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

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

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 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 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 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 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 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 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 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 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 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 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

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