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Strontium in PDB 4ms9: Native Rna-10MER Structure: Ccggcgccgg

Protein crystallography data

The structure of Native Rna-10MER Structure: Ccggcgccgg, PDB code: 4ms9 was solved by J.Sheng, L.Li, Engelhart A.E., J.Gan, J.Wang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.91 / 1.32
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 22.708, 22.708, 77.721, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.8

Strontium Binding Sites:

The binding sites of Strontium atom in the Native Rna-10MER Structure: Ccggcgccgg (pdb code 4ms9). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 3 binding sites of Strontium where determined in the Native Rna-10MER Structure: Ccggcgccgg, PDB code: 4ms9:
Jump to Strontium binding site number: 1; 2; 3;

Strontium binding site 1 out of 3 in 4ms9

Go back to Strontium Binding Sites List in 4ms9
Strontium binding site 1 out of 3 in the Native Rna-10MER Structure: Ccggcgccgg


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Native Rna-10MER Structure: Ccggcgccgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:13.4
occ:0.65
O A:HOH246 2.4 30.5 1.0
O A:HOH247 2.5 26.7 1.0
O A:HOH206 2.5 15.3 1.0
O A:HOH227 2.6 16.8 1.0
O A:HOH202 2.7 17.0 1.0
O6 A:G4 2.7 10.7 1.0
C6 A:G4 3.8 9.9 1.0
N7 A:G4 4.2 10.4 1.0
O6 A:G3 4.2 10.1 1.0
C5 A:G4 4.4 10.3 1.0
O A:HOH205 4.6 15.4 1.0
N7 A:G3 4.6 10.3 1.0
O A:HOH204 4.6 18.3 1.0
N4 A:C5 4.7 11.6 1.0
O A:HOH211 4.8 26.4 1.0
C6 A:G3 4.8 9.7 1.0
O A:HOH213 4.9 18.1 1.0
N1 A:G4 5.0 9.9 1.0

Strontium binding site 2 out of 3 in 4ms9

Go back to Strontium Binding Sites List in 4ms9
Strontium binding site 2 out of 3 in the Native Rna-10MER Structure: Ccggcgccgg


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Native Rna-10MER Structure: Ccggcgccgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr102

b:16.6
occ:0.40
SR A:SR103 2.0 17.3 0.4
O A:HOH210 2.2 32.6 1.0
O3' A:G10 2.6 21.7 1.0
O A:HOH249 2.8 25.6 1.0
O2' A:G10 3.4 21.3 1.0
C3' A:G10 3.7 22.5 1.0
C4' A:G10 4.0 18.9 1.0
C2' A:G10 4.2 18.1 1.0
C5' A:G10 4.8 17.3 1.0

Strontium binding site 3 out of 3 in 4ms9

Go back to Strontium Binding Sites List in 4ms9
Strontium binding site 3 out of 3 in the Native Rna-10MER Structure: Ccggcgccgg


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Native Rna-10MER Structure: Ccggcgccgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr103

b:17.3
occ:0.40
SR A:SR102 2.0 16.6 0.4
O2' A:G10 2.5 21.3 1.0
O3' A:G10 2.7 21.7 1.0
O A:HOH210 3.4 32.6 1.0
C2' A:G10 3.4 18.1 1.0
C3' A:G10 3.6 22.5 1.0
O A:HOH249 4.1 25.6 1.0
O A:HOH250 4.2 38.7 1.0
C4' A:G10 4.4 18.9 1.0
C1' A:G10 4.7 18.4 1.0

Reference:

J.Sheng, L.Li, A.E.Engelhart, J.Gan, J.Wang, J.W.Szostak. Structural Insights Into the Effects of 2'-5' Linkages on the Rna Duplex. Proc.Natl.Acad.Sci.Usa V. 111 3050 2014.
ISSN: ISSN 0027-8424
PubMed: 24516151
DOI: 10.1073/PNAS.1317799111
Page generated: Wed Dec 16 02:24:00 2020

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