Phosphorus in PDB 133d: The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)

Protein crystallography data

The structure of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg), PDB code: 133d was solved by A.R.Cervi, A.Guy, G.A.Leonard, R.Teoule, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 17.980, 30.770, 44.760, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) (pdb code 133d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 10 binding sites of Phosphorus where determined in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg), PDB code: 133d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 10 in 133d

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Phosphorus binding site 1 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:14.0
occ:1.00
 P A:DG2 0.0 14.0 1.0
OP1 A:DG2 1.5 19.0 1.0
OP2 A:DG2 1.5 10.2 1.0
O5' A:DG2 1.6 22.2 1.0
O3' A:DC1 1.6 8.9 1.0
C5' A:DG2 2.7 2.1 1.0
C3' A:DC1 2.7 6.0 1.0
C4' A:DC1 3.5 10.3 1.0
C4' A:DG2 3.8 7.0 1.0
O A:HOH14 3.9 12.2 1.0
C2' A:DC1 4.0 2.0 1.0
O4' A:DG2 4.0 2.0 1.0
O A:HOH28 4.0 48.6 1.0
C5' A:DC1 4.4 2.3 1.0
O4' A:DC1 4.5 9.3 1.0
O A:HOH56 4.5 59.3 1.0
O A:HOH16 4.6 12.6 1.0
C1' A:DC1 4.7 14.9 1.0

Phosphorus binding site 2 out of 10 in 133d

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Phosphorus binding site 2 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:56.8
occ:1.00
 P A:DC3 0.0 56.8 1.0
OP2 A:DC3 1.5 13.8 1.0
OP1 A:DC3 1.5 35.3 1.0
O3' A:DG2 1.6 33.8 1.0
O5' A:DC3 1.6 25.2 1.0
C5' A:DC3 2.6 24.0 1.0
C3' A:DG2 2.7 6.4 1.0
O A:HOH53 3.4 49.8 1.0
C4' A:DC3 3.8 4.5 1.0
C4' A:DG2 3.8 7.0 1.0
C2' A:DG2 3.8 9.4 1.0
O4' A:DC3 4.1 13.2 1.0
C5' A:DG2 4.2 2.1 1.0
C3' A:DC3 4.2 2.0 1.0
O A:HOH43 4.5 25.4 1.0
C2' A:DC3 4.6 6.8 1.0
O A:HOH16 4.6 12.6 1.0

Phosphorus binding site 3 out of 10 in 133d

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Phosphorus binding site 3 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:31.8
occ:1.00
 P A:DG4 0.0 31.8 1.0
OP1 A:DG4 1.5 30.2 1.0
OP2 A:DG4 1.5 18.9 1.0
O5' A:DG4 1.6 39.2 1.0
O3' A:DC3 1.6 17.4 1.0
C3' A:DC3 2.6 2.0 1.0
C5' A:DG4 2.7 16.4 1.0
C4' A:DC3 3.2 4.5 1.0
C4' A:DG4 3.8 20.6 1.0
C2' A:DC3 4.0 6.8 1.0
C5' A:DC3 4.0 24.0 1.0
O A:HOH35 4.0 29.7 1.0
O4' A:DG4 4.1 4.7 1.0
O A:HOH50 4.3 30.6 1.0
O A:HOH15 4.3 7.6 1.0
O4' A:DC3 4.3 13.2 1.0
O A:HOH49 4.4 43.3 1.0
C1' A:DC3 4.5 5.2 1.0
O A:HOH34 4.6 23.9 1.0
O A:HOH19 4.6 43.1 1.0
O A:HOH58 4.7 64.6 1.0
O A:HOH26 4.9 45.7 1.0

Phosphorus binding site 4 out of 10 in 133d

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Phosphorus binding site 4 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:53.0
occ:1.00
 P A:C345 0.0 53.0 1.0
OP1 A:C345 1.5 44.4 1.0
OP2 A:C345 1.5 32.4 1.0
O3' A:DG4 1.6 37.8 1.0
O5' A:C345 1.6 19.5 1.0
C5' A:C345 2.6 7.1 1.0
C3' A:DG4 2.7 20.3 1.0
C4' A:DG4 3.6 20.6 1.0
O A:HOH19 3.9 43.1 1.0
C4' A:C345 3.9 2.0 1.0
C2' A:DG4 3.9 16.9 1.0
C5' A:DG4 4.0 16.4 1.0
C3' A:C345 4.2 9.3 1.0
O4' A:C345 4.4 2.3 1.0
C2' A:C345 4.6 2.0 1.0
O4' A:DG4 4.9 4.7 1.0
C6 A:C345 5.0 2.0 1.0

Phosphorus binding site 5 out of 10 in 133d

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Phosphorus binding site 5 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:25.6
occ:1.00
 P A:DG6 0.0 25.6 1.0
OP1 A:DG6 1.5 10.5 1.0
OP2 A:DG6 1.5 18.5 1.0
O5' A:DG6 1.6 35.3 1.0
O3' A:C345 1.6 12.4 1.0
C3' A:C345 2.7 9.3 1.0
C5' A:DG6 2.7 25.0 1.0
C4' A:C345 3.2 2.0 1.0
C4' A:DG6 3.7 11.8 1.0
C2' A:C345 3.9 2.0 1.0
O4' A:DG6 4.0 29.1 1.0
O A:HOH52 4.1 45.0 1.0
C5' A:C345 4.3 7.1 1.0
O4' A:C345 4.3 2.3 1.0
C1' A:C345 4.3 18.1 1.0
O A:HOH38 4.6 10.9 1.0
N3 A:DG6 4.8 9.1 1.0

Phosphorus binding site 6 out of 10 in 133d

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Phosphorus binding site 6 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:19.5
occ:1.00
 P B:DG8 0.0 19.5 1.0
OP2 B:DG8 1.5 21.8 1.0
OP1 B:DG8 1.5 33.9 1.0
O3' B:DC7 1.6 10.4 1.0
O5' B:DG8 1.7 11.8 1.0
C5' B:DG8 2.6 12.8 1.0
C3' B:DC7 2.7 2.0 1.0
C4' B:DC7 3.6 3.6 1.0
C2' B:DC7 3.8 2.0 1.0
C4' B:DG8 3.9 8.1 1.0
O B:HOH31 4.0 31.5 1.0
O4' B:DG8 4.2 8.3 1.0
O B:HOH25 4.5 13.0 1.0
O5' B:DC7 4.5 9.6 1.0
C1' B:DC7 4.5 2.0 1.0
C5' B:DC7 4.6 2.7 1.0
O4' B:DC7 4.6 11.5 1.0
O B:HOH21 4.8 8.2 1.0

Phosphorus binding site 7 out of 10 in 133d

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Phosphorus binding site 7 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:34.7
occ:1.00
 P B:DC9 0.0 34.7 1.0
OP1 B:DC9 1.5 34.0 1.0
OP2 B:DC9 1.5 9.6 1.0
O3' B:DG8 1.6 24.6 1.0
O5' B:DC9 1.6 15.3 1.0
C5' B:DC9 2.6 8.7 1.0
C3' B:DG8 2.8 21.1 1.0
C4' B:DG8 3.8 8.1 1.0
C4' B:DC9 3.8 4.3 1.0
C2' B:DG8 3.9 4.4 1.0
O B:HOH48 3.9 63.4 1.0
C3' B:DC9 4.1 8.6 1.0
C2' B:DC9 4.1 2.7 1.0
O B:HOH23 4.1 22.0 1.0
O4' B:DC9 4.2 11.4 1.0
C5' B:DG8 4.3 12.8 1.0
O B:HOH22 4.4 33.3 1.0
O B:HOH40 4.7 33.9 1.0
C6 B:DC9 4.8 7.1 1.0
C1' B:DC9 4.9 3.2 1.0

Phosphorus binding site 8 out of 10 in 133d

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Phosphorus binding site 8 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:34.6
occ:1.00
 P B:DG10 0.0 34.6 1.0
OP2 B:DG10 1.5 18.3 1.0
OP1 B:DG10 1.5 27.7 1.0
O5' B:DG10 1.6 23.2 1.0
O3' B:DC9 1.7 11.7 1.0
C3' B:DC9 2.5 8.6 1.0
C5' B:DG10 2.6 28.9 1.0
C4' B:DC9 3.2 4.3 1.0
C4' B:DG10 3.9 25.9 1.0
C2' B:DC9 3.9 2.7 1.0
C5' B:DC9 4.2 8.7 1.0
O4' B:DG10 4.2 9.4 1.0
O4' B:DC9 4.3 11.4 1.0
O B:HOH60 4.3 50.0 1.0
C1' B:DC9 4.4 3.2 1.0
O B:HOH37 4.6 37.5 1.0
O B:HOH17 4.8 17.5 1.0
O5' B:DC9 4.9 15.3 1.0

Phosphorus binding site 9 out of 10 in 133d

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Phosphorus binding site 9 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:32.1
occ:1.00
 P B:C3411 0.0 32.1 1.0
OP2 B:C3411 1.5 29.6 1.0
OP1 B:C3411 1.5 38.0 1.0
O5' B:C3411 1.6 18.8 1.0
O3' B:DG10 1.6 19.3 1.0
C3' B:DG10 2.6 18.2 1.0
C5' B:C3411 2.7 15.5 1.0
C4' B:C3411 3.6 2.0 1.0
C4' B:DG10 3.7 25.9 1.0
C2' B:DG10 3.8 8.2 1.0
C3' B:C3411 3.9 2.0 1.0
C5' B:DG10 4.0 28.9 1.0
C2' B:C3411 4.1 2.0 1.0
O4' B:C3411 4.4 20.1 1.0
O B:HOH17 4.5 17.5 1.0
C1' B:C3411 4.9 5.3 1.0
O4' B:DG10 4.9 9.4 1.0
C1' B:DG10 5.0 6.9 1.0

Phosphorus binding site 10 out of 10 in 133d

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Phosphorus binding site 10 out of 10 in the The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Crystal Structure of N4-Methylcytosine.Guanosin Base- Pairs in the Synthetic Hexanucleotide D(Cgcgm(4)Cg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:18.3
occ:1.00
 P B:DG12 0.0 18.3 1.0
OP2 B:DG12 1.5 23.1 1.0
OP1 B:DG12 1.5 24.4 1.0
O5' B:DG12 1.6 9.1 1.0
O3' B:C3411 1.6 12.9 1.0
C5' B:DG12 2.6 2.0 1.0
C3' B:C3411 2.6 2.0 1.0
C4' B:C3411 3.4 2.0 1.0
C4' B:DG12 3.7 2.0 1.0
O B:HOH51 3.8 58.6 1.0
C2' B:C3411 4.0 2.0 1.0
O4' B:DG12 4.0 3.6 1.0
O B:HOH13 4.2 37.3 1.0
C5' B:C3411 4.2 15.5 1.0
O4' B:C3411 4.4 20.1 1.0
O B:HOH36 4.6 16.6 1.0
C1' B:C3411 4.6 5.3 1.0

Reference:

A.R.Cervi, A.Guy, G.A.Leonard, R.Teoule, W.N.Hunter. The Crystal Structure of N4-Methylcytosine.Guanosine Base-Pairs in the Synthetic Hexanucleotide D(CGCGM4CG). Nucleic Acids Res. V. 21 5623 1993.
ISSN: ISSN 0305-1048
PubMed: 8284207
DOI: 10.1093/NAR/21.24.5623
Page generated: Fri Sep 25 11:19:19 2020

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