
O A:HOH81 4.5 33.4 1.0
C5' A:DG1 4.5 16.2 1.0
C3' A:DG2 4.5 16.2 1.0
O A:HOH58 4.7 33.4 1.0
C1' A:DG1 4.8 16.2 1.0
O4' A:DG1 4.9 16.2 1.0

Phosphorus binding site 2 out of 14 in 115d

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Phosphorus binding site 2 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:17.8
occ:1.00
 P A:BRU3 0.0 17.8 1.0
OP2 A:BRU3 1.4 17.8 1.0
OP1 A:BRU3 1.4 17.8 1.0
O3' A:DG2 1.6 16.2 1.0
O5' A:BRU3 1.6 16.2 1.0
C3' A:DG2 2.6 16.2 1.0
C5' A:BRU3 2.7 16.2 1.0
C2' A:DG2 3.5 16.2 1.0
O A:HOH34 3.8 33.4 1.0
C4' A:DG2 3.9 16.2 1.0
C4' A:BRU3 4.0 16.2 1.0
O A:HOH70 4.4 33.4 1.0
O4' A:BRU3 4.4 16.2 1.0
C5' A:DG2 4.5 16.2 1.0
C6 A:BRU3 4.5 14.6 1.0
BR A:BRU3 4.6 14.6 1.0
C3' A:BRU3 4.6 16.2 1.0
O A:HOH81 4.6 33.4 1.0
O5' A:DG2 4.8 16.2 1.0
C1' A:DG2 4.8 16.2 1.0
O A:HOH92 4.8 33.4 1.0
O4' A:DG2 5.0 16.2 1.0

Phosphorus binding site 3 out of 14 in 115d

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Phosphorus binding site 3 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:17.8
occ:1.00
 P A:DA4 0.0 17.8 1.0
OP2 A:DA4 1.4 17.8 1.0
OP1 A:DA4 1.4 17.8 1.0
O3' A:BRU3 1.6 16.2 1.0
O5' A:DA4 1.7 16.2 1.0
C3' A:BRU3 2.6 16.2 1.0
C5' A:DA4 2.7 16.2 1.0
C2' A:BRU3 3.6 16.2 1.0
O A:HOH89 3.7 33.4 1.0
O A:HOH86 3.8 33.4 1.0
C4' A:BRU3 3.8 16.2 1.0
C4' A:DA4 4.0 16.2 1.0
O A:HOH34 4.2 33.4 1.0
O4' A:DA4 4.2 16.2 1.0
O A:HOH49 4.3 33.4 1.0
C5' A:BRU3 4.3 16.2 1.0
C8 A:DA4 4.5 14.6 1.0
C3' A:DA4 4.6 16.2 1.0
O5' A:BRU3 4.6 16.2 1.0
C1' A:BRU3 4.8 16.2 1.0
O4' A:BRU3 4.9 16.2 1.0

Phosphorus binding site 4 out of 14 in 115d

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Phosphorus binding site 4 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:17.8
occ:1.00
 P A:BRU5 0.0 17.8 1.0
OP2 A:BRU5 1.4 17.8 1.0
OP1 A:BRU5 1.4 17.8 1.0
O3' A:DA4 1.5 16.2 1.0
O5' A:BRU5 1.6 16.2 1.0
C3' A:DA4 2.6 16.2 1.0
C5' A:BRU5 2.7 16.2 1.0
C2' A:DA4 3.4 16.2 1.0
C4' A:DA4 3.8 16.2 1.0
O A:HOH49 3.9 33.4 1.0
O A:HOH100 4.0 33.4 1.0
O A:HOH56 4.0 33.4 1.0
C4' A:BRU5 4.0 16.2 1.0
O A:HOH82 4.1 33.4 1.0
O4' A:BRU5 4.3 16.2 1.0
C6 A:BRU5 4.4 14.6 1.0
C5' A:DA4 4.4 16.2 1.0
O A:HOH89 4.5 33.4 1.0
O A:HOH98 4.5 33.4 1.0
C3' A:BRU5 4.6 16.2 1.0
BR A:BRU5 4.6 14.6 1.0
C1' A:DA4 4.7 16.2 1.0
O5' A:DA4 4.8 16.2 1.0
O4' A:DA4 4.9 16.2 1.0

Phosphorus binding site 5 out of 14 in 115d

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Phosphorus binding site 5 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:17.8
occ:1.00
 P A:DA6 0.0 17.8 1.0
OP1 A:DA6 1.5 17.8 1.0
OP2 A:DA6 1.5 17.8 1.0
O3' A:BRU5 1.5 16.2 1.0
O5' A:DA6 1.6 16.2 1.0
C3' A:BRU5 2.5 16.2 1.0
C5' A:DA6 2.7 16.2 1.0
C2' A:BRU5 3.4 16.2 1.0
O A:HOH44 3.7 33.4 1.0
C4' A:BRU5 3.8 16.2 1.0
C4' A:DA6 3.9 16.2 1.0
O A:HOH38 4.1 33.4 1.0
C8 A:DA6 4.2 14.6 1.0
O4' A:DA6 4.3 16.2 1.0
O A:HOH56 4.4 33.4 1.0
C3' A:DA6 4.4 16.2 1.0
C5' A:BRU5 4.4 16.2 1.0
O5' A:BRU5 4.6 16.2 1.0
C1' A:BRU5 4.7 16.2 1.0
O4' A:BRU5 4.8 16.2 1.0

Phosphorus binding site 6 out of 14 in 115d

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Phosphorus binding site 6 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:17.8
occ:1.00
 P A:DC7 0.0 17.8 1.0
OP1 A:DC7 1.5 17.8 1.0
OP2 A:DC7 1.5 17.8 1.0
O5' A:DC7 1.6 16.2 1.0
O3' A:DA6 1.6 16.2 1.0
C3' A:DA6 2.6 16.2 1.0
C5' A:DC7 2.7 16.2 1.0
C2' A:DA6 3.5 16.2 1.0
C4' A:DA6 3.9 16.2 1.0
C4' A:DC7 3.9 16.2 1.0
O A:HOH46 4.1 33.4 1.0
O4' A:DC7 4.1 16.2 1.0
O A:HOH44 4.3 33.4 1.0
C6 A:DC7 4.4 14.6 1.0
O A:HOH66 4.4 33.4 1.0
C5' A:DA6 4.4 16.2 1.0
C3' A:DC7 4.5 16.2 1.0
O A:HOH38 4.5 33.4 1.0
O5' A:DA6 4.5 16.2 1.0
C1' A:DA6 4.8 16.2 1.0
O4' A:DA6 4.9 16.2 1.0

Phosphorus binding site 7 out of 14 in 115d

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Phosphorus binding site 7 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:17.8
occ:1.00
 P A:DC8 0.0 17.8 1.0
OP2 A:DC8 1.4 17.8 1.0
OP1 A:DC8 1.5 17.8 1.0
O5' A:DC8 1.6 16.2 1.0
O3' A:DC7 1.6 16.2 1.0
C3' A:DC7 2.7 16.2 1.0
C5' A:DC8 2.7 16.2 1.0
C2' A:DC7 3.5 16.2 1.0
O A:HOH46 3.8 33.4 1.0
C4' A:DC7 3.9 16.2 1.0
C4' A:DC8 3.9 16.2 1.0
O4' A:DC8 4.2 16.2 1.0
C3' A:DC8 4.4 16.2 1.0
C5' A:DC7 4.5 16.2 1.0
O5' A:DC7 4.6 16.2 1.0
C6 A:DC8 4.7 14.6 1.0
O A:HOH30 4.7 33.4 1.0
C1' A:DC7 4.9 16.2 1.0
O4' A:DC7 5.0 16.2 1.0
O3' A:DC8 5.0 16.2 1.0

Phosphorus binding site 8 out of 14 in 115d

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Phosphorus binding site 8 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:17.8
occ:1.00
 P B:DG10 0.0 17.8 1.0
OP2 B:DG10 1.4 17.8 1.0
OP1 B:DG10 1.5 17.8 1.0
O3' B:DG9 1.6 16.2 1.0
O5' B:DG10 1.6 16.2 1.0
C5' B:DG10 2.6 16.2 1.0
C3' B:DG9 2.7 16.2 1.0
C2' B:DG9 3.6 16.2 1.0
O B:HOH65 3.8 33.4 1.0
C4' B:DG9 3.9 16.2 1.0
C4' B:DG10 3.9 16.2 1.0
O4' B:DG10 4.1 16.2 1.0
O B:HOH32 4.1 33.4 1.0
C5' B:DG9 4.2 16.2 1.0
C8 B:DG10 4.3 14.6 1.0
C3' B:DG10 4.6 16.2 1.0
O5' B:DG9 4.8 16.2 1.0
C1' B:DG9 4.9 16.2 1.0
O4' B:DG9 5.0 16.2 1.0

Phosphorus binding site 9 out of 14 in 115d

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Phosphorus binding site 9 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:17.8
occ:1.00
 P B:BRU11 0.0 17.8 1.0
OP2 B:BRU11 1.4 17.8 1.0
OP1 B:BRU11 1.5 17.8 1.0
O3' B:DG10 1.5 16.2 1.0
O5' B:BRU11 1.6 16.2 1.0
C3' B:DG10 2.6 16.2 1.0
C5' B:BRU11 2.6 16.2 1.0
C2' B:DG10 3.5 16.2 1.0
O B:HOH48 3.7 33.4 1.0
O B:HOH47 3.8 33.4 1.0
C4' B:DG10 3.8 16.2 1.0
C4' B:BRU11 3.9 16.2 1.0
O B:HOH88 3.9 33.4 1.0
O B:HOH32 4.1 33.4 1.0
O4' B:BRU11 4.2 16.2 1.0
C6 B:BRU11 4.3 14.6 1.0
C5' B:DG10 4.3 16.2 1.0
C3' B:BRU11 4.4 16.2 1.0
O B:HOH85 4.4 33.4 1.0
BR B:BRU11 4.5 14.6 1.0
C1' B:DG10 4.8 16.2 1.0
O5' B:DG10 4.8 16.2 1.0
O B:HOH52 4.9 33.4 1.0
OP2 B:DA12 4.9 17.8 1.0
C5 B:BRU11 4.9 14.6 1.0
O4' B:DG10 4.9 16.2 1.0

Phosphorus binding site 10 out of 14 in 115d

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Phosphorus binding site 10 out of 14 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:17.8
occ:1.00
 P B:DA12 0.0 17.8 1.0
OP1 B:DA12 1.5 17.8 1.0
OP2 B:DA12 1.5 17.8 1.0
O3' B:BRU11 1.6 16.2 1.0
O5' B:DA12 1.6 16.2 1.0
C3' B:BRU11 2.6 16.2 1.0
C5' B:DA12 2.7 16.2 1.0
C2' B:BRU11 3.4 16.2 1.0
O B:HOH97 3.8 33.4 1.0
C4' B:BRU11 3.9 16.2 1.0
C4' B:DA12 3.9 16.2 1.0
O B:HOH47 4.0 33.4 1.0
O B:HOH52 4.1 33.4 1.0
O B:HOH74 4.2 33.4 1.0
O4' B:DA12 4.3 16.2 1.0
C5' B:BRU11 4.5 16.2 1.0
O B:HOH48 4.5 33.4 1.0
O5' B:BRU11 4.6 16.2 1.0
C8 B:DA12 4.7 14.6 1.0
C1' B:BRU11 4.7 16.2 1.0
C3' B:DA12 4.7 16.2 1.0
O4' B:BRU11 4.9 16.2 1.0

Reference:

O.Kennard, W.B.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich. Ordered Water Structure in An A-Dna Octamer at 1.7 A Resolution. J.Biomol.Struct.Dyn. V. 3 623 1986.
ISSN: ISSN 0739-1102
PubMed: 3271041
Page generated: Fri Sep 25 11:10:24 2020

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