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Strontium in PDB 7dfy: Novel Motif For Left-Handed G-Quadruplex Formation

Protein crystallography data

The structure of Novel Motif For Left-Handed G-Quadruplex Formation, PDB code: 7dfy was solved by P.Das, F.R.Winnerdy, A.Maity, Y.Mechulam, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.99 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 28.405, 31.601, 77.764, 90, 98.07, 90
R / Rfree (%) 20.1 / 25.9

Other elements in 7dfy:

The structure of Novel Motif For Left-Handed G-Quadruplex Formation also contains other interesting chemical elements:

Potassium (K) 11 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Novel Motif For Left-Handed G-Quadruplex Formation (pdb code 7dfy). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 10 binding sites of Strontium where determined in the Novel Motif For Left-Handed G-Quadruplex Formation, PDB code: 7dfy:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 10 in 7dfy

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Strontium binding site 1 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr107

b:9.7
occ:0.55
 O A:HOH240 2.5 20.8 1.0
O A:HOH239 2.7 17.8 1.0
O A:HOH224 2.9 14.2 1.0
OP1 A:DG15 4.4 20.8 1.0
O3' A:DG26 4.7 7.5 1.0
N2 A:DG24 4.7 5.9 1.0
OP2 A:DT25 4.8 10.9 1.0
OP2 A:DG15 4.8 13.2 1.0
N3 A:DG24 4.9 3.9 1.0
C2' A:DG26 5.0 7.3 1.0

Strontium binding site 2 out of 10 in 7dfy

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Strontium binding site 2 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr108

b:44.7
occ:1.00
 O A:HOH245 2.7 15.5 1.0
O A:HOH259 2.7 18.1 1.0
O2 A:DT11 2.7 21.4 1.0
C2 A:DT11 3.9 18.6 1.0
O4 A:DT14 4.5 14.3 1.0
C1' A:DT11 4.6 13.6 1.0
C4 A:DT14 4.8 15.8 1.0
O A:HOH220 4.8 21.7 1.0
N1 A:DT11 4.8 14.4 1.0
N3 A:DT11 4.9 15.7 1.0
C2' A:DT11 4.9 11.9 1.0
O2 A:DT13 4.9 14.9 1.0
N3 A:DT14 5.0 14.3 1.0

Strontium binding site 3 out of 10 in 7dfy

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Strontium binding site 3 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr109

b:15.3
occ:0.46
 SR A:SR109 0.0 15.3 0.5
SR A:SR109 1.8 18.5 0.5
O A:HOH236 2.6 17.6 1.0
O2 A:DT20 2.8 6.5 1.0
C2 A:DT20 3.7 9.3 1.0
N3 A:DT20 4.0 10.3 1.0
O A:HOH257 4.3 20.7 1.0
O A:HOH263 4.7 12.8 1.0
N1 A:DT20 4.9 6.7 1.0
O A:HOH244 4.9 10.7 1.0

Strontium binding site 4 out of 10 in 7dfy

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Strontium binding site 4 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr109

b:18.5
occ:0.54
 SR A:SR109 0.0 18.5 0.5
SR A:SR109 1.8 15.3 0.5
O2 A:DT20 2.7 6.5 1.0
O A:HOH257 2.8 20.7 1.0
O A:HOH236 3.0 17.6 1.0
C2 A:DT20 3.6 9.3 1.0
N1 A:DT20 4.4 6.7 1.0
C1' A:DT20 4.4 7.1 1.0
N3 A:DT20 4.4 10.3 1.0

Strontium binding site 5 out of 10 in 7dfy

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Strontium binding site 5 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr110

b:21.3
occ:0.42
 O A:HOH206 2.4 10.7 1.0
OP1 A:DT6 4.3 23.6 1.0
OP1 A:DG7 4.7 16.6 1.0

Strontium binding site 6 out of 10 in 7dfy

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Strontium binding site 6 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr111

b:44.5
occ:0.57
 O A:HOH205 2.6 25.1 1.0
O A:HOH203 3.0 10.6 1.0
OP2 A:DT6 4.7 8.0 1.0
OP1 A:DT20 4.7 9.3 1.0
OP2 A:DG5 4.8 16.8 1.0
C5' A:DG5 5.0 7.0 1.0

Strontium binding site 7 out of 10 in 7dfy

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Strontium binding site 7 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr112

b:13.2
occ:1.00
 O A:HOH234 2.4 9.6 1.0
OP1 A:DT14 2.4 7.2 1.0
O A:HOH238 2.6 5.7 1.0
O A:HOH253 2.7 10.3 1.0
P A:DT14 3.7 12.8 1.0
OP2 A:DT14 4.0 8.8 1.0
O3' A:DT13 4.6 12.7 1.0
C5' A:DT25 4.7 10.0 1.0
O5' A:DT14 4.8 12.3 1.0
C4' A:DT13 4.9 15.1 1.0
OP2 A:DT25 4.9 10.9 1.0

Strontium binding site 8 out of 10 in 7dfy

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Strontium binding site 8 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr113

b:12.2
occ:1.00
 O B:HOH215 2.5 11.2 1.0
OP2 B:DG26 2.5 14.1 1.0
OP2 B:DT13 2.5 9.7 1.0
O2 A:DT3 2.5 11.6 1.0
O A:HOH230 2.6 11.1 1.0
O B:HOH208 2.6 8.2 1.0
O B:HOH206 2.7 11.3 1.0
O B:HOH212 2.7 7.9 1.0
C2 A:DT3 3.5 10.4 1.0
O B:HOH217 3.8 14.4 0.7
P B:DG26 3.8 13.1 1.0
P B:DT13 3.9 12.3 1.0
N3 A:DT3 4.1 8.8 1.0
O3' B:DG12 4.2 21.9 1.0
OP1 B:DG26 4.3 12.7 1.0
N1 A:DT3 4.4 14.1 1.0
O A:HOH222 4.4 7.5 1.0
C1' A:DT3 4.6 10.1 1.0
O B:HOH205 4.7 9.4 1.0
O3' B:DT25 4.7 17.2 1.0
SR B:SR106 4.8 33.6 0.3
OP1 B:DT13 4.8 10.1 1.0
O5' B:DG26 4.9 18.1 1.0
C5' B:DT13 4.9 10.3 1.0
O5' B:DT13 4.9 10.3 1.0

Strontium binding site 9 out of 10 in 7dfy

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Strontium binding site 9 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr114

b:45.3
occ:1.00
 O B:HOH203 2.5 22.2 1.0
O2 B:DT13 2.6 15.2 1.0
O A:HOH223 2.6 24.6 1.0
OP2 A:DT3 2.7 4.2 1.0
C2 B:DT13 3.7 11.7 1.0
P A:DT3 4.0 14.8 1.0
OP1 A:DT3 4.4 15.6 1.0
OP2 A:DG2 4.4 21.9 1.0
N3 B:DT13 4.5 12.8 1.0
O A:HOH228 4.5 26.1 1.0
C1' B:DT13 4.5 12.8 1.0
N1 B:DT13 4.6 9.7 1.0
O3' A:DG2 4.7 16.3 1.0
C3' A:DG2 4.8 7.8 1.0

Strontium binding site 10 out of 10 in 7dfy

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Strontium binding site 10 out of 10 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr106

b:33.6
occ:0.28
 O5' B:DG1 2.6 21.0 1.0
O B:HOH206 2.8 11.3 1.0
O4' B:DG26 2.9 14.0 1.0
N3 B:DG12 2.9 21.1 1.0
C5' B:DG1 3.3 21.0 1.0
O B:HOH217 3.4 14.4 0.7
O5' B:DG26 3.4 18.1 1.0
N2 B:DG12 3.5 17.5 1.0
C2 B:DG12 3.7 20.2 1.0
C8 B:DG26 3.8 17.7 1.0
C1' B:DG12 3.9 14.9 1.0
C1' B:DG26 3.9 15.2 1.0
N9 B:DG26 3.9 22.9 1.0
C4' B:DG26 4.0 15.8 1.0
OP2 B:DG26 4.0 14.1 1.0
P B:DG26 4.0 13.1 1.0
C4 B:DG12 4.0 18.9 1.0
OP1 B:DG26 4.0 12.7 1.0
O B:HOH208 4.1 8.2 1.0
O4' B:DG12 4.2 23.1 1.0
C5' B:DG26 4.3 25.5 1.0
C8 B:DG1 4.3 18.8 1.0
N9 B:DG12 4.4 16.3 1.0
N7 B:DG26 4.5 19.6 1.0
C4' B:DG1 4.7 14.9 1.0
O3' B:DG12 4.7 21.9 1.0
O4' B:DG1 4.8 23.2 1.0
SR A:SR113 4.8 12.2 1.0
C4 B:DG26 4.8 23.1 1.0
N7 B:DG1 4.9 24.3 1.0
C2' B:DG12 5.0 14.0 1.0

Reference:

P.Das, F.R.Winnerdy, A.Maity, Y.Mechulam, A.T.Phan. A Novel Minimal Motif For Left-Handed G-Quadruplex Formation. Chem.Commun.(Camb.) V. 57 2527 2021.
ISSN: ESSN 1364-548X
PubMed: 33690751
DOI: 10.1039/D0CC08146A
Page generated: Fri Oct 11 06:51:54 2024

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