Phosphorus in PDB 153d: Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine

Protein crystallography data

The structure of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine, PDB code: 153d was solved by S.L.Ginell, J.Vojtechovsky, B.Gaffney, R.Jones, H.M.Berman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.130, 40.450, 64.510, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine (pdb code 153d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine, PDB code: 153d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 153d

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Phosphorus binding site 1 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:12.2
occ:1.00
P A:DG2 0.0 12.2 1.0
OP1 A:DG2 1.5 14.6 1.0
OP2 A:DG2 1.5 10.2 1.0
O5' A:DG2 1.6 10.8 1.0
O3' A:DC1 1.6 7.3 1.0
C5' A:DG2 2.6 9.4 1.0
C3' A:DC1 2.6 7.1 1.0
C2' A:DC1 3.5 6.8 1.0
C4' A:DG2 3.6 9.5 1.0
O4' A:DG2 3.7 8.6 1.0
C4' A:DC1 3.9 7.4 1.0
C1' A:DC1 4.2 6.8 1.0
C3' A:DG2 4.4 8.9 1.0
O4' A:DC1 4.6 7.5 1.0
O5' A:DC1 4.6 9.4 1.0
C5' A:DC1 5.0 7.8 1.0

Phosphorus binding site 2 out of 22 in 153d

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Phosphorus binding site 2 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:15.7
occ:1.00
P A:DA3 0.0 15.7 1.0
OP2 A:DA3 1.5 16.8 1.0
OP1 A:DA3 1.5 10.6 1.0
O3' A:DG2 1.6 9.5 1.0
O5' A:DA3 1.6 12.6 1.0
C5' A:DA3 2.6 11.5 1.0
C3' A:DG2 2.6 8.9 1.0
C2' A:DG2 3.7 8.5 1.0
O4' A:DA3 3.7 10.5 1.0
C4' A:DG2 3.7 9.5 1.0
C4' A:DA3 3.7 10.8 1.0
C5' A:DG2 4.1 9.4 1.0
N3 A:DA3 4.1 10.4 1.0
O5' A:DG2 4.5 10.8 1.0
C2 A:DA3 4.6 10.7 1.0
C1' A:DG2 4.8 8.5 1.0
C3' A:DA3 4.9 11.4 1.0
O4' A:DG2 4.9 8.6 1.0

Phosphorus binding site 3 out of 22 in 153d

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Phosphorus binding site 3 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:16.0
occ:1.00
P A:DG4 0.0 16.0 1.0
OP1 A:DG4 1.5 13.2 1.0
OP2 A:DG4 1.5 14.3 1.0
O5' A:DG4 1.6 8.9 1.0
O3' A:DA3 1.6 12.7 1.0
C3' A:DA3 2.6 11.4 1.0
C5' A:DG4 2.6 8.8 1.0
O A:HOH27 2.8 25.4 1.0
C2' A:DA3 3.2 11.0 1.0
C4' A:DG4 3.9 9.1 1.0
C4' A:DA3 3.9 10.8 1.0
O A:HOH30 4.0 33.6 1.0
C3' A:DG4 4.1 9.1 1.0
C1' A:DA3 4.2 10.4 1.0
O A:HOH26 4.3 24.7 1.0
C2' A:DG4 4.6 9.2 1.0
O4' A:DG4 4.7 8.5 1.0
O4' A:DA3 4.8 10.5 1.0
C5' A:DA3 4.8 11.5 1.0

Phosphorus binding site 4 out of 22 in 153d

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Phosphorus binding site 4 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:11.4
occ:1.00
P A:DA5 0.0 11.4 1.0
OP2 A:DA5 1.5 7.7 1.0
OP1 A:DA5 1.5 14.9 1.0
O5' A:DA5 1.6 6.8 1.0
O3' A:DG4 1.6 9.9 1.0
C5' A:DA5 2.6 6.2 1.0
C3' A:DG4 2.7 9.1 1.0
C2' A:DG4 3.1 9.2 1.0
C4' A:DA5 3.9 6.8 1.0
C1' A:DG4 3.9 8.5 1.0
C4' A:DG4 3.9 9.1 1.0
C8 A:DA5 4.0 5.1 1.0
O4' A:DA5 4.1 7.6 1.0
O4' A:DG4 4.5 8.5 1.0
C2' A:DA5 4.5 7.0 1.0
C3' A:DA5 4.5 7.1 1.0
C1' A:DA5 4.8 6.5 1.0
N9 A:DA5 4.8 5.4 1.0
N7 A:DA5 4.9 5.0 1.0

Phosphorus binding site 5 out of 22 in 153d

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Phosphorus binding site 5 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:11.8
occ:1.00
P A:DA6 0.0 11.8 1.0
OP2 A:DA6 1.5 9.3 1.0
OP1 A:DA6 1.5 14.6 1.0
O5' A:DA6 1.6 8.8 1.0
O3' A:DA5 1.6 6.7 1.0
C5' A:DA6 2.6 8.9 1.0
C3' A:DA5 2.6 7.1 1.0
O A:HOH37 3.0 23.7 1.0
O A:HOH33 3.0 18.9 1.0
C2' A:DA5 3.3 7.0 1.0
C4' A:DA6 3.8 8.1 1.0
O4' A:DA6 3.9 7.9 1.0
O A:HOH34 3.9 28.9 1.0
C4' A:DA5 3.9 6.8 1.0
O A:HOH36 4.0 21.7 1.0
C1' A:DA5 4.3 6.5 1.0
O A:HOH29 4.4 34.1 1.0
C3' A:DA6 4.6 7.3 1.0
O4' A:DA5 4.7 7.6 1.0
C5' A:DA5 5.0 6.2 1.0

Phosphorus binding site 6 out of 22 in 153d

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Phosphorus binding site 6 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:9.3
occ:1.00
P A:DT7 0.0 9.3 1.0
OP2 A:DT7 1.5 10.5 1.0
OP1 A:DT7 1.5 8.2 1.0
O3' A:DA6 1.6 7.7 1.0
O5' A:DT7 1.6 8.3 1.0
C5' A:DT7 2.6 8.0 1.0
C3' A:DA6 2.7 7.3 1.0
C2' A:DA6 3.4 7.5 1.0
C4' A:DT7 3.8 7.9 1.0
C4' A:DA6 3.9 8.1 1.0
O A:HOH40 4.0 19.9 1.0
C3' A:DT7 4.1 7.6 1.0
O4' A:DT7 4.4 7.7 1.0
C1' A:DA6 4.5 7.4 1.0
C5' A:DA6 4.8 8.9 1.0
O4' A:DA6 4.9 7.9 1.0
O A:HOH35 5.0 23.4 1.0

Phosphorus binding site 7 out of 22 in 153d

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Phosphorus binding site 7 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:10.6
occ:1.00
P A:DT8 0.0 10.6 1.0
OP2 A:DT8 1.5 9.4 1.0
OP1 A:DT8 1.5 11.1 1.0
O3' A:DT7 1.6 8.8 1.0
O5' A:DT8 1.6 11.1 1.0
C5' A:DT8 2.6 10.7 1.0
C3' A:DT7 2.7 7.6 1.0
C2' A:DT7 3.3 7.2 1.0
C4' A:DT8 4.0 10.6 1.0
C4' A:DT7 4.0 7.9 1.0
O A:HOH39 4.2 32.7 1.0
C1' A:DT7 4.5 7.1 1.0
C3' A:DT8 4.5 10.8 1.0
O4' A:DT8 4.6 10.0 1.0
O5' A:DT7 4.7 8.3 1.0
C5' A:DT7 4.8 8.0 1.0
C2' A:DT8 4.9 10.4 1.0
O4' A:DT7 4.9 7.7 1.0

Phosphorus binding site 8 out of 22 in 153d

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Phosphorus binding site 8 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:15.7
occ:1.00
P A:DC9 0.0 15.7 1.0
OP2 A:DC9 1.5 10.6 1.0
OP1 A:DC9 1.5 14.4 1.0
O3' A:DT8 1.6 11.7 1.0
O5' A:DC9 1.6 10.5 1.0
C5' A:DC9 2.6 9.8 1.0
C3' A:DT8 2.7 10.8 1.0
C2' A:DT8 3.3 10.4 1.0
C4' A:DC9 3.8 9.6 1.0
C4' A:DT8 4.0 10.6 1.0
C3' A:DC9 4.0 9.5 1.0
C1' A:DT8 4.0 10.3 1.0
O A:HOH47 4.3 32.2 1.0
C6 A:DC9 4.3 9.6 1.0
C2' A:DC9 4.4 9.8 1.0
O4' A:DT8 4.5 10.0 1.0
O4' A:DC9 4.7 9.3 1.0

Phosphorus binding site 9 out of 22 in 153d

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Phosphorus binding site 9 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:13.6
occ:1.00
P A:6OG10 0.0 13.6 1.0
OP2 A:6OG10 1.5 12.7 1.0
OP1 A:6OG10 1.5 12.6 1.0
O3' A:DC9 1.6 10.0 1.0
O5' A:6OG10 1.6 14.1 1.0
C5' A:6OG10 2.6 13.6 1.0
C3' A:DC9 2.7 9.5 1.0
O A:HOH47 3.1 32.2 1.0
C2' A:DC9 3.1 9.8 1.0
O A:HOH45 3.5 22.5 1.0
C4' A:6OG10 3.8 13.9 1.0
C3' A:6OG10 3.9 14.1 1.0
C4' A:DC9 3.9 9.6 1.0
C1' A:DC9 4.0 9.2 1.0
O A:HOH48 4.0 25.9 1.0
O A:HOH46 4.0 21.2 1.0
C2' A:6OG10 4.2 13.6 1.0
O4' A:DC9 4.4 9.3 1.0
O4' A:6OG10 4.7 13.8 1.0

Phosphorus binding site 10 out of 22 in 153d

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Phosphorus binding site 10 out of 22 in the Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:13.6
occ:1.00
P A:DC11 0.0 13.6 1.0
OP2 A:DC11 1.5 7.8 1.0
OP1 A:DC11 1.5 9.9 1.0
O3' A:6OG10 1.6 15.0 1.0
O5' A:DC11 1.6 11.2 1.0
C5' A:DC11 2.5 12.3 1.0
C3' A:6OG10 2.8 14.1 1.0
C2' A:6OG10 3.5 13.6 1.0
C6 A:DC11 3.8 13.3 1.0
C4' A:DC11 3.8 12.8 1.0
C4' A:6OG10 4.0 13.9 1.0
O A:HOH49 4.0 17.5 1.0
O4' A:DC11 4.1 13.4 1.0
C1' A:6OG10 4.2 13.3 1.0
C5 A:DC11 4.4 13.9 1.0
O4' A:6OG10 4.4 13.8 1.0
N1 A:DC11 4.7 13.7 1.0
C3' A:DC11 4.7 12.5 1.0
C1' A:DC11 4.8 13.5 1.0
C2' A:DC11 4.9 12.9 1.0

Reference:

S.L.Ginell, J.Vojtechovsky, B.Gaffney, R.Jones, H.M.Berman. Crystal Structure of A Mispaired Dodecamer, D(Cgagaattc(O6ME)Gcg)2, Containing A Carcinogenic O6-Methylguanine Biochemistry V. 33 3487 1994.
ISSN: ISSN 0006-2960
PubMed: 8142345
DOI: 10.1021/BI00178A004
Page generated: Fri Sep 25 11:32:23 2020

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