Phosphorus in PDB 116d: Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis

Protein crystallography data

The structure of Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis, PDB code: 116d was solved by C.A.Bingman, G.Zon, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 46.200, 46.200, 71.500, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis (pdb code 116d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 11 binding sites of Phosphorus where determined in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis, PDB code: 116d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 11 in 116d

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Phosphorus binding site 1 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:45.5
occ:1.00
P A:DC2 0.0 45.5 1.0
OP2 A:DC2 1.5 43.7 1.0
OP1 A:DC2 1.5 46.9 1.0
O5' A:DC2 1.6 45.3 1.0
O3' A:DC1 1.6 46.6 1.0
C3' A:DC1 2.5 48.2 1.0
C5' A:DC2 2.7 41.6 1.0
O A:HOH21 3.3 52.4 1.0
C2' A:DC1 3.5 47.5 1.0
C4' A:DC1 3.8 49.4 1.0
C4' A:DC2 3.9 40.8 1.0
O4' A:DC2 4.0 39.3 1.0
C5' A:DC1 4.2 50.5 1.0
O A:HOH32 4.5 76.2 1.0
C6 A:DC2 4.5 38.2 1.0
C3' A:DC2 4.7 40.9 1.0
C1' A:DC1 4.8 46.8 1.0
O4' A:DC1 4.8 49.4 1.0

Phosphorus binding site 2 out of 11 in 116d

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Phosphorus binding site 2 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:41.1
occ:1.00
P A:DG3 0.0 41.1 1.0
OP2 A:DG3 1.5 39.4 1.0
OP1 A:DG3 1.5 42.1 1.0
O5' A:DG3 1.6 38.8 1.0
O3' A:DC2 1.7 40.7 1.0
C3' A:DC2 2.5 40.9 1.0
C5' A:DG3 2.6 38.2 1.0
C2' A:DC2 3.5 39.3 1.0
C4' A:DC2 3.8 40.8 1.0
C4' A:DG3 3.8 36.2 1.0
O4' A:DG3 4.0 34.9 1.0
C5' A:DC2 4.2 41.6 1.0
C8 A:DG3 4.3 32.2 1.0
O A:HOH21 4.6 52.4 1.0
C3' A:DG3 4.6 35.3 1.0
O5' A:DC2 4.6 45.3 1.0
C1' A:DC2 4.7 38.5 1.0
O4' A:DC2 4.8 39.3 1.0

Phosphorus binding site 3 out of 11 in 116d

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Phosphorus binding site 3 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:32.8
occ:1.00
P A:DT4 0.0 32.8 1.0
OP1 A:DT4 1.4 32.7 1.0
OP2 A:DT4 1.5 34.5 1.0
O5' A:DT4 1.6 32.6 1.0
O3' A:DG3 1.7 36.1 1.0
C5' A:DT4 2.5 32.6 1.0
C3' A:DG3 2.6 35.3 1.0
C2' A:DG3 3.4 34.3 1.0
C4' A:DT4 3.8 33.1 1.0
C4' A:DG3 3.9 36.2 1.0
O A:HOH23 3.9 57.0 1.0
O4' A:DT4 4.2 32.0 1.0
O A:HOH45 4.3 54.3 1.0
C3' A:DT4 4.3 34.9 1.0
C5' A:DG3 4.3 38.2 1.0
C6 A:DT4 4.4 24.7 1.0
C7 A:DT4 4.7 24.4 1.0
C1' A:DG3 4.7 33.0 1.0
O5' A:DG3 4.9 38.8 1.0
O4' A:DG3 4.9 34.9 1.0
OP2 A:DA5 5.0 39.5 1.0
O3' A:DT4 5.0 39.5 1.0

Phosphorus binding site 4 out of 11 in 116d

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Phosphorus binding site 4 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:41.4
occ:1.00
P A:DA5 0.0 41.4 1.0
OP1 A:DA5 1.5 42.5 1.0
OP2 A:DA5 1.5 39.5 1.0
O5' A:DA5 1.6 38.6 1.0
O3' A:DT4 1.7 39.5 1.0
C3' A:DT4 2.6 34.9 1.0
C5' A:DA5 2.7 37.0 1.0
C2' A:DT4 3.3 33.0 1.0
C4' A:DA5 3.9 36.1 1.0
C4' A:DT4 3.9 33.1 1.0
O4' A:DA5 4.1 35.8 1.0
O A:HOH23 4.1 57.0 1.0
C8 A:DA5 4.3 27.7 1.0
O A:HOH34 4.5 44.7 1.0
O A:HOH24 4.5 67.5 1.0
C3' A:DA5 4.5 36.4 1.0
C5' A:DT4 4.5 32.6 1.0
C1' A:DT4 4.6 27.3 1.0
O5' A:DT4 4.7 32.6 1.0
OP2 A:DC6 4.8 41.7 1.0
O4' A:DT4 4.8 32.0 1.0

Phosphorus binding site 5 out of 11 in 116d

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Phosphorus binding site 5 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:41.6
occ:1.00
P A:DC6 0.0 41.6 1.0
OP1 A:DC6 1.5 43.6 1.0
OP2 A:DC6 1.5 41.7 1.0
O5' A:DC6 1.6 40.0 1.0
O3' A:DA5 1.6 39.4 1.0
C3' A:DA5 2.5 36.4 1.0
C5' A:DC6 2.6 38.7 1.0
O A:HOH25 3.2 44.3 1.0
C2' A:DA5 3.5 34.9 1.0
C4' A:DA5 3.8 36.1 1.0
C4' A:DC6 3.8 36.9 1.0
O A:HOH42 4.0 63.6 1.0
C3' A:DC6 4.2 37.3 1.0
C5' A:DA5 4.2 37.0 1.0
O4' A:DC6 4.3 36.6 1.0
O A:HOH34 4.3 44.7 1.0
C6 A:DC6 4.3 29.0 1.0
O A:HOH24 4.4 67.5 1.0
OP2 A:DG7 4.7 39.6 1.0
C1' A:DA5 4.7 31.7 1.0
O5' A:DA5 4.8 38.6 1.0
O4' A:DA5 4.8 35.8 1.0
O3' A:DC6 4.9 40.2 1.0
C5 A:DC6 5.0 28.8 1.0

Phosphorus binding site 6 out of 11 in 116d

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Phosphorus binding site 6 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:40.4
occ:1.00
P A:DG7 0.0 40.4 1.0
OP1 A:DG7 1.5 42.3 1.0
OP2 A:DG7 1.5 39.6 1.0
O5' A:DG7 1.6 37.4 1.0
O3' A:DC6 1.6 40.2 1.0
C5' A:DG7 2.6 36.0 1.0
C3' A:DC6 2.7 37.3 1.0
O A:HOH20 3.4 77.3 1.0
C2' A:DC6 3.5 36.0 1.0
C4' A:DG7 3.9 33.5 1.0
C4' A:DC6 4.0 36.9 1.0
O4' A:DG7 4.1 32.0 1.0
O5' A:DC6 4.3 40.0 1.0
O A:HOH18 4.4 60.4 1.0
C8 A:DG7 4.5 25.7 1.0
C5' A:DC6 4.6 38.7 1.0
C3' A:DG7 4.6 33.2 1.0
O A:HOH25 4.6 44.3 1.0
C1' A:DC6 4.8 32.9 1.0
O4' A:DC6 5.0 36.6 1.0

Phosphorus binding site 7 out of 11 in 116d

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Phosphorus binding site 7 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:35.7
occ:1.00
P A:DT8 0.0 35.7 1.0
OP1 A:DT8 1.5 37.1 1.0
OP2 A:DT8 1.5 35.9 1.0
O5' A:DT8 1.6 34.5 1.0
O3' A:DG7 1.6 34.9 1.0
C3' A:DG7 2.6 33.2 1.0
C5' A:DT8 2.6 35.3 1.0
C2' A:DG7 3.5 31.1 1.0
C4' A:DG7 3.8 33.5 1.0
C4' A:DT8 3.9 35.6 1.0
C5' A:DG7 4.3 36.0 1.0
C3' A:DT8 4.4 36.5 1.0
O4' A:DT8 4.4 34.1 1.0
O A:HOH35 4.4 45.6 1.0
C6 A:DT8 4.5 30.4 1.0
C7 A:DT8 4.6 28.4 1.0
O A:HOH20 4.8 77.3 1.0
OP2 A:DA9 4.8 43.6 1.0
C1' A:DG7 4.8 29.8 1.0
O4' A:DG7 4.9 32.0 1.0
O3' A:DT8 4.9 41.6 1.0
O5' A:DG7 5.0 37.4 1.0

Phosphorus binding site 8 out of 11 in 116d

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Phosphorus binding site 8 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:44.8
occ:1.00
P A:DA9 0.0 44.8 1.0
OP1 A:DA9 1.5 44.5 1.0
OP2 A:DA9 1.5 43.6 1.0
O5' A:DA9 1.6 42.2 1.0
O3' A:DT8 1.7 41.6 1.0
C5' A:DA9 2.6 39.3 1.0
C3' A:DT8 2.6 36.5 1.0
O A:HOH35 2.9 45.6 1.0
C2' A:DT8 3.5 33.4 1.0
O A:HOH27 3.8 52.5 1.0
C4' A:DA9 3.9 39.4 1.0
C4' A:DT8 3.9 35.6 1.0
O4' A:DA9 4.0 38.4 1.0
O A:HOH28 4.1 47.2 1.0
O5' A:DT8 4.3 34.5 1.0
O A:HOH49 4.4 69.1 1.0
C8 A:DA9 4.4 34.0 1.0
C5' A:DT8 4.5 35.3 1.0
C3' A:DA9 4.6 41.5 1.0
C1' A:DT8 4.8 31.5 1.0
O4' A:DT8 5.0 34.1 1.0

Phosphorus binding site 9 out of 11 in 116d

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Phosphorus binding site 9 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:44.5
occ:1.00
P A:DC10 0.0 44.5 1.0
OP2 A:DC10 1.5 41.4 1.0
OP1 A:DC10 1.5 46.6 1.0
O5' A:DC10 1.6 44.0 1.0
O3' A:DA9 1.6 43.4 1.0
C3' A:DA9 2.6 41.5 1.0
C5' A:DC10 2.6 42.3 1.0
O A:HOH37 3.0 61.2 1.0
O A:HOH36 3.5 65.2 1.0
C2' A:DA9 3.5 40.7 1.0
C4' A:DA9 3.8 39.4 1.0
C4' A:DC10 3.9 40.0 1.0
O A:HOH28 4.0 47.2 1.0
O4' A:DC10 4.1 39.0 1.0
C6 A:DC10 4.1 33.2 1.0
C5' A:DA9 4.3 39.3 1.0
C3' A:DC10 4.5 40.3 1.0
O5' A:DA9 4.7 42.2 1.0
C1' A:DA9 4.7 36.0 1.0
C5 A:DC10 4.8 32.7 1.0
O4' A:DA9 4.8 38.4 1.0

Phosphorus binding site 10 out of 11 in 116d

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Phosphorus binding site 10 out of 11 in the Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis


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 the A-Dna Dodecamer D(Ccgtacgtacgg): Choice of Fragment Helical Axis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:42.7
occ:1.00
P A:DG11 0.0 42.7 1.0
OP2 A:DG11 1.5 42.3 1.0
OP1 A:DG11 1.5 43.5 1.0
O5' A:DG11 1.6 42.4 1.0
O3' A:DC10 1.6 43.1 1.0
C5' A:DG11 2.6 40.6 1.0
C3' A:DC10 2.7 40.3 1.0
C2' A:DC10 3.5 37.5 1.0
O A:HOH51 3.7 75.1 1.0
C4' A:DG11 3.9 38.6 1.0
C4' A:DC10 4.0 40.0 1.0
O4' A:DG11 4.3 37.3 1.0
C3' A:DG11 4.3 38.0 1.0
C8 A:DG11 4.4 32.7 1.0
C5' A:DC10 4.5 42.3 1.0
O A:HOH30 4.6 54.5 1.0
C1' A:DC10 4.8 36.4 1.0
O5' A:DC10 4.9 44.0 1.0
O A:HOH36 4.9 65.2 1.0
O3' A:DG11 4.9 38.4 1.0
OP2 A:DG12 5.0 36.4 1.0
O4' A:DC10 5.0 39.0 1.0

Reference:

C.A.Bingman, G.Zon, M.Sundaralingam. Crystal and Molecular Structure of the A-Dna Dodecamer D(Ccgtacgtacgg). Choice of Fragment Helical Axis. J.Mol.Biol. V. 227 738 1992.
ISSN: ISSN 0022-2836
PubMed: 1404387
DOI: 10.1016/0022-2836(92)90221-5
Page generated: Fri Sep 25 11:11:13 2020

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