Phosphorus in PDB 161d: A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet

Protein crystallography data

The structure of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet, PDB code: 161d was solved by C.Ban, B.Ramakrishnan, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 26.630, 45.240, 47.990, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet (pdb code 161d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet, PDB code: 161d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 161d

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Phosphorus binding site 1 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:36.4
occ:1.00
P A:DC2 0.0 36.4 1.0
OP2 A:DC2 1.5 34.3 1.0
OP1 A:DC2 1.5 33.5 1.0
O3' A:DC1 1.6 34.2 1.0
O5' A:DC2 1.6 35.0 1.0
C3' A:DC1 2.7 35.8 1.0
C5' A:DC2 2.7 32.3 1.0
C2' A:DC1 3.4 34.4 1.0
C4' A:DC1 3.9 38.3 1.0
C4' A:DC2 4.0 30.6 1.0
O A:HOH38 4.0 50.3 1.0
O A:HOH51 4.1 60.5 1.0
O4' A:DC2 4.3 28.1 1.0
C5' A:DC1 4.5 38.8 1.0
C3' A:DC2 4.6 29.2 1.0
C6 A:DC2 4.6 22.1 1.0
C1' A:DC1 4.8 34.9 1.0
O4' A:DC1 5.0 39.0 1.0

Phosphorus binding site 2 out of 18 in 161d

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Phosphorus binding site 2 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:33.5
occ:1.00
P A:DG3 0.0 33.5 1.0
OP1 A:DG3 1.5 34.3 1.0
OP2 A:DG3 1.5 28.7 1.0
O3' A:DC2 1.6 30.1 1.0
O5' A:DG3 1.6 28.5 1.0
C3' A:DC2 2.6 29.2 1.0
C5' A:DG3 2.7 26.3 1.0
C2' A:DC2 3.3 26.5 1.0
C4' A:DC2 3.9 30.6 1.0
C4' A:DG3 4.0 26.6 1.0
O4' A:DG3 4.2 24.4 1.0
O A:HOH51 4.2 60.5 1.0
O A:HOH35 4.3 64.3 1.0
O A:HOH58 4.4 52.5 1.0
O A:HOH50 4.4 52.5 1.0
C5' A:DC2 4.5 32.3 1.0
C1' A:DC2 4.7 26.9 1.0
C3' A:DG3 4.8 25.1 1.0
O5' A:DC2 4.8 35.0 1.0
O4' A:DC2 4.9 28.1 1.0
C8 A:DG3 4.9 18.3 1.0

Phosphorus binding site 3 out of 18 in 161d

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Phosphorus binding site 3 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:33.6
occ:1.00
P A:DG4 0.0 33.6 1.0
OP1 A:DG4 1.5 37.1 1.0
OP2 A:DG4 1.5 39.9 1.0
O5' A:DG4 1.6 34.0 1.0
O3' A:DG3 1.7 27.9 1.0
C3' A:DG3 2.8 25.1 1.0
C5' A:DG4 2.8 28.3 1.0
C2' A:DG3 3.5 21.6 1.0
O A:HOH21 3.9 36.5 1.0
C4' A:DG3 4.0 26.6 1.0
C4' A:DG4 4.1 25.5 1.0
O A:HOH76 4.4 86.9 1.0
C3' A:DG4 4.5 26.7 1.0
O4' A:DG4 4.5 24.7 1.0
C8 A:DG4 4.5 18.7 1.0
O A:HOH27 4.5 32.3 1.0
C5' A:DG3 4.7 26.3 1.0
C1' A:DG3 4.9 21.9 1.0
OP2 A:DC5 4.9 29.3 1.0

Phosphorus binding site 4 out of 18 in 161d

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Phosphorus binding site 4 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:32.1
occ:1.00
P A:DC5 0.0 32.1 1.0
OP2 A:DC5 1.5 29.3 1.0
OP1 A:DC5 1.5 31.3 1.0
O5' A:DC5 1.6 29.6 1.0
O3' A:DG4 1.6 31.5 1.0
C3' A:DG4 2.7 26.7 1.0
C5' A:DC5 2.7 25.8 1.0
C2' A:DG4 3.5 23.0 1.0
O A:HOH21 3.7 36.5 1.0
O A:HOH39 3.9 53.9 1.0
C4' A:DG4 4.0 25.5 1.0
C4' A:DC5 4.0 26.3 1.0
O4' A:DC5 4.3 25.6 1.0
C5' A:DG4 4.4 28.3 1.0
O A:HOH78 4.5 80.6 1.0
O5' A:DG4 4.5 34.0 1.0
C1' A:DG4 4.8 22.8 1.0
O4' A:DG4 5.0 24.7 1.0

Phosphorus binding site 5 out of 18 in 161d

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Phosphorus binding site 5 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:27.9
occ:1.00
P A:G6 0.0 27.9 1.0
OP1 A:G6 1.5 30.6 1.0
OP2 A:G6 1.5 30.7 1.0
O5' A:G6 1.6 29.6 1.0
O3' A:DC5 1.6 27.6 1.0
C3' A:DC5 2.6 25.9 1.0
C5' A:G6 2.7 27.0 1.0
C2' A:DC5 3.6 22.3 1.0
C4' A:DC5 3.8 26.3 1.0
O A:HOH26 4.0 40.8 1.0
C4' A:G6 4.0 25.2 1.0
C5' A:DC5 4.2 25.8 1.0
O A:HOH44 4.3 52.3 1.0
O4' A:G6 4.3 25.7 1.0
C8 A:G6 4.4 19.1 1.0
C3' A:G6 4.5 25.5 1.0
OP2 A:DC7 4.7 31.9 1.0
C1' A:DC5 4.8 24.1 1.0
O4' A:DC5 4.9 25.6 1.0

Phosphorus binding site 6 out of 18 in 161d

Go back to Phosphorus Binding Sites List in 161d
Phosphorus binding site 6 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:27.8
occ:1.00
P A:DC7 0.0 27.8 1.0
OP2 A:DC7 1.5 31.9 1.0
OP1 A:DC7 1.5 29.2 1.0
O3' A:G6 1.6 25.8 1.0
O5' A:DC7 1.6 25.4 1.0
C3' A:G6 2.6 25.5 1.0
C5' A:DC7 2.7 22.5 1.0
C2' A:G6 3.6 24.5 1.0
C4' A:G6 3.9 25.2 1.0
O A:HOH26 3.9 40.8 1.0
C4' A:DC7 4.0 19.9 1.0
O2' A:G6 4.2 24.1 1.0
C5' A:G6 4.2 27.0 1.0
O4' A:DC7 4.2 21.7 1.0
O A:HOH33 4.3 44.3 1.0
O5' A:G6 4.3 29.6 1.0
C6 A:DC7 4.4 20.1 1.0
C3' A:DC7 4.6 19.3 1.0
C1' A:G6 4.8 23.1 1.0
O4' A:G6 5.0 25.7 1.0

Phosphorus binding site 7 out of 18 in 161d

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Phosphorus binding site 7 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:27.8
occ:1.00
P A:DC8 0.0 27.8 1.0
OP2 A:DC8 1.5 28.7 1.0
OP1 A:DC8 1.5 27.4 1.0
O3' A:DC7 1.6 22.2 1.0
O5' A:DC8 1.7 28.9 1.0
C3' A:DC7 2.6 19.3 1.0
C5' A:DC8 2.7 21.4 1.0
C2' A:DC7 3.4 18.0 1.0
C4' A:DC7 3.8 19.9 1.0
O A:HOH68 4.0 71.9 1.0
C4' A:DC8 4.0 19.6 1.0
C5' A:DC7 4.3 22.5 1.0
O4' A:DC8 4.3 17.8 1.0
O5' A:DC7 4.7 25.4 1.0
C3' A:DC8 4.7 18.1 1.0
C1' A:DC7 4.7 20.0 1.0
C6 A:DC8 4.7 17.2 1.0
O4' A:DC7 4.8 21.7 1.0

Phosphorus binding site 8 out of 18 in 161d

Go back to Phosphorus Binding Sites List in 161d
Phosphorus binding site 8 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:25.9
occ:1.00
P A:DG9 0.0 25.9 1.0
OP1 A:DG9 1.5 27.2 1.0
OP2 A:DG9 1.5 25.8 1.0
O5' A:DG9 1.6 23.1 1.0
O3' A:DC8 1.6 24.2 1.0
C5' A:DG9 2.7 23.2 1.0
C3' A:DC8 2.7 18.1 1.0
C2' A:DC8 3.6 18.5 1.0
C4' A:DG9 4.0 25.2 1.0
C4' A:DC8 4.0 19.6 1.0
O A:HOH75 4.2 86.2 1.0
O4' A:DG9 4.3 23.8 1.0
O A:HOH55 4.3 59.0 1.0
C5' A:DC8 4.5 21.4 1.0
C3' A:DG9 4.5 26.3 1.0
C8 A:DG9 4.6 13.9 1.0
C1' A:DC8 4.9 18.2 1.0
O5' A:DC8 4.9 28.9 1.0

Phosphorus binding site 9 out of 18 in 161d

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Phosphorus binding site 9 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:24.8
occ:1.00
P A:DG10 0.0 24.8 1.0
OP2 A:DG10 1.5 23.6 1.0
OP1 A:DG10 1.5 25.3 1.0
O3' A:DG9 1.6 29.8 1.0
O5' A:DG10 1.6 23.8 1.0
C3' A:DG9 2.7 26.3 1.0
C5' A:DG10 2.7 22.0 1.0
C2' A:DG9 3.6 24.4 1.0
O A:HOH22 3.9 54.9 1.0
C4' A:DG9 4.0 25.2 1.0
O A:HOH36 4.0 53.8 1.0
C4' A:DG10 4.0 22.2 1.0
C5' A:DG9 4.5 23.2 1.0
C3' A:DG10 4.5 24.5 1.0
O A:HOH55 4.6 59.0 1.0
O4' A:DG10 4.6 23.4 1.0
O5' A:DG9 4.7 23.1 1.0
C8 A:DG10 4.8 19.2 1.0
C1' A:DG9 4.9 20.9 1.0

Phosphorus binding site 10 out of 18 in 161d

Go back to Phosphorus Binding Sites List in 161d
Phosphorus binding site 10 out of 18 in the A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna: Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc) R(G)D(Ccgg) with A Novel Intermolecular G.C Base-Paired Quadruplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:42.5
occ:1.00
P B:DC12 0.0 42.5 1.0
OP1 B:DC12 1.5 45.1 1.0
OP2 B:DC12 1.5 44.5 1.0
O3' B:DC11 1.6 42.0 1.0
O5' B:DC12 1.6 42.1 1.0
C3' B:DC11 2.7 43.4 1.0
C5' B:DC12 2.7 35.5 1.0
C2' B:DC11 3.5 41.9 1.0
O B:HOH32 3.7 47.6 1.0
O B:HOH46 3.7 53.1 1.0
C4' B:DC11 3.9 45.7 1.0
C4' B:DC12 4.0 32.8 1.0
O B:HOH80 4.0 94.6 1.0
O4' B:DC12 4.3 29.6 1.0
C5' B:DC11 4.4 50.2 1.0
C6 B:DC12 4.5 22.7 1.0
C3' B:DC12 4.5 32.3 1.0
O5' B:DC11 4.5 55.6 1.0
C1' B:DC11 4.8 41.7 1.0
O B:HOH29 4.9 48.5 1.0
OP2 B:DG13 5.0 35.8 1.0

Reference:

C.Ban, B.Ramakrishnan, M.Sundaralingam. A Single 2'-Hydroxyl Group Converts B-Dna to A-Dna. Crystal Structure of the Dna-Rna Chimeric Decamer Duplex D(Ccggc)R(G)D(Ccgg) with A Novel Intermolecular G-C Base-Paired Quadruplet. J.Mol.Biol. V. 236 275 1994.
ISSN: ISSN 0022-2836
PubMed: 7508984
DOI: 10.1006/JMBI.1994.1134
Page generated: Fri Sep 25 11:35:54 2020

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