Phosphorus in PDB 157d: Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs

Protein crystallography data

The structure of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs, PDB code: 157d was solved by G.A.Leonard, K.E.Mcauley-Hecht, S.Ebel, D.M.Lough, T.Brown, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.690, 34.620, 32.130, 90.00, 127.60, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs (pdb code 157d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs, PDB code: 157d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 157d

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Phosphorus binding site 1 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:27.1
occ:1.00
P A:G2 0.0 27.1 1.0
OP2 A:G2 1.5 32.4 1.0
OP1 A:G2 1.5 41.8 1.0
O3' A:C1 1.6 21.2 1.0
O5' A:G2 1.6 25.9 1.0
C5' A:G2 2.6 20.3 1.0
C3' A:C1 2.7 24.4 1.0
C2' A:C1 3.3 21.0 1.0
O2' A:C1 3.7 25.0 1.0
C4' A:G2 3.8 18.9 1.0
C4' A:C1 4.0 20.4 1.0
O A:HOH75 4.1 32.7 1.0
C3' A:G2 4.2 20.6 1.0
O A:HOH99 4.3 54.9 1.0
C8 A:G2 4.3 13.8 1.0
O4' A:G2 4.3 25.6 1.0
O5' A:C1 4.6 25.1 1.0
O A:HOH46 4.7 45.5 1.0
C1' A:C1 4.7 17.6 1.0
C5' A:C1 4.7 14.5 1.0
O3' A:G2 4.8 24.3 1.0
O4' A:C1 4.9 20.0 1.0

Phosphorus binding site 2 out of 22 in 157d

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Phosphorus binding site 2 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:24.2
occ:1.00
P A:C3 0.0 24.2 1.0
OP2 A:C3 1.5 18.5 1.0
OP1 A:C3 1.5 30.2 1.0
O3' A:G2 1.6 24.3 1.0
O5' A:C3 1.6 29.7 1.0
C5' A:C3 2.6 21.5 1.0
C3' A:G2 2.6 20.6 1.0
C2' A:G2 3.3 23.0 1.0
O2' A:G2 3.5 25.6 1.0
C4' A:C3 3.9 24.0 1.0
C4' A:G2 4.0 18.9 1.0
O4' A:C3 4.2 23.8 1.0
OP2 A:G4 4.2 22.1 1.0
C6 A:C3 4.4 16.4 1.0
C3' A:C3 4.5 19.0 1.0
O5' A:G2 4.6 25.9 1.0
C1' A:G2 4.6 23.5 1.0
O A:HOH75 4.6 32.7 1.0
C5' A:G2 4.7 20.3 1.0
O4' A:G2 4.9 25.6 1.0
C5 A:C3 5.0 20.7 1.0

Phosphorus binding site 3 out of 22 in 157d

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Phosphorus binding site 3 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:28.1
occ:1.00
P A:G4 0.0 28.1 1.0
OP2 A:G4 1.5 22.1 1.0
OP1 A:G4 1.5 32.7 1.0
O5' A:G4 1.6 18.7 1.0
O3' A:C3 1.6 26.8 1.0
C5' A:G4 2.6 15.6 1.0
C3' A:C3 2.6 19.0 1.0
O4' A:G4 3.6 16.1 1.0
C4' A:G4 3.7 12.5 1.0
C4' A:C3 3.7 24.0 1.0
C2' A:C3 3.8 15.7 1.0
C5' A:C3 4.0 21.5 1.0
C8 A:G4 4.1 14.5 1.0
O2' A:C3 4.3 18.6 1.0
O A:HOH56 4.5 32.4 1.0
C3' A:G4 4.5 11.6 1.0
O5' A:C3 4.5 29.7 1.0
C1' A:G4 4.8 20.1 1.0
O4' A:C3 4.9 23.8 1.0
N9 A:G4 4.9 19.0 1.0
C1' A:C3 4.9 19.3 1.0
OP1 A:C3 5.0 30.2 1.0

Phosphorus binding site 4 out of 22 in 157d

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Phosphorus binding site 4 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:27.3
occ:1.00
P A:A5 0.0 27.3 1.0
OP1 A:A5 1.5 23.5 1.0
OP2 A:A5 1.5 21.5 1.0
O5' A:A5 1.6 17.1 1.0
O3' A:G4 1.6 25.7 1.0
C5' A:A5 2.6 12.9 1.0
C3' A:G4 2.6 11.6 1.0
C2' A:G4 3.4 17.8 1.0
O2' A:G4 3.8 15.9 1.0
C4' A:A5 3.9 22.8 1.0
O4' A:A5 3.9 21.4 1.0
C4' A:G4 4.0 12.5 1.0
C3' A:A5 4.5 21.9 1.0
C8 A:A5 4.5 15.3 1.0
O A:HOH87 4.6 37.6 1.0
C5' A:G4 4.6 15.6 1.0
C1' A:G4 4.7 20.1 1.0
O5' A:G4 4.8 18.7 1.0
OP2 A:A6 4.9 37.0 1.0
O A:HOH47 4.9 46.8 1.0
O4' A:G4 4.9 16.1 1.0

Phosphorus binding site 5 out of 22 in 157d

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Phosphorus binding site 5 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:27.7
occ:1.00
P A:A6 0.0 27.7 1.0
OP2 A:A6 1.5 37.0 1.0
OP1 A:A6 1.5 33.1 1.0
O5' A:A6 1.6 23.3 1.0
O3' A:A5 1.6 27.3 1.0
C5' A:A6 2.6 18.6 1.0
C3' A:A5 2.7 21.9 1.0
C2' A:A5 3.7 16.5 1.0
C4' A:A6 3.8 16.5 1.0
C4' A:A5 3.9 22.8 1.0
O A:HOH53 3.9 35.3 1.0
O2' A:A5 4.1 27.9 1.0
C8 A:A6 4.1 20.9 1.0
C5' A:A5 4.2 12.9 1.0
O4' A:A6 4.2 19.6 1.0
O A:HOH47 4.3 46.8 1.0
C3' A:A6 4.4 30.2 1.0
O5' A:A5 4.6 17.1 1.0
O A:HOH88 4.6 40.8 1.0
OP2 A:U7 4.7 41.2 1.0
O4' A:A5 4.9 21.4 1.0
C1' A:A5 4.9 14.9 1.0
N7 A:A6 5.0 18.6 1.0

Phosphorus binding site 6 out of 22 in 157d

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Phosphorus binding site 6 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:36.5
occ:1.00
P A:U7 0.0 36.5 1.0
OP1 A:U7 1.5 52.6 1.0
OP2 A:U7 1.5 41.2 1.0
O5' A:U7 1.6 19.7 1.0
O3' A:A6 1.6 38.7 1.0
C5' A:U7 2.6 21.2 1.0
C3' A:A6 2.6 30.2 1.0
C2' A:A6 3.5 28.2 1.0
O4' A:U7 3.7 19.4 1.0
C4' A:U7 3.8 21.4 1.0
C4' A:A6 3.9 16.5 1.0
O2' A:A6 4.0 35.4 1.0
O5' A:A6 4.3 23.3 1.0
C6 A:U7 4.3 17.1 1.0
C5' A:A6 4.4 18.6 1.0
C3' A:U7 4.5 30.5 1.0
O A:HOH88 4.5 40.8 1.0
C1' A:A6 4.7 17.5 1.0
O4' A:A6 4.9 19.6 1.0
OP2 A:U8 4.9 46.9 1.0

Phosphorus binding site 7 out of 22 in 157d

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Phosphorus binding site 7 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:27.4
occ:1.00
P A:U8 0.0 27.4 1.0
OP1 A:U8 1.5 43.6 1.0
OP2 A:U8 1.5 46.9 1.0
O5' A:U8 1.6 18.9 1.0
O3' A:U7 1.6 42.7 1.0
C3' A:U7 2.6 30.5 1.0
C5' A:U8 2.6 19.3 1.0
C2' A:U7 3.7 19.0 1.0
C4' A:U7 3.8 21.4 1.0
C4' A:U8 3.9 23.6 1.0
O2' A:U7 3.9 12.1 1.0
C5' A:U7 4.1 21.2 1.0
O A:HOH103 4.2 40.9 1.0
C3' A:U8 4.5 26.8 1.0
O5' A:U7 4.6 19.7 1.0
OP2 A:A9 4.6 38.9 1.0
C6 A:U8 4.7 23.7 1.0
O4' A:U8 4.7 35.5 1.0
O4' A:U7 4.8 19.4 1.0
C1' A:U7 4.9 21.7 1.0

Phosphorus binding site 8 out of 22 in 157d

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Phosphorus binding site 8 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:26.3
occ:1.00
P A:A9 0.0 26.3 1.0
OP1 A:A9 1.5 51.5 1.0
OP2 A:A9 1.5 38.9 1.0
O5' A:A9 1.6 27.0 1.0
O3' A:U8 1.6 29.4 1.0
C5' A:A9 2.6 10.6 1.0
C3' A:U8 2.7 26.8 1.0
C2' A:U8 3.6 28.1 1.0
C4' A:A9 3.8 13.3 1.0
C4' A:U8 3.8 23.6 1.0
O4' A:A9 3.9 19.6 1.0
O2' A:U8 3.9 31.7 1.0
O5' A:U8 4.2 18.9 1.0
C5' A:U8 4.4 19.3 1.0
O A:HOH48 4.5 31.5 1.0
C8 A:A9 4.6 12.7 1.0
C3' A:A9 4.6 17.0 1.0
C1' A:U8 4.9 29.8 1.0
O4' A:U8 5.0 35.5 1.0

Phosphorus binding site 9 out of 22 in 157d

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Phosphorus binding site 9 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:21.0
occ:1.00
P A:G10 0.0 21.0 1.0
OP1 A:G10 1.5 21.9 1.0
OP2 A:G10 1.5 24.0 1.0
O5' A:G10 1.6 16.0 1.0
O3' A:A9 1.6 26.2 1.0
C5' A:G10 2.6 13.6 1.0
C3' A:A9 2.6 17.0 1.0
C2' A:A9 3.5 16.3 1.0
C4' A:G10 3.8 19.0 1.0
O A:HOH50 3.9 53.7 1.0
C4' A:A9 3.9 13.3 1.0
O4' A:G10 4.0 17.4 1.0
O2' A:A9 4.0 23.6 1.0
O A:HOH48 4.3 31.5 1.0
C5' A:A9 4.4 10.6 1.0
C3' A:G10 4.4 24.5 1.0
C8 A:G10 4.5 12.9 1.0
O A:HOH105 4.6 42.4 1.0
O A:HOH77 4.8 32.0 1.0
C1' A:A9 4.8 18.0 1.0
O5' A:A9 4.8 27.0 1.0
O4' A:A9 4.9 19.6 1.0
OP2 A:C11 5.0 12.3 1.0

Phosphorus binding site 10 out of 22 in 157d

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Phosphorus binding site 10 out of 22 in the Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:23.1
occ:1.00
P A:C11 0.0 23.1 1.0
OP1 A:C11 1.5 30.0 1.0
OP2 A:C11 1.5 12.3 1.0
O5' A:C11 1.6 16.8 1.0
O3' A:G10 1.6 19.0 1.0
C3' A:G10 2.6 24.5 1.0
C5' A:C11 2.7 25.4 1.0
C2' A:G10 3.6 19.6 1.0
C4' A:G10 3.9 19.0 1.0
O2' A:G10 3.9 25.4 1.0
C4' A:C11 3.9 24.4 1.0
O A:HOH104 4.0 51.9 1.0
C5' A:G10 4.2 13.6 1.0
O4' A:C11 4.3 23.6 1.0
O A:HOH106 4.3 29.0 1.0
C6 A:C11 4.4 15.2 1.0
C3' A:C11 4.4 23.2 1.0
O5' A:G10 4.6 16.0 1.0
C1' A:G10 4.8 11.5 1.0
O4' A:G10 4.9 17.4 1.0

Reference:

G.A.Leonard, K.E.Mcauley-Hecht, S.Ebel, D.M.Lough, T.Brown, W.N.Hunter. Crystal and Molecular Structure of R(Cgcgaauuagcg): An Rna Duplex Containing Two G(Anti).A(Anti) Base Pairs. Structure V. 2 483 1994.
ISSN: ISSN 0969-2126
PubMed: 7922026
DOI: 10.1016/S0969-2126(00)00049-6
Page generated: Fri Sep 25 11:33:13 2020

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