Phosphorus in PDB 117d: Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)

Protein crystallography data

The structure of Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg), PDB code: 117d was solved by C.Bingman, S.Jain, 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 / 2.55
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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) (pdb code 117d). 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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg), PDB code: 117d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 11 in 117d

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Phosphorus binding site 1 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:30.4
occ:1.00
P A:DC2 0.0 30.4 1.0
OP1 A:DC2 1.5 25.4 1.0
OP2 A:DC2 1.5 29.5 1.0
O5' A:DC2 1.6 28.1 1.0
O3' A:DG1 1.7 30.3 1.0
C5' A:DC2 2.5 25.3 1.0
C3' A:DG1 2.6 31.9 1.0
O A:HOH35 3.2 63.2 1.0
O A:HOH13 3.3 37.8 1.0
C4' A:DG1 3.5 34.5 1.0
C5' A:DG1 3.6 36.9 1.0
C4' A:DC2 3.7 21.9 1.0
O4' A:DC2 3.8 20.0 1.0
C2' A:DG1 3.8 32.6 1.0
O A:HOH24 4.1 59.8 1.0
C6 A:DC2 4.3 18.7 1.0
O A:HOH14 4.5 62.5 1.0
C3' A:DC2 4.6 21.6 1.0
O4' A:DG1 4.7 35.3 1.0
C1' A:DG1 4.9 32.9 1.0
C1' A:DC2 5.0 21.5 1.0

Phosphorus binding site 2 out of 11 in 117d

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Phosphorus binding site 2 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:26.9
occ:1.00
P A:DG3 0.0 26.9 1.0
OP1 A:DG3 1.5 25.1 1.0
OP2 A:DG3 1.5 27.8 1.0
O5' A:DG3 1.6 21.8 1.0
O3' A:DC2 1.6 23.8 1.0
C3' A:DC2 2.5 21.6 1.0
C5' A:DG3 2.6 23.0 1.0
C2' A:DC2 3.4 19.4 1.0
C4' A:DC2 3.8 21.9 1.0
C4' A:DG3 3.8 23.7 1.0
O4' A:DG3 4.0 24.6 1.0
C5' A:DC2 4.1 25.3 1.0
C8 A:DG3 4.2 23.7 1.0
O5' A:DC2 4.4 28.1 1.0
C3' A:DG3 4.5 23.1 1.0
C1' A:DC2 4.6 21.5 1.0
O A:HOH24 4.6 59.8 1.0
O4' A:DC2 4.7 20.0 1.0
O A:HOH35 5.0 63.2 1.0
O A:HOH45 5.0 47.5 1.0

Phosphorus binding site 3 out of 11 in 117d

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Phosphorus binding site 3 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:18.6
occ:1.00
P A:DT4 0.0 18.6 1.0
OP2 A:DT4 1.5 16.2 1.0
OP1 A:DT4 1.5 18.2 1.0
O5' A:DT4 1.6 17.3 1.0
O3' A:DG3 1.7 24.2 1.0
C3' A:DG3 2.6 23.1 1.0
C5' A:DT4 2.6 18.4 1.0
C2' A:DG3 3.4 22.6 1.0
C4' A:DT4 3.9 16.7 1.0
O A:HOH26 3.9 47.8 1.0
C4' A:DG3 3.9 23.7 1.0
O A:HOH36 4.0 23.4 1.0
C3' A:DT4 4.3 18.9 1.0
O4' A:DT4 4.3 16.2 1.0
C5' A:DG3 4.5 23.0 1.0
C6 A:DT4 4.6 12.3 1.0
C1' A:DG3 4.7 23.0 1.0
O4' A:DG3 4.9 24.6 1.0
O3' A:DT4 4.9 22.8 1.0
O5' A:DG3 4.9 21.8 1.0
C7 A:DT4 4.9 11.6 1.0

Phosphorus binding site 4 out of 11 in 117d

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Phosphorus binding site 4 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:22.2
occ:1.00
P A:DA5 0.0 22.2 1.0
OP1 A:DA5 1.5 25.8 1.0
OP2 A:DA5 1.5 21.8 1.0
O5' A:DA5 1.6 23.1 1.0
O3' A:DT4 1.7 22.8 1.0
C5' A:DA5 2.6 20.6 1.0
C3' A:DT4 2.7 18.9 1.0
C2' A:DT4 3.3 16.9 1.0
C4' A:DA5 3.9 19.5 1.0
C4' A:DT4 4.0 16.7 1.0
O A:HOH19 4.2 29.8 1.0
C8 A:DA5 4.2 16.0 1.0
C3' A:DA5 4.3 23.1 1.0
O4' A:DA5 4.3 19.8 1.0
O A:HOH26 4.4 47.8 1.0
C1' A:DT4 4.7 13.7 1.0
C5' A:DT4 4.7 18.4 1.0
O5' A:DT4 4.8 17.3 1.0
OP2 A:DC6 4.8 31.2 1.0
O4' A:DT4 4.9 16.2 1.0

Phosphorus binding site 5 out of 11 in 117d

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Phosphorus binding site 5 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:28.3
occ:1.00
P A:DC6 0.0 28.3 1.0
OP1 A:DC6 1.5 30.2 1.0
OP2 A:DC6 1.5 31.2 1.0
O5' A:DC6 1.6 29.7 1.0
O3' A:DA5 1.6 26.9 1.0
C3' A:DA5 2.6 23.1 1.0
C5' A:DC6 2.6 29.2 1.0
C2' A:DA5 3.3 23.7 1.0
C4' A:DC6 3.8 27.5 1.0
C4' A:DA5 3.9 19.5 1.0
C6 A:DC6 4.0 23.5 1.0
O4' A:DC6 4.0 24.8 1.0
C3' A:DC6 4.4 25.9 1.0
O5' A:DA5 4.5 23.1 1.0
C5' A:DA5 4.6 20.6 1.0
C1' A:DA5 4.7 20.5 1.0
C5 A:DC6 4.7 22.6 1.0
O A:HOH28 4.7 64.6 1.0
O A:HOH19 4.9 29.8 1.0
O4' A:DA5 4.9 19.8 1.0
N1 A:DC6 4.9 21.8 1.0
OP2 A:DG7 4.9 29.2 1.0
C1' A:DC6 5.0 23.7 1.0

Phosphorus binding site 6 out of 11 in 117d

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Phosphorus binding site 6 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:30.0
occ:1.00
P A:DG7 0.0 30.0 1.0
OP1 A:DG7 1.5 32.2 1.0
OP2 A:DG7 1.5 29.2 1.0
O5' A:DG7 1.6 29.9 1.0
O3' A:DC6 1.6 28.5 1.0
C3' A:DC6 2.6 25.9 1.0
C5' A:DG7 2.7 25.4 1.0
C2' A:DC6 3.5 23.9 1.0
C4' A:DC6 3.9 27.5 1.0
C4' A:DG7 3.9 23.9 1.0
O A:HOH29 4.1 57.9 1.0
O4' A:DG7 4.2 24.6 1.0
C5' A:DC6 4.3 29.2 1.0
O A:HOH28 4.4 64.6 1.0
C3' A:DG7 4.5 20.7 1.0
C8 A:DG7 4.7 18.5 1.0
O5' A:DC6 4.7 29.7 1.0
C1' A:DC6 4.8 23.7 1.0
OP2 A:DT8 4.8 22.8 1.0
O4' A:DC6 4.9 24.8 1.0

Phosphorus binding site 7 out of 11 in 117d

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Phosphorus binding site 7 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:21.6
occ:1.00
P A:DT8 0.0 21.6 1.0
OP1 A:DT8 1.5 19.2 1.0
OP2 A:DT8 1.5 22.8 1.0
O3' A:DG7 1.6 23.0 1.0
O5' A:DT8 1.6 22.8 1.0
C3' A:DG7 2.6 20.7 1.0
C5' A:DT8 2.6 20.5 1.0
C2' A:DG7 3.6 17.8 1.0
C4' A:DG7 3.8 23.9 1.0
C4' A:DT8 3.9 21.5 1.0
C5' A:DG7 4.1 25.4 1.0
O4' A:DT8 4.3 21.2 1.0
C6 A:DT8 4.3 17.3 1.0
C3' A:DT8 4.4 21.9 1.0
O5' A:DG7 4.5 29.9 1.0
C7 A:DT8 4.6 14.8 1.0
C1' A:DG7 4.8 20.8 1.0
O4' A:DG7 4.9 24.6 1.0
C5 A:DT8 5.0 17.5 1.0

Phosphorus binding site 8 out of 11 in 117d

Go back to Phosphorus Binding Sites List in 117d
Phosphorus binding site 8 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:27.4
occ:1.00
P A:DA9 0.0 27.4 1.0
OP1 A:DA9 1.5 31.4 1.0
OP2 A:DA9 1.5 30.4 1.0
O5' A:DA9 1.6 24.1 1.0
O3' A:DT8 1.6 24.2 1.0
C5' A:DA9 2.6 24.0 1.0
C3' A:DT8 2.6 21.9 1.0
C2' A:DT8 3.3 18.3 1.0
C4' A:DA9 3.9 21.7 1.0
C4' A:DT8 4.0 21.5 1.0
O A:HOH31 4.0 35.0 1.0
C3' A:DA9 4.3 23.8 1.0
C8 A:DA9 4.4 18.7 1.0
O4' A:DA9 4.4 24.4 1.0
O5' A:DT8 4.6 22.8 1.0
C1' A:DT8 4.7 20.1 1.0
C5' A:DT8 4.7 20.5 1.0
O3' A:DA9 4.9 24.4 1.0
O4' A:DT8 4.9 21.2 1.0
O A:HOH22 5.0 33.1 1.0

Phosphorus binding site 9 out of 11 in 117d

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Phosphorus binding site 9 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:21.4
occ:1.00
P A:DC10 0.0 21.4 1.0
OP2 A:DC10 1.5 19.5 1.0
OP1 A:DC10 1.5 26.6 1.0
O5' A:DC10 1.6 23.6 1.0
O3' A:DA9 1.6 24.4 1.0
C5' A:DC10 2.6 22.3 1.0
C3' A:DA9 2.6 23.8 1.0
C2' A:DA9 3.2 20.1 1.0
C4' A:DC10 3.9 16.9 1.0
C4' A:DA9 3.9 21.7 1.0
O A:HOH32 3.9 61.1 1.0
O4' A:DC10 4.0 17.6 1.0
C6 A:DC10 4.5 14.9 1.0
O A:HOH31 4.5 35.0 1.0
C1' A:DA9 4.6 17.8 1.0
C5' A:DA9 4.6 24.0 1.0
O5' A:DA9 4.7 24.1 1.0
C3' A:DC10 4.7 16.6 1.0
O4' A:DA9 4.9 24.4 1.0

Phosphorus binding site 10 out of 11 in 117d

Go back to Phosphorus Binding Sites List in 117d
Phosphorus binding site 10 out of 11 in the Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg)


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 Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:23.5
occ:1.00
P A:DG11 0.0 23.5 1.0
OP2 A:DG11 1.5 24.5 1.0
OP1 A:DG11 1.5 22.3 1.0
O3' A:DC10 1.6 21.0 1.0
O5' A:DG11 1.6 26.7 1.0
C3' A:DC10 2.6 16.6 1.0
C5' A:DG11 2.7 22.8 1.0
C2' A:DC10 3.5 13.7 1.0
C4' A:DC10 3.9 16.9 1.0
C4' A:DG11 3.9 21.9 1.0
O A:HOH33 4.0 30.6 1.0
O A:HOH34 4.2 14.5 1.0
C3' A:DG11 4.3 20.8 1.0
C8 A:DG11 4.3 21.6 1.0
C5' A:DC10 4.3 22.3 1.0
O4' A:DG11 4.3 21.5 1.0
C1' A:DC10 4.8 13.8 1.0
O4' A:DC10 4.9 17.6 1.0
O3' A:DG11 4.9 19.9 1.0

Reference:

C.Bingman, S.Jain, G.Zon, M.Sundaralingam. Crystal and Molecular Structure of the Alternating Dodecamer D(Gcgtacgtacgc) in the A-Dna Form: Comparison with the Isomorphous Non-Alternating Dodecamer D(Ccgtacgtacgg). Nucleic Acids Res. V. 20 6637 1992.
ISSN: ISSN 0305-1048
PubMed: 1480485
DOI: 10.1093/NAR/20.24.6637
Page generated: Fri Sep 25 11:11:46 2020

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