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Strontium in PDB 5v1l: Structure of S-Gna Dodecamer

Protein crystallography data

The structure of Structure of S-Gna Dodecamer, PDB code: 5v1l was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 34.951, 46.239, 82.928, 90.00, 100.09, 90.00
R / Rfree (%) 13.3 / 15.3

Strontium Binding Sites:

The binding sites of Strontium atom in the Structure of S-Gna Dodecamer (pdb code 5v1l). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the Structure of S-Gna Dodecamer, PDB code: 5v1l:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 5v1l

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Strontium binding site 1 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:16.6
occ:0.45
 O6 A:G104 2.5 17.5 1.0
O A:HOH357 2.6 41.0 1.0
O A:HOH354 2.7 22.2 1.0
O A:HOH350 2.7 19.6 1.0
O A:HOH352 2.8 19.6 1.0
O A:HOH340 3.1 23.3 1.0
C6 A:G104 3.7 13.1 1.0
C5 A:G104 4.5 12.2 1.0
OP2 A:C103 4.5 14.0 1.0
N7 A:G104 4.5 13.0 1.0
OP2 A:G102 4.6 20.4 1.0
N1 A:G104 4.6 13.5 1.0
C5 A:C103 4.7 12.6 1.0
O A:HOH329 4.8 42.1 1.0
O A:HOH305 4.9 45.6 1.0
O A:HOH341 4.9 30.4 1.0
N4 A:C103 4.9 12.7 1.0

Strontium binding site 2 out of 8 in 5v1l

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Strontium binding site 2 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr301

b:17.7
occ:0.39
 SR B:SR302 1.4 26.5 0.5
O B:HOH433 2.4 21.6 1.0
O6 B:G204 2.5 13.5 1.0
O B:HOH447 2.7 22.3 1.0
O B:HOH434 2.9 19.9 1.0
O B:HOH457 3.3 58.7 1.0
O A:HOH344 3.5 28.9 1.0
C6 B:G204 3.6 13.0 1.0
O B:HOH462 3.7 20.6 1.0
OP2 B:C203 4.3 12.5 1.0
C5 B:G204 4.3 12.6 1.0
N7 B:G204 4.4 13.0 1.0
OP2 B:G202 4.5 15.7 1.0
C5 B:C203 4.5 11.4 1.0
N1 B:G204 4.6 13.3 1.0
C5 A:U107 4.8 13.3 0.5
O4 A:U107 4.8 14.5 0.5
O B:HOH414 4.9 23.3 1.0
C6 A:U107 4.9 12.4 0.5
N4 B:C203 4.9 11.2 1.0

Strontium binding site 3 out of 8 in 5v1l

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Strontium binding site 3 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr302

b:26.5
occ:0.45
 SR B:SR301 1.4 17.7 0.4
O B:HOH457 2.4 58.7 1.0
O A:HOH344 2.5 28.9 1.0
O B:HOH462 2.6 20.6 1.0
O B:HOH434 2.6 19.9 1.0
O6 B:G204 2.9 13.5 1.0
O B:HOH433 3.4 21.6 1.0
C6 B:G204 4.0 13.0 1.0
C5 A:U107 4.0 13.3 0.5
O B:HOH447 4.1 22.3 1.0
O4 A:U107 4.1 14.5 0.5
C5 A:U107 4.4 10.7 0.5
N7 B:G204 4.5 13.0 1.0
C6 A:U107 4.5 12.4 0.5
OP2 B:C203 4.5 12.5 1.0
C4 A:U107 4.5 11.2 0.5
C5 B:G204 4.6 12.6 1.0
C4 A:U107 4.7 12.0 0.5
OP2 A:A106 4.7 15.2 1.0
OP2 A:U107 4.8 14.7 0.5
O4 A:U107 4.9 15.9 0.5

Strontium binding site 4 out of 8 in 5v1l

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Strontium binding site 4 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr401

b:16.2
occ:0.42
 SR C:SR402 2.4 13.9 0.4
O6 C:G304 2.6 13.7 1.0
O C:HOH508 2.7 56.2 1.0
O C:HOH572 2.8 34.4 0.5
O C:HOH538 2.8 16.9 1.0
O C:HOH536 2.8 15.1 1.0
O C:HOH567 2.9 18.5 1.0
C6 C:G304 3.8 12.1 1.0
O C:HOH541 4.2 36.1 1.0
O C:HOH584 4.3 19.1 1.0
OP2 C:C303 4.4 11.6 1.0
C5 C:G304 4.5 11.6 1.0
N7 C:G304 4.5 11.6 1.0
C5 C:C303 4.7 10.5 1.0
OP2 C:G302 4.7 16.1 1.0
N1 C:G304 4.8 12.7 1.0
O C:HOH569 4.9 93.0 1.0
O D:HOH654 4.9 26.3 1.0
O D:HOH691 5.0 36.5 1.0

Strontium binding site 5 out of 8 in 5v1l

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Strontium binding site 5 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr402

b:13.9
occ:0.38
 SR C:SR401 2.4 16.2 0.4
O6 C:G304 2.6 13.7 1.0
O C:HOH567 2.6 18.5 1.0
O D:HOH691 2.8 36.5 1.0
O C:HOH572 3.0 34.4 0.5
O C:HOH569 3.1 93.0 1.0
C6 C:G304 3.6 12.1 1.0
O C:HOH508 4.0 56.2 1.0
N1 C:G304 4.0 12.7 1.0
O D:HOH645 4.1 40.5 1.0
O D:HOH694 4.3 53.5 1.0
O C:HOH538 4.5 16.9 1.0
O C:HOH539 4.6 21.4 1.0
O D:HOH625 4.7 31.2 1.0
O D:HOH654 4.8 26.3 1.0
N4 C:C303 4.8 10.8 1.0
O C:HOH536 4.8 15.1 1.0
C5 C:G304 4.9 11.6 1.0

Strontium binding site 6 out of 8 in 5v1l

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Strontium binding site 6 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr403

b:18.8
occ:0.30
 O2' C:G302 2.7 11.8 1.0
O C:HOH573 2.7 36.9 1.0
N3 C:G302 2.9 10.6 1.0
C2' C:G302 3.1 11.1 1.0
O D:HOH662 3.2 26.3 1.0
C1' C:G302 3.3 11.1 1.0
O D:HOH634 3.4 46.2 1.0
O4' C:C303 3.4 12.0 1.0
O C:HOH559 3.4 25.6 1.0
N2 C:G302 3.8 12.1 1.0
C2 C:G302 3.8 11.0 1.0
C4 C:G302 3.9 9.6 1.0
N9 C:G302 4.0 10.4 1.0
C1' C:C303 4.2 11.1 1.0
N2 D:G412 4.4 10.4 1.0
C4' C:C303 4.4 11.8 1.0
O4' C:G302 4.5 11.4 1.0
N3 D:G412 4.6 10.9 1.0
C3' C:G302 4.7 10.8 1.0
N1 C:C303 4.8 10.0 1.0
C5' C:C303 4.8 11.8 1.0
C2 D:G412 4.8 10.0 1.0

Strontium binding site 7 out of 8 in 5v1l

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Strontium binding site 7 out of 8 in the Structure of S-Gna Dodecamer


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr404

b:17.8
occ:0.39
 O C:HOH511 2.4 38.0 1.0
O C:HOH520 2.5 27.4 1.0
O C:HOH575 2.6 51.2 1.0
O C:HOH560 2.7 34.2 1.0
O C:HOH524 2.7 21.3 1.0
O C:HOH517 2.8 34.4 1.0
O C:HOH594 3.7 91.3 1.0
O C:HOH503 4.2 38.9 1.0
O D:HOH630 4.3 20.7 1.0
N7 C:G310 4.5 11.5 1.0
O D:HOH672 4.5 27.6 1.0
OP2 C:A309 4.7 17.1 1.0
N4 C:C311 4.8 11.3 1.0
O6 C:G310 4.8 11.7 1.0
O C:HOH547 4.9 18.4 1.0
OP2 C:G310 4.9 15.6 1.0
O D:HOH646 4.9 31.4 1.0

Strontium binding site 8 out of 8 in 5v1l

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Strontium binding site 8 out of 8 in the Structure of S-Gna Dodecamer


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Structure of S-Gna Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr501

b:16.5
occ:0.44
 O D:HOH605 2.4 6.8 1.0
O D:HOH635 2.6 16.1 1.0
O6 D:G404 2.6 13.9 1.0
O D:HOH681 2.6 41.3 1.0
O D:HOH638 2.7 23.9 1.0
O D:HOH663 2.8 18.5 1.0
O D:HOH643 2.9 15.5 1.0
O D:HOH647 3.7 38.9 1.0
C6 D:G404 3.8 12.2 1.0
O D:HOH686 4.2 8.2 1.0
OP2 D:C403 4.3 10.7 1.0
O D:HOH669 4.5 30.0 1.0
C5 D:G404 4.5 11.1 1.0
N7 D:G404 4.6 10.7 1.0
OP2 D:G402 4.6 14.2 1.0
C5 D:C403 4.7 9.9 1.0
N1 D:G404 4.8 12.3 1.0
O C:HOH512 5.0 41.0 1.0
N4 D:C403 5.0 10.4 1.0
O D:HOH603 5.0 32.3 1.0

Reference:

M.K.Schlegel, D.J.Foster, A.V.Kel'in, I.Zlatev, A.Bisbe, M.Jayaraman, J.G.Lackey, K.G.Rajeev, K.Charisse, J.Harp, P.S.Pallan, M.A.Maier, M.Egli, M.Manoharan. Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on Sirna. J. Am. Chem. Soc. V. 139 8537 2017.
ISSN: ESSN 1520-5126
PubMed: 28570818
DOI: 10.1021/JACS.7B02694
Page generated: Fri Oct 11 06:31:47 2024

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