Phosphorus in PDB 168d: Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines

Protein crystallography data

The structure of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines, PDB code: 168d was solved by P.Lubini, W.Zuercher, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.130, 45.649, 47.554, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines (pdb code 168d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines, PDB code: 168d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 168d

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Phosphorus binding site 1 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:32.1
occ:1.00
P A:DC2 0.0 32.1 1.0
OP1 A:DC2 1.4 32.5 1.0
OP2 A:DC2 1.5 32.2 1.0
O3' A:DG1 1.6 31.7 1.0
O5' A:DC2 1.7 30.8 1.0
C5' A:DC2 2.6 28.3 1.0
C3' A:DG1 2.6 31.2 1.0
C2' A:DG1 3.6 30.5 1.0
C4' A:DG1 3.8 31.5 1.0
C4' A:DC2 3.8 26.3 1.0
O4' A:DC2 4.1 25.1 1.0
C5' A:DG1 4.2 32.0 1.0
C6 A:DC2 4.2 22.7 1.0
C3' A:DC2 4.5 25.9 1.0
O B:HOH51 4.8 57.8 1.0
C5 A:DC2 4.9 22.7 1.0
C1' A:DG1 4.9 29.7 1.0
O4' A:DG1 4.9 31.0 1.0

Phosphorus binding site 2 out of 18 in 168d

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Phosphorus binding site 2 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:27.6
occ:1.00
P A:DG3 0.0 27.6 1.0
OP1 A:DG3 1.4 27.9 1.0
OP2 A:DG3 1.5 27.9 1.0
O3' A:DC2 1.6 26.8 1.0
O5' A:DG3 1.6 26.4 1.0
C3' A:DC2 2.5 25.9 1.0
C5' A:DG3 2.6 24.5 1.0
C2' A:DC2 3.3 25.1 1.0
C4' A:DC2 3.8 26.3 1.0
C4' A:DG3 3.9 23.3 1.0
O4' A:DG3 4.0 22.4 1.0
C5' A:DC2 4.4 28.3 1.0
C8 A:DG3 4.5 19.0 1.0
O5' A:DC2 4.5 30.8 1.0
C3' A:DG3 4.6 23.3 1.0
C1' A:DC2 4.6 23.9 1.0
O A:HOH36 4.7 36.4 1.0
O4' A:DC2 4.8 25.1 1.0

Phosphorus binding site 3 out of 18 in 168d

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Phosphorus binding site 3 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:25.5
occ:1.00
P A:DT4 0.0 25.5 1.0
OP2 A:DT4 1.4 25.4 1.0
OP1 A:DT4 1.5 26.2 1.0
O3' A:DG3 1.6 24.7 1.0
O5' A:DT4 1.6 25.2 1.0
C5' A:DT4 2.5 24.4 1.0
C3' A:DG3 2.6 23.3 1.0
C2' A:DG3 3.4 22.0 1.0
C4' A:DT4 3.9 23.8 1.0
C4' A:DG3 3.9 23.3 1.0
C3' A:DT4 4.3 24.0 1.0
C6 A:DT4 4.4 19.8 1.0
C5' A:DG3 4.5 24.5 1.0
C7 A:DT4 4.5 19.2 1.0
O4' A:DT4 4.6 23.1 1.0
OP2 A:A2M5 4.7 26.1 1.0
C1' A:DG3 4.7 20.7 1.0
O3' A:DT4 4.7 25.1 1.0
O4' A:DG3 4.9 22.4 1.0
O5' A:DG3 5.0 26.4 1.0
C5 A:DT4 5.0 19.5 1.0

Phosphorus binding site 4 out of 18 in 168d

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Phosphorus binding site 4 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:26.0
occ:1.00
P A:A2M5 0.0 26.0 1.0
OP1 A:A2M5 1.4 25.6 1.0
OP2 A:A2M5 1.5 26.1 1.0
O3' A:DT4 1.6 25.1 1.0
O5' A:A2M5 1.7 25.2 1.0
C5' A:A2M5 2.6 24.0 1.0
C3' A:DT4 2.7 24.0 1.0
C2' A:DT4 3.5 23.0 1.0
C4' A:A2M5 3.9 23.0 1.0
C4' A:DT4 4.0 23.8 1.0
O4' A:A2M5 4.4 22.1 1.0
O5' A:DT4 4.4 25.2 1.0
C5' A:DT4 4.6 24.4 1.0
C1' A:DT4 4.8 21.5 1.0

Phosphorus binding site 5 out of 18 in 168d

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Phosphorus binding site 5 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:25.6
occ:1.00
P A:DT6 0.0 25.6 1.0
OP1 A:DT6 1.4 25.8 1.0
OP2 A:DT6 1.5 25.9 1.0
O3' A:A2M5 1.6 24.6 1.0
O5' A:DT6 1.6 25.5 1.0
C5' A:DT6 2.5 25.2 1.0
C3' A:A2M5 2.6 23.1 1.0
C2' A:A2M5 3.6 22.2 1.0
O A:HOH52 3.8 39.1 1.0
C4' A:A2M5 3.8 23.0 1.0
C4' A:DT6 3.9 24.9 1.0
O2' A:A2M5 4.0 22.5 1.0
C7 A:DT6 4.2 21.8 1.0
C5' A:A2M5 4.3 24.0 1.0
C6 A:DT6 4.3 22.4 1.0
O4' A:DT6 4.5 24.6 1.0
C3' A:DT6 4.5 25.1 1.0
C5 A:DT6 4.8 22.2 1.0
C1' A:A2M5 4.9 20.9 1.0
O4' A:A2M5 4.9 22.1 1.0

Phosphorus binding site 6 out of 18 in 168d

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Phosphorus binding site 6 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:26.2
occ:1.00
P A:DA7 0.0 26.2 1.0
OP1 A:DA7 1.4 26.4 1.0
OP2 A:DA7 1.5 26.1 1.0
O3' A:DT6 1.6 25.6 1.0
O5' A:DA7 1.6 25.7 1.0
C3' A:DT6 2.7 25.1 1.0
C5' A:DA7 2.7 23.9 1.0
C2' A:DT6 3.5 24.5 1.0
O A:HOH66 3.5 44.1 1.0
O A:HOH48 3.8 35.4 1.0
C4' A:DA7 3.9 23.0 1.0
C4' A:DT6 4.0 24.9 1.0
O A:HOH71 4.2 45.3 1.0
O4' A:DA7 4.4 22.3 1.0
C3' A:DA7 4.4 23.0 1.0
O5' A:DT6 4.5 25.5 1.0
C8 A:DA7 4.6 20.1 1.0
C5' A:DT6 4.6 25.2 1.0
O A:HOH67 4.6 53.0 1.0
O A:HOH52 4.7 39.1 1.0
C1' A:DT6 4.9 23.5 1.0
O3' A:DA7 4.9 24.3 1.0
O A:HOH68 5.0 66.2 1.0

Phosphorus binding site 7 out of 18 in 168d

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Phosphorus binding site 7 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:25.1
occ:1.00
P A:DC8 0.0 25.1 1.0
OP1 A:DC8 1.4 25.5 1.0
OP2 A:DC8 1.5 25.2 1.0
O3' A:DA7 1.6 24.3 1.0
O5' A:DC8 1.6 23.7 1.0
C3' A:DA7 2.7 23.0 1.0
C5' A:DC8 2.7 22.0 1.0
C2' A:DA7 3.4 22.0 1.0
C4' A:DC8 3.9 21.4 1.0
C4' A:DA7 3.9 23.0 1.0
O4' A:DC8 4.0 20.9 1.0
O A:HOH50 4.1 55.9 1.0
O A:HOH48 4.3 35.4 1.0
O A:HOH71 4.3 45.3 1.0
O5' A:DA7 4.4 25.7 1.0
C6 A:DC8 4.5 19.8 1.0
O A:HOH49 4.5 39.9 1.0
C5' A:DA7 4.6 23.9 1.0
C3' A:DC8 4.7 21.3 1.0
C1' A:DA7 4.8 21.2 1.0
O A:HOH32 4.8 39.5 1.0
O4' A:DA7 4.9 22.3 1.0

Phosphorus binding site 8 out of 18 in 168d

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Phosphorus binding site 8 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:22.4
occ:1.00
P A:DG9 0.0 22.4 1.0
OP1 A:DG9 1.4 23.3 1.0
OP2 A:DG9 1.5 22.9 1.0
O3' A:DC8 1.6 21.6 1.0
O5' A:DG9 1.6 21.9 1.0
C3' A:DC8 2.5 21.3 1.0
C5' A:DG9 2.6 20.9 1.0
C2' A:DC8 3.4 20.8 1.0
C4' A:DC8 3.8 21.4 1.0
C4' A:DG9 3.9 19.9 1.0
O A:HOH32 4.0 39.5 1.0
O A:HOH58 4.1 31.2 1.0
O4' A:DG9 4.1 19.9 1.0
C5' A:DC8 4.3 22.0 1.0
C3' A:DG9 4.4 19.9 1.0
C8 A:DG9 4.4 17.6 1.0
O A:HOH33 4.6 49.5 1.0
C1' A:DC8 4.8 20.3 1.0
O4' A:DC8 4.8 20.9 1.0
O5' A:DC8 4.8 23.7 1.0
OP2 A:DC10 4.9 20.4 1.0
O3' A:DG9 5.0 19.9 1.0

Phosphorus binding site 9 out of 18 in 168d

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Phosphorus binding site 9 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:20.1
occ:1.00
P A:DC10 0.0 20.1 1.0
OP1 A:DC10 1.4 20.7 1.0
OP2 A:DC10 1.5 20.4 1.0
O3' A:DG9 1.6 19.9 1.0
O5' A:DC10 1.6 19.9 1.0
C5' A:DC10 2.6 19.4 1.0
C3' A:DG9 2.6 19.9 1.0
C2' A:DG9 3.5 19.5 1.0
C4' A:DG9 3.9 19.9 1.0
C4' A:DC10 3.9 18.8 1.0
O A:HOH58 4.0 31.2 1.0
O A:HOH33 4.0 49.5 1.0
O4' A:DC10 4.2 19.1 1.0
C6 A:DC10 4.4 18.8 1.0
C5' A:DG9 4.4 20.9 1.0
O5' A:DG9 4.4 21.9 1.0
C3' A:DC10 4.5 18.2 1.0
O A:HOH23 4.8 25.2 1.0
C1' A:DG9 4.8 18.7 1.0
O4' A:DG9 4.9 19.9 1.0
C5 A:DC10 5.0 18.4 1.0

Phosphorus binding site 10 out of 18 in 168d

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Phosphorus binding site 10 out of 18 in the Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:32.8
occ:1.00
P B:DC12 0.0 32.8 1.0
OP1 B:DC12 1.4 33.1 1.0
OP2 B:DC12 1.5 33.2 1.0
O3' B:DG11 1.6 33.1 1.0
O5' B:DC12 1.6 31.3 1.0
C3' B:DG11 2.6 33.9 1.0
C5' B:DC12 2.6 28.6 1.0
C2' B:DG11 3.5 33.6 1.0
C4' B:DC12 3.9 26.9 1.0
C4' B:DG11 3.9 34.5 1.0
O B:HOH44 4.0 49.4 1.0
O4' B:DC12 4.1 26.3 1.0
C6 B:DC12 4.3 24.9 1.0
C3' B:DC12 4.5 26.4 1.0
C5' B:DG11 4.5 35.3 1.0
C1' B:DG11 4.8 33.2 1.0
C5 B:DC12 4.9 24.8 1.0
O4' B:DG11 5.0 34.1 1.0

Reference:

P.Lubini, W.Zurcher, M.Egli. Stabilizing Effects of the Rna 2'-Substituent: Crystal Structure of An Oligodeoxynucleotide Duplex Containing 2'-O-Methylated Adenosines. Chem.Biol. V. 1 39 1994.
ISSN: ISSN 1074-5521
PubMed: 9383369
DOI: 10.1016/1074-5521(94)90039-6
Page generated: Fri Sep 25 11:38:05 2020

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