Phosphorus in PDB 165d: The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure

Protein crystallography data

The structure of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure, PDB code: 165d was solved by W.Cruse, P.Saludjian, E.Biala, P.Strazewski, T.Prange, O.Kennard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.800, 19.400, 50.140, 90.00, 109.90, 90.00
R / Rfree (%) 18 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Phosphorus atom in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure (pdb code 165d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 17 binding sites of Phosphorus where determined in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure, PDB code: 165d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 17 in 165d

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Phosphorus binding site 1 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:17.3
occ:1.00
P A:C2 0.0 17.3 1.0
OP1 A:C2 1.5 17.4 1.0
OP2 A:C2 1.5 16.8 1.0
O3' A:G1 1.6 19.1 1.0
O5' A:C2 1.6 15.6 1.0
C3' A:G1 2.7 19.5 1.0
C5' A:C2 2.7 13.7 1.0
C2' A:G1 3.5 19.5 1.0
O2' A:G1 3.9 20.1 1.0
C4' A:G1 4.0 20.1 1.0
C4' A:C2 4.0 12.5 1.0
O A:HOH60 4.1 38.1 1.0
C6 A:C2 4.3 11.6 1.0
C5' A:G1 4.4 20.3 1.0
O4' A:C2 4.4 12.1 1.0
C3' A:C2 4.6 11.3 1.0
O5' A:G1 4.7 20.6 1.0
C1' A:G1 4.8 19.7 1.0
C5 A:C2 4.9 11.6 1.0
OP2 A:U3 4.9 8.3 1.0

Phosphorus binding site 2 out of 17 in 165d

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Phosphorus binding site 2 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:8.5
occ:1.00
P A:U3 0.0 8.5 1.0
OP1 A:U3 1.5 8.7 1.0
OP2 A:U3 1.5 8.3 1.0
O5' A:U3 1.6 8.1 1.0
O3' A:C2 1.6 10.2 1.0
C5' A:U3 2.6 7.5 1.0
C3' A:C2 2.7 11.3 1.0
C2' A:C2 3.6 11.4 1.0
C4' A:U3 3.9 7.1 1.0
C4' A:C2 3.9 12.5 1.0
O4' A:U3 4.1 7.0 1.0
O2' A:C2 4.2 11.0 1.0
C6 A:U3 4.2 7.3 1.0
C5' A:C2 4.3 13.7 1.0
C3' A:U3 4.5 6.9 1.0
O5' A:C2 4.5 15.6 1.0
C5 A:U3 4.8 7.8 1.0
C1' A:C2 4.9 11.6 1.0

Phosphorus binding site 3 out of 17 in 165d

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Phosphorus binding site 3 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:6.7
occ:1.00
P A:U4 0.0 6.7 1.0
OP1 A:U4 1.5 7.2 1.0
OP2 A:U4 1.5 6.6 1.0
O5' A:U4 1.6 7.0 1.0
O3' A:U3 1.6 7.0 1.0
C3' A:U3 2.6 6.9 1.0
C5' A:U4 2.7 6.4 1.0
C2' A:U3 3.3 6.7 1.0
O2' A:U3 3.7 7.1 1.0
O A:HOH59 3.8 21.5 1.0
O A:HOH54 3.9 27.6 1.0
C4' A:U3 4.0 7.1 1.0
C4' A:U4 4.0 6.6 1.0
O A:HOH36 4.1 14.0 1.0
C6 A:U4 4.3 5.9 1.0
O4' A:U4 4.5 6.5 1.0
C3' A:U4 4.5 6.4 1.0
C5' A:U3 4.6 7.5 1.0
C1' A:U3 4.7 6.9 1.0
OP2 A:C5 4.8 5.6 1.0
C5 A:U4 4.8 6.2 1.0
O5' A:U3 4.9 8.1 1.0
O4' A:U3 5.0 7.0 1.0

Phosphorus binding site 4 out of 17 in 165d

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Phosphorus binding site 4 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:5.8
occ:1.00
P A:C5 0.0 5.8 1.0
OP1 A:C5 1.5 6.4 1.0
OP2 A:C5 1.5 5.6 1.0
O5' A:C5 1.6 5.3 1.0
O3' A:U4 1.6 6.7 1.0
C5' A:C5 2.6 5.2 1.0
C3' A:U4 2.6 6.4 1.0
C2' A:U4 3.5 6.4 1.0
N1 A:RHD19 3.7 13.0 1.0
O A:HOH48 3.8 20.3 1.0
C4' A:U4 3.9 6.6 1.0
C4' A:C5 3.9 4.7 1.0
O2' A:U4 4.0 7.5 1.0
C5' A:U4 4.3 6.4 1.0
O4' A:C5 4.3 4.5 1.0
C6 A:C5 4.3 4.2 1.0
C3' A:C5 4.4 4.7 1.0
O A:HOH59 4.5 21.5 1.0
O5' A:U4 4.5 7.0 1.0
OP2 A:G6 4.6 5.5 1.0
C1' A:U4 4.8 6.6 1.0
O3' A:C5 4.9 5.4 1.0
C5 A:C5 4.9 4.1 1.0
N5 A:RHD19 5.0 13.4 1.0
O4' A:U4 5.0 6.5 1.0

Phosphorus binding site 5 out of 17 in 165d

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Phosphorus binding site 5 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:5.5
occ:1.00
P A:G6 0.0 5.5 1.0
OP1 A:G6 1.5 6.0 1.0
OP2 A:G6 1.5 5.5 1.0
O5' A:G6 1.6 5.5 1.0
O3' A:C5 1.6 5.4 1.0
C3' A:C5 2.6 4.7 1.0
C5' A:G6 2.6 5.4 1.0
C2' A:C5 3.5 4.5 1.0
C4' A:C5 3.8 4.7 1.0
C4' A:G6 3.9 5.1 1.0
O2' A:C5 4.0 4.8 1.0
C5' A:C5 4.1 5.2 1.0
O5' A:C5 4.2 5.3 1.0
N1 A:RHD19 4.3 13.0 1.0
N4 A:RHD19 4.3 13.1 1.0
C8 A:G6 4.3 4.4 1.0
O4' A:G6 4.3 5.0 1.0
C3' A:G6 4.5 5.0 1.0
C1' A:C5 4.7 4.5 1.0
OP2 A:G7 4.8 6.3 1.0
O4' A:C5 4.9 4.5 1.0
N5 A:RHD19 4.9 13.4 1.0

Phosphorus binding site 6 out of 17 in 165d

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Phosphorus binding site 6 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:5.6
occ:1.00
P A:G7 0.0 5.6 1.0
OP1 A:G7 1.5 6.2 1.0
OP2 A:G7 1.5 6.3 1.0
O5' A:G7 1.6 6.0 1.0
O3' A:G6 1.6 5.1 1.0
C5' A:G7 2.6 5.9 1.0
C3' A:G6 2.7 5.0 1.0
C2' A:G6 3.6 4.9 1.0
C4' A:G7 3.9 5.5 1.0
O A:HOH56 3.9 15.1 1.0
C4' A:G6 4.0 5.1 1.0
O2' A:G6 4.2 5.4 1.0
O4' A:G7 4.2 5.4 1.0
C8 A:G7 4.2 5.3 1.0
C5' A:G6 4.3 5.4 1.0
C3' A:G7 4.5 5.4 1.0
O5' A:G6 4.5 5.5 1.0
C1' A:G6 4.9 4.7 1.0

Phosphorus binding site 7 out of 17 in 165d

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Phosphorus binding site 7 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:5.4
occ:1.00
P A:C8 0.0 5.4 1.0
OP2 A:C8 1.5 5.5 1.0
OP1 A:C8 1.5 5.6 1.0
O3' A:G7 1.6 5.1 1.0
O5' A:C8 1.6 5.2 1.0
C5' A:C8 2.7 5.5 1.0
C3' A:G7 2.7 5.4 1.0
C2' A:G7 3.5 5.3 1.0
O A:HOH63 3.8 27.5 1.0
O A:HOH37 3.9 18.4 1.0
O A:HOH35 3.9 18.7 1.0
C4' A:G7 3.9 5.5 1.0
O A:HOH33 4.0 11.5 1.0
C4' A:C8 4.0 5.8 1.0
O2' A:G7 4.0 5.3 1.0
C5' A:G7 4.3 5.9 1.0
O4' A:C8 4.4 5.5 1.0
C3' A:C8 4.5 5.9 1.0
OP2 A:BRU9 4.5 7.5 1.0
O5' A:G7 4.7 6.0 1.0
C6 A:C8 4.7 5.7 1.0
C1' A:G7 4.8 5.3 1.0

Phosphorus binding site 8 out of 17 in 165d

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Phosphorus binding site 8 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:7.4
occ:1.00
P A:BRU9 0.0 7.4 1.0
OP1 A:BRU9 1.5 7.5 1.0
OP2 A:BRU9 1.5 7.5 1.0
O3' A:C8 1.6 6.5 1.0
O5' A:BRU9 1.6 7.6 1.0
C3' A:C8 2.7 5.9 1.0
C5' A:BRU9 2.7 7.4 1.0
O A:HOH64 3.5 33.2 1.0
C2' A:C8 3.7 5.5 1.0
C4' A:C8 3.8 5.8 1.0
O A:HOH33 3.9 11.5 1.0
C4' A:BRU9 3.9 7.5 1.0
C6 A:BRU9 4.0 11.6 1.0
O A:HOH63 4.0 27.5 1.0
C5' A:C8 4.0 5.5 1.0
O2' A:C8 4.1 5.4 1.0
O4' A:BRU9 4.2 7.5 1.0
BR A:BRU9 4.4 16.6 1.0
O5' A:C8 4.5 5.2 1.0
C3' A:BRU9 4.5 7.4 1.0
C2' A:BRU9 4.6 7.7 1.0
C5 A:BRU9 4.7 12.9 1.0
C1' A:BRU9 4.8 8.4 1.0
N1 A:BRU9 4.9 10.1 1.0
O4' A:C8 5.0 5.5 1.0
C1' A:C8 5.0 5.7 1.0

Phosphorus binding site 9 out of 17 in 165d

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Phosphorus binding site 9 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:10.9
occ:1.00
P B:C11 0.0 10.9 1.0
OP2 B:C11 1.5 10.5 1.0
OP1 B:C11 1.5 10.3 1.0
O5' B:C11 1.6 9.7 1.0
O3' B:G10 1.6 10.9 1.0
C5' B:C11 2.7 8.3 1.0
C3' B:G10 2.7 11.3 1.0
C2' B:G10 3.6 11.0 1.0
O B:HOH58 3.6 27.4 1.0
O B:HOH62 3.7 27.2 1.0
C4' B:C11 3.9 7.5 1.0
C4' B:G10 4.0 11.4 1.0
O2' B:G10 4.1 10.8 1.0
O4' B:C11 4.3 7.1 1.0
C6 B:C11 4.3 5.7 1.0
O B:HOH71 4.4 32.0 1.0
C3' B:C11 4.4 6.8 1.0
C5' B:G10 4.4 12.0 1.0
O5' B:G10 4.9 12.6 1.0
C5 B:C11 4.9 5.4 1.0
C1' B:G10 4.9 10.9 1.0
OP2 B:U12 5.0 7.5 1.0

Phosphorus binding site 10 out of 17 in 165d

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Phosphorus binding site 10 out of 17 in the The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Structure of A Mispaired Rna Double Helix at 1.6 Angstroms Resolution and Implications For the Prediction of Rna Secondary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:7.2
occ:1.00
P B:U12 0.0 7.2 1.0
OP2 B:U12 1.5 7.5 1.0
OP1 B:U12 1.5 7.1 1.0
O5' B:U12 1.6 6.4 1.0
O3' B:C11 1.6 7.0 1.0
C5' B:U12 2.7 5.6 1.0
C3' B:C11 2.7 6.8 1.0
C2' B:C11 3.6 6.5 1.0
O B:HOH55 3.8 23.1 1.0
C4' B:U12 4.0 5.2 1.0
O B:HOH58 4.0 27.4 1.0
C4' B:C11 4.0 7.5 1.0
O2' B:C11 4.0 5.7 1.0
O B:HOH32 4.3 16.6 1.0
O4' B:U12 4.4 5.1 1.0
C6 B:U12 4.4 4.8 1.0
O B:HOH62 4.4 27.2 1.0
C5' B:C11 4.5 8.3 1.0
C3' B:U12 4.5 5.2 1.0
O5' B:C11 4.7 9.7 1.0
C1' B:C11 4.9 6.3 1.0
C5 B:U12 5.0 4.7 1.0

Reference:

W.B.Cruse, P.Saludjian, E.Biala, P.Strazewski, T.Prange, O.Kennard. Structure of A Mispaired Rna Double Helix at 1.6-A Resolution and Implications For the Prediction of Rna Secondary Structure. Proc.Natl.Acad.Sci.Usa V. 91 4160 1994.
ISSN: ISSN 0027-8424
PubMed: 7514296
DOI: 10.1073/PNAS.91.10.4160
Page generated: Fri Sep 25 11:36:24 2020

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