Phosphorus in PDB 1a34: Satellite Tobacco Mosaic Virus/Rna Complex

Protein crystallography data

The structure of Satellite Tobacco Mosaic Virus/Rna Complex, PDB code: 1a34 was solved by S.B.Larson, J.Day, A.J.Greenwood, A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.81
Space group I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.270, 191.770, 202.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 18.4

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Satellite Tobacco Mosaic Virus/Rna Complex (pdb code 1a34). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 21 binding sites of Phosphorus where determined in the Satellite Tobacco Mosaic Virus/Rna Complex, PDB code: 1a34:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 21 in 1a34

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Phosphorus binding site 1 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P1

b:0.7
occ:0.50
P B:A1 0.0 0.7 0.5
OP2 B:A1 1.5 0.9 0.5
OP1 B:A1 1.5 0.6 0.5
O5' B:A1 1.6 0.4 0.5
OP3 B:A1 1.6 0.9 0.5
HOP3 B:A1 2.2 0.2 0.5
C5' B:A1 2.7 0.6 0.5
H5'' B:A1 2.7 0.2 0.5
H5' B:A1 3.0 0.2 0.5
H8 B:A1 3.8 0.9 0.5
C4' B:A1 4.0 0.5 0.5
O4' B:A1 4.2 0.9 0.5
H4' B:A1 4.6 0.2 0.5
C8 B:A1 4.9 0.6 0.5
H3' B:A1 4.9 0.2 0.5

Phosphorus binding site 2 out of 21 in 1a34

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Phosphorus binding site 2 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:0.9
occ:0.50
P B:A2 0.0 0.9 0.5
OP2 B:A2 1.5 0.4 0.5
OP1 B:A2 1.5 0.7 0.5
O5' B:A2 1.6 1.0 0.5
O3' B:A1 1.6 0.9 0.5
C5' B:A2 2.7 1.0 0.5
C3' B:A1 2.8 1.0 0.5
H5'' B:A2 2.9 0.6 0.5
H5' B:A2 3.2 0.6 0.5
H3' B:A1 3.3 0.2 0.5
C2' B:A1 3.5 0.4 0.5
O2' B:A1 3.6 0.4 0.5
HO2' B:A1 3.7 0.2 0.5
H3' B:A2 3.8 0.6 0.5
H8 B:A2 3.8 0.3 0.5
H2' B:A1 3.9 0.2 0.5
H4' B:A1 4.0 0.2 0.5
C4' B:A2 4.0 0.2 0.5
C4' B:A1 4.0 0.5 0.5
C3' B:A2 4.4 0.6 0.5
OP1 C:U2 4.6 0.6 0.5
O4' B:A2 4.7 0.0 0.5
H5' B:A1 4.8 0.2 0.5
H4' B:A2 4.8 0.6 0.5
C8 B:A2 4.8 0.4 0.5
OP2 C:U2 4.8 0.4 0.5
O3' B:A2 4.8 0.4 0.5
C5' B:A1 4.8 0.6 0.5
H5'' B:A1 4.9 0.2 0.5
C1' B:A1 5.0 0.2 0.5
OP2 B:A3 5.0 0.7 0.5

Phosphorus binding site 3 out of 21 in 1a34

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Phosphorus binding site 3 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:0.7
occ:0.50
P B:A3 0.0 0.7 0.5
OP2 B:A3 1.5 0.7 0.5
OP1 B:A3 1.5 0.1 0.5
O5' B:A3 1.6 0.3 0.5
O3' B:A2 1.7 0.4 0.5
C5' B:A3 2.7 0.4 0.5
H5'' B:A3 2.8 0.7 0.5
C3' B:A2 2.8 0.6 0.5
H5' B:A3 2.8 0.7 0.5
H3' B:A2 3.0 0.6 0.5
H2' B:A2 3.5 0.6 0.5
C2' B:A2 3.6 0.0 0.5
H8 B:A3 3.9 93.2 0.5
H3' B:A3 4.0 0.7 0.5
C4' B:A3 4.0 0.2 0.5
C4' B:A2 4.1 0.2 0.5
O2' B:A2 4.1 0.3 0.5
H4' B:A2 4.2 0.6 0.5
HO2' B:A2 4.3 0.6 0.5
H5'' B:A2 4.5 0.6 0.5
C3' B:A3 4.5 99.3 0.5
OP2 B:A4 4.6 80.0 0.5
O4' B:A3 4.6 0.5 0.5
O5' B:A2 4.7 1.0 0.5
C5' B:A2 4.7 1.0 0.5
H4' B:A3 4.8 0.7 0.5
O3' B:A3 4.9 89.7 0.5
C8 B:A3 4.9 94.5 0.5
C1' B:A2 5.0 0.8 0.5

Phosphorus binding site 4 out of 21 in 1a34

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Phosphorus binding site 4 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:80.7
occ:0.50
P B:A4 0.0 80.7 0.5
OP2 B:A4 1.5 80.0 0.5
OP1 B:A4 1.5 82.8 0.5
O5' B:A4 1.6 72.8 0.5
O3' B:A3 1.6 89.7 0.5
C5' B:A4 2.7 55.9 0.5
H3' B:A3 2.7 0.7 0.5
C3' B:A3 2.7 99.3 0.5
H5' B:A4 2.9 44.0 0.5
H5'' B:A4 2.9 44.0 0.5
H8 B:A4 3.4 26.0 0.5
H2' B:A3 3.7 0.7 0.5
C2' B:A3 3.8 99.2 0.5
H3' B:A4 4.0 44.0 0.5
C4' B:A3 4.0 0.2 0.5
C4' B:A4 4.0 45.2 0.5
H5'' B:A3 4.1 0.7 0.5
O5' B:A3 4.3 0.3 0.5
H4' B:A3 4.3 0.7 0.5
C5' B:A3 4.4 0.4 0.5
O2' B:A3 4.4 98.4 0.5
C8 B:A4 4.5 30.6 0.5
O4' B:A4 4.5 41.8 0.5
C3' B:A4 4.5 38.9 0.5
H4' B:A4 4.8 44.0 0.5
HO2' B:A3 4.9 0.7 0.5
OP2 B:A5 4.9 27.8 0.5

Phosphorus binding site 5 out of 21 in 1a34

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Phosphorus binding site 5 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P5

b:27.8
occ:0.50
P B:A5 0.0 27.8 0.5
OP2 B:A5 1.5 27.8 0.5
OP1 B:A5 1.5 29.0 0.5
O5' B:A5 1.6 24.2 0.5
O3' B:A4 1.6 32.8 0.5
C5' B:A5 2.6 19.9 0.5
C3' B:A4 2.7 38.9 0.5
H3' B:A4 2.7 44.0 0.5
H2 B:HOH2202 2.8 42.0 1.0
H5'' B:A5 2.9 18.4 0.5
H5' B:A5 3.0 18.4 0.5
H8 B:A5 3.4 19.1 0.5
H2' B:A4 3.5 44.0 0.5
C2' B:A4 3.6 37.1 0.5
O B:HOH2202 3.7 42.0 1.0
H1 B:HOH2202 3.7 42.0 1.0
H3' B:A5 3.9 18.4 0.5
O2' B:A4 3.9 34.0 0.5
C4' B:A4 3.9 45.2 0.5
C4' B:A5 3.9 19.1 0.5
H5'' B:A4 4.0 44.0 0.5
H4' B:A4 4.1 44.0 0.5
C8 B:A5 4.3 19.2 0.5
H1 B:HOH2201 4.4 64.7 1.0
C3' B:A5 4.4 17.6 0.5
C5' B:A4 4.5 55.9 0.5
O4' B:A5 4.5 17.2 0.5
OP2 B:A6 4.5 15.6 0.5
O5' B:A4 4.5 72.8 0.5
O B:HOH2201 4.6 64.7 1.0
H2 B:HOH2201 4.6 64.7 1.0
H4' B:A5 4.7 18.4 0.5
HO2' B:A4 4.8 44.0 0.5
C1' B:A4 4.9 37.1 0.5
N7 B:A5 4.9 19.8 0.5
O3' B:A5 5.0 16.4 0.5

Phosphorus binding site 6 out of 21 in 1a34

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Phosphorus binding site 6 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:16.4
occ:0.50
P B:A6 0.0 16.4 0.5
OP2 B:A6 1.5 15.6 0.5
OP1 B:A6 1.5 15.8 0.5
O5' B:A6 1.6 17.8 0.5
O3' B:A5 1.6 16.4 0.5
C5' B:A6 2.6 16.0 0.5
H2 B:HOH2203 2.6 33.5 1.0
C3' B:A5 2.6 17.6 0.5
H3' B:A5 2.7 18.4 0.5
H5' B:A6 2.8 17.0 0.5
H5'' B:A6 2.9 17.0 0.5
H2 B:HOH2604 3.0 20.6 1.0
H8 B:A6 3.1 22.2 0.5
H1 A:HOH2901 3.2 11.7 1.0
H1 B:HOH2201 3.2 64.7 1.0
H1 B:HOH2202 3.4 42.0 1.0
H2' B:A5 3.5 18.4 0.5
O B:HOH2203 3.5 33.5 1.0
C2' B:A5 3.5 16.9 0.5
H1 B:HOH2203 3.6 33.5 1.0
O B:HOH2604 3.8 20.6 1.0
H3' B:A6 3.8 17.0 0.5
O A:HOH2901 3.9 11.7 1.0
C4' B:A5 3.9 19.1 0.5
C4' B:A6 3.9 17.1 0.5
C8 B:A6 4.0 21.1 0.5
H1 B:HOH2604 4.1 20.6 1.0
H4' B:A5 4.1 18.4 0.5
O B:HOH2201 4.1 64.7 1.0
H5'' B:A5 4.1 18.4 0.5
H1 A:HOH2105 4.1 14.2 1.0
O2' B:A5 4.2 15.1 0.5
O B:HOH2202 4.3 42.0 1.0
O4' B:A6 4.3 17.9 0.5
HO2' B:A5 4.3 18.4 0.5
C3' B:A6 4.4 17.2 0.5
C5' B:A5 4.4 19.9 0.5
O5' B:A5 4.4 24.2 0.5
H2 A:HOH2105 4.5 14.2 1.0
H1 A:HOH2104 4.5 19.2 1.0
HG1 A:THR36 4.5 8.2 1.0
H2 A:HOH2901 4.6 11.7 1.0
H2 B:HOH2201 4.6 64.7 1.0
O A:HOH2105 4.6 14.2 1.0
H4' B:A6 4.7 17.0 0.5
OG1 A:THR36 4.7 9.0 1.0
H2 B:HOH2202 4.7 42.0 1.0
O A:HOH2104 4.7 19.2 1.0
N7 B:A6 4.8 21.8 0.5
C1' B:A5 4.8 19.1 0.5
OP2 B:A7 4.8 23.6 0.5
O4' B:A5 5.0 17.2 0.5
N9 B:A6 5.0 20.7 0.5

Phosphorus binding site 7 out of 21 in 1a34

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Phosphorus binding site 7 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:20.5
occ:0.50
P B:A7 0.0 20.5 0.5
OP2 B:A7 1.5 23.6 0.5
OP1 B:A7 1.5 19.1 0.5
O5' B:A7 1.6 21.3 0.5
O3' B:A6 1.6 18.7 0.5
C5' B:A7 2.6 22.5 0.5
C3' B:A6 2.7 17.2 0.5
H5' B:A7 2.7 25.1 0.5
H3' B:A6 2.8 17.0 0.5
H1 B:HOH2210 2.8 67.4 1.0
H5'' B:A7 2.8 25.1 0.5
H2 B:HOH2602 3.1 15.7 1.0
H2 B:HOH2211 3.3 66.1 1.0
H1 B:HOH2603 3.5 8.7 1.0
H2 B:HOH2603 3.6 8.7 1.0
H8 B:A7 3.6 19.4 0.5
C2' B:A6 3.6 16.5 0.5
HO2' B:A6 3.6 17.0 0.5
H2' B:A6 3.6 17.0 0.5
O B:HOH2602 3.7 15.7 1.0
O B:HOH2210 3.7 67.4 1.0
H1 B:HOH2203 3.7 33.5 1.0
H2 B:HOH2210 3.8 67.4 1.0
O B:HOH2603 3.8 8.7 1.0
C4' B:A7 3.9 25.2 0.5
H3' B:A7 3.9 25.1 0.5
C4' B:A6 3.9 17.1 0.5
H5'' B:A6 4.1 17.0 0.5
O4' B:A7 4.1 24.4 0.5
O B:HOH2211 4.1 66.1 1.0
O2' B:A6 4.2 14.2 0.5
H4' B:A6 4.2 17.0 0.5
H2 A:HOH2104 4.3 19.2 1.0
C5' B:A6 4.4 16.0 0.5
H1 A:HOH2103 4.5 25.9 1.0
C3' B:A7 4.5 27.3 0.5
H1 B:HOH2602 4.5 15.7 1.0
O5' B:A6 4.5 17.8 0.5
C8 B:A7 4.5 19.7 0.5
H1 A:HOH2104 4.6 19.2 1.0
H4' B:A7 4.6 25.1 0.5
O B:HOH2203 4.7 33.5 1.0
H1 B:HOH2211 4.7 66.1 1.0
O A:HOH2104 4.8 19.2 1.0
C1' B:A6 4.9 17.3 0.5

Phosphorus binding site 8 out of 21 in 1a34

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Phosphorus binding site 8 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:37.7
occ:0.50
P B:A8 0.0 37.7 0.5
OP1 B:A8 1.5 39.3 0.5
OP2 B:A8 1.5 37.7 0.5
O5' B:A8 1.6 46.7 0.5
O3' B:A7 1.6 33.5 0.5
C5' B:A8 2.5 60.7 0.5
H5' B:A8 2.5 73.8 0.5
C3' B:A7 2.6 27.3 0.5
H5'' B:A8 2.8 73.8 0.5
H3' B:A7 2.9 25.1 0.5
C2' B:A7 3.5 23.6 0.5
H2' B:A7 3.5 25.1 0.5
H2 B:HOH2210 3.6 67.4 1.0
C4' B:A8 3.8 72.9 0.5
H8 B:A8 3.8 71.9 0.5
C4' B:A7 3.9 25.2 0.5
H3' B:A8 3.9 73.8 0.5
O2' B:A7 4.0 24.3 0.5
O4' B:A8 4.1 74.0 0.5
H4' B:A7 4.3 25.1 0.5
HO2' B:A7 4.4 25.1 0.5
H5'' B:A7 4.4 25.1 0.5
C3' B:A8 4.4 81.4 0.5
C5' B:A7 4.6 22.5 0.5
O B:HOH2210 4.6 67.4 1.0
H4' B:A8 4.6 73.8 0.5
H1 A:HOH2207 4.7 59.2 1.0
C1' B:A7 4.8 23.9 0.5
O5' B:A7 4.8 21.3 0.5
C8 B:A8 4.8 71.4 0.5
H1 B:HOH2210 4.9 67.4 1.0
O4' B:A7 4.9 24.4 0.5

Phosphorus binding site 9 out of 21 in 1a34

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Phosphorus binding site 9 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:0.3
occ:0.50
P B:A9 0.0 0.3 0.5
OP2 B:A9 1.5 0.3 0.5
OP1 B:A9 1.5 0.3 0.5
O5' B:A9 1.6 0.4 0.5
HO2' B:U11 1.6 50.4 0.4
O3' B:A8 1.6 96.7 0.5
O2' B:U11 2.1 53.7 0.4
C5' B:A9 2.6 1.0 0.5
C3' B:A8 2.7 81.4 0.5
H5'' B:A9 2.8 0.4 0.5
H3' B:A8 2.8 73.8 0.5
H5' B:A9 3.0 0.4 0.5
C2' B:U11 3.3 50.6 0.4
H2' B:A8 3.5 73.8 0.5
C2' B:A8 3.6 78.8 0.5
H3' B:A9 3.6 0.4 0.5
H1' B:U11 3.7 50.4 0.4
C4' B:A9 3.9 0.6 0.5
C4' B:A8 4.0 72.9 0.5
H8 B:A9 4.1 0.6 0.5
C3' B:A9 4.1 0.6 0.5
C3' B:U11 4.2 50.1 0.4
H3' B:U11 4.3 50.4 0.4
O2' B:A8 4.3 78.5 0.5
H4' B:A8 4.5 73.8 0.5
O3' B:A9 4.5 0.8 0.5
C1' B:U11 4.5 49.0 0.4
H5'' B:A8 4.5 73.8 0.5
O5' B:A8 4.5 46.7 0.5
HO3' B:U11 4.6 50.4 0.4
C5' B:A8 4.6 60.7 0.5
O4' B:A9 4.6 0.0 0.5
H4' B:A9 4.7 0.4 0.5
HO2' B:A8 4.8 73.8 0.5
C1' B:A8 4.8 74.7 0.5
N1 B:U11 4.9 48.5 0.4
O4' B:A8 5.0 74.0 0.5

Phosphorus binding site 10 out of 21 in 1a34

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Phosphorus binding site 10 out of 21 in the Satellite Tobacco Mosaic Virus/Rna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Satellite Tobacco Mosaic Virus/Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:0.0
occ:0.50
P B:A10 0.0 0.0 0.5
OP1 B:A10 1.5 0.0 0.5
OP2 B:A10 1.5 0.3 0.5
O3' B:A9 1.6 0.8 0.5
O5' B:A10 1.6 0.5 0.5
C3' B:A9 2.7 0.6 0.5
C5' B:A10 2.8 0.1 0.5
H3' B:A9 3.0 0.4 0.5
H5' B:A10 3.1 0.5 0.5
H5'' B:A10 3.1 0.5 0.5
C2' B:A9 3.4 0.6 0.5
H2' B:A9 3.5 0.4 0.5
O2' B:A9 3.5 0.5 0.5
H3' B:A10 3.8 0.5 0.5
C4' B:A9 4.0 0.6 0.5
H4' B:A9 4.1 0.4 0.5
C4' B:A10 4.1 0.3 0.5
H8 B:A10 4.2 0.7 0.5
HO2' B:A9 4.2 0.4 0.5
C3' B:A10 4.5 0.2 0.5
O5' B:A9 4.6 0.4 0.5
H5'' B:A9 4.7 0.4 0.5
C5' B:A9 4.7 1.0 0.5
O4' B:A10 4.7 0.2 0.5
C1' B:A9 4.8 0.7 0.5
H4' B:A10 4.9 0.5 0.5

Reference:

S.B.Larson, J.Day, A.Greenwood, A.Mcpherson. Refined Structure of Satellite Tobacco Mosaic Virus at 1.8 A Resolution. J.Mol.Biol. V. 277 37 1998.
ISSN: ISSN 0022-2836
PubMed: 9514737
DOI: 10.1006/JMBI.1997.1570
Page generated: Fri Sep 25 12:04:39 2020

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