Phosphorus in PDB 184d: Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution

Protein crystallography data

The structure of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution, PDB code: 184d was solved by G.A.Leonard, S.Zhang, M.R.Peterson, S.J.Harrop, J.R.Helliwell, W.B.T.Cruse, B.Langlois D'estaintot, O.Kennard, 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 C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 22.520, 59.370, 24.350, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution (pdb code 184d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution, PDB code: 184d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 184d

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Phosphorus binding site 1 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:16.9
occ:1.00
P A:DC2 0.0 16.9 1.0
OP2 A:DC2 1.5 17.1 1.0
OP1 A:DC2 1.5 19.7 1.0
O5' A:DC2 1.6 15.1 1.0
O3' A:DG1 1.6 15.6 1.0
C5' A:DC2 2.6 11.7 1.0
C3' A:DG1 2.7 14.1 1.0
C2' A:DG1 3.4 11.2 1.0
O A:HOH40 3.8 48.1 1.0
MG A:MG9 3.8 17.8 0.5
C4' A:DC2 3.9 16.5 1.0
C4' A:DG1 4.0 16.6 1.0
C1' A:DG1 4.1 12.4 1.0
O A:HOH57 4.1 46.9 1.0
C3' A:DC2 4.3 11.8 1.0
O4' A:DC2 4.3 20.3 1.0
O4' A:DG1 4.4 14.4 1.0
O A:HOH24 4.5 28.8 1.0
O3' A:DG5 4.6 19.1 1.0
C5' A:DC6 4.6 17.5 1.0
OP1 A:DC6 4.6 13.7 1.0
C2' A:DC2 4.9 12.3 1.0

Phosphorus binding site 2 out of 6 in 184d

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Phosphorus binding site 2 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:12.0
occ:1.00
P A:DA3 0.0 12.0 1.0
OP2 A:DA3 1.5 7.6 1.0
OP1 A:DA3 1.5 14.4 1.0
O5' A:DA3 1.6 16.6 1.0
O3' A:DC2 1.6 15.8 1.0
C5' A:DA3 2.6 12.5 1.0
C3' A:DC2 2.7 11.8 1.0
O A:HOH42 3.7 43.9 1.0
C2' A:DC2 3.8 12.3 1.0
C4' A:DA3 3.8 3.5 1.0
C4' A:DC2 3.8 16.5 1.0
O A:HOH13 3.9 10.6 0.5
O A:HOH24 4.1 28.8 1.0
O4' A:DA3 4.2 9.4 1.0
C3' A:DA3 4.4 7.6 1.0
C8 A:DA3 4.4 9.0 1.0
O4' A:DG5 4.4 7.2 1.0
C5' A:DC2 4.4 11.7 1.0
C2' A:DA3 4.6 2.0 1.0
O5' A:DC2 4.7 15.1 1.0
C1' A:DC2 4.7 12.8 1.0
O A:HOH26 4.8 29.4 1.0
O4' A:DC2 4.9 20.3 1.0
C1' A:DA3 4.9 7.5 1.0

Phosphorus binding site 3 out of 6 in 184d

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Phosphorus binding site 3 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:14.5
occ:1.00
P A:DT4 0.0 14.5 1.0
OP1 A:DT4 1.5 18.1 1.0
OP2 A:DT4 1.5 18.6 1.0
O5' A:DT4 1.6 11.8 1.0
O3' A:DA3 1.6 13.1 1.0
C5' A:DT4 2.6 13.6 1.0
C3' A:DA3 2.7 7.6 1.0
C2' A:DA3 3.6 2.0 1.0
O A:HOH18 3.7 23.1 1.0
O A:HOH25 3.8 21.1 1.0
C4' A:DT4 3.8 14.3 1.0
C4' A:DA3 3.9 3.5 1.0
O A:HOH11 3.9 32.9 0.5
C6 A:DT4 4.2 7.3 1.0
O4' A:DT4 4.3 11.6 1.0
C3' A:DT4 4.4 20.1 1.0
C1' A:DA3 4.4 7.5 1.0
C2' A:DT4 4.4 13.4 1.0
O4' A:DA3 4.6 9.4 1.0
O A:HOH10 4.6 29.2 0.5
O A:HOH39 4.7 45.9 1.0
O A:HOH12 4.8 14.4 0.5
C7 A:DT4 4.8 10.8 1.0
O A:HOH16 4.8 21.9 1.0
C1' A:DT4 4.9 10.6 1.0
C5' A:DA3 4.9 12.5 1.0
O A:HOH19 5.0 18.6 1.0

Phosphorus binding site 4 out of 6 in 184d

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Phosphorus binding site 4 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:17.3
occ:1.00
P A:DG5 0.0 17.3 1.0
OP1 A:DG5 1.5 17.1 1.0
OP2 A:DG5 1.5 13.1 1.0
O5' A:DG5 1.6 14.2 1.0
O3' A:DT4 1.6 15.6 1.0
C5' A:DG5 2.6 10.5 1.0
C3' A:DT4 2.7 20.1 1.0
O A:HOH44 3.3 35.1 1.0
C4' A:DT4 3.4 14.3 1.0
O A:HOH23 3.6 37.0 1.0
C4' A:DG5 3.8 11.1 1.0
C2' A:DT4 4.0 13.4 1.0
C8 A:DG5 4.2 3.4 1.0
C3' A:DG5 4.3 10.7 1.0
C2' A:DG5 4.3 6.5 1.0
O4' A:DG5 4.3 7.2 1.0
O4' A:DT4 4.4 11.6 1.0
C1' A:DT4 4.5 10.6 1.0
C5' A:DT4 4.5 13.6 1.0
C1' A:DG5 4.8 11.0 1.0
O A:HOH27 4.8 25.8 1.0
N9 A:DG5 4.9 8.0 1.0
O A:HOH37 5.0 45.4 1.0

Phosphorus binding site 5 out of 6 in 184d

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Phosphorus binding site 5 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:18.8
occ:1.00
P A:DC6 0.0 18.8 1.0
OP1 A:DC6 1.5 13.7 1.0
OP2 A:DC6 1.5 17.7 1.0
O3' A:DG5 1.6 19.1 1.0
O5' A:DC6 1.6 19.7 1.0
C5' A:DC6 2.6 17.5 1.0
C3' A:DG5 2.7 10.7 1.0
C2' A:DG5 3.6 6.5 1.0
C4' A:DC6 3.7 9.8 1.0
C4' A:DG5 3.9 11.1 1.0
O A:HOH54 3.9 42.1 0.5
O4' A:DC6 4.1 13.3 1.0
O A:HOH20 4.2 23.7 1.0
C3' A:DC6 4.3 21.1 1.0
MG A:MG9 4.3 17.8 0.5
OP1 A:DC2 4.4 19.7 1.0
C1' A:DG5 4.4 11.0 1.0
O A:HOH30 4.4 20.5 1.0
O A:HOH56 4.4 62.4 1.0
O4' A:DG5 4.6 7.2 1.0
O3' A:DG1 4.7 15.6 1.0
O A:HOH22 4.7 35.9 1.0
C5' A:DC2 4.7 11.7 1.0
C2' A:DC6 4.9 17.7 1.0
C5' A:DG5 4.9 10.5 1.0

Phosphorus binding site 6 out of 6 in 184d

Go back to Phosphorus Binding Sites List in 184d
Phosphorus binding site 6 out of 6 in the Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:24.9
occ:1.00
P A:DT7 0.0 24.9 1.0
OP1 A:DT7 1.5 16.0 1.0
OP2 A:DT7 1.5 17.4 1.0
O5' A:DT7 1.6 16.9 1.0
O3' A:DC6 1.6 18.1 1.0
C5' A:DT7 2.6 13.4 1.0
C3' A:DC6 2.7 21.1 1.0
C2' A:DC6 3.7 17.7 1.0
C4' A:DT7 3.8 16.7 1.0
C4' A:DC6 3.8 9.8 1.0
O4' A:DT7 3.9 12.2 1.0
C6 A:DT7 4.1 14.2 1.0
O A:HOH36 4.1 47.1 1.0
O A:HOH30 4.3 20.5 1.0
C3' A:DT7 4.4 21.5 1.0
C7 A:DT7 4.6 16.9 1.0
C5' A:DC6 4.6 17.5 1.0
C1' A:DC6 4.7 19.8 1.0
C5 A:DT7 4.8 16.2 1.0
O5' A:DC6 4.8 19.7 1.0
C2' A:DT7 4.8 16.7 1.0
C1' A:DT7 4.9 16.1 1.0
N1 A:DT7 4.9 16.4 1.0
O4' A:DC6 4.9 13.3 1.0
O4' A:DG1 4.9 14.4 1.0

Reference:

G.A.Leonard, S.Zhang, M.R.Peterson, S.J.Harrop, J.R.Helliwell, W.B.Cruse, B.L.D'estaintot, O.Kennard, T.Brown, W.N.Hunter. Self-Association of A Dna Loop Creates A Quadruplex: Crystal Structure of D(Gcatgct) at 1.8 A Resolution. Structure V. 3 335 1995.
ISSN: ISSN 0969-2126
PubMed: 7613864
DOI: 10.1016/S0969-2126(01)00165-4
Page generated: Fri Sep 25 11:47:18 2020

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