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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Go back to Phosphorus Binding Sites List in 153d
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy