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Strontium in PDB 1ybc: Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*)

Protein crystallography data

The structure of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*), PDB code: 1ybc was solved by M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.063, 44.365, 45.458, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.3

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*) (pdb code 1ybc). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total only one binding site of Strontium was determined in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*), PDB code: 1ybc:

Strontium binding site 1 out of 1 in 1ybc

Go back to Strontium Binding Sites List in 1ybc
Strontium binding site 1 out of 1 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Benzyloxy)Ethyl] Thymidine (T*) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr100

b:52.1
occ:1.00
O A:HOH101 2.4 36.4 1.0
O A:HOH105 2.5 35.8 1.0
O B:HOH102 2.6 27.8 1.0
O B:HOH106 2.6 23.2 0.5
O A:HOH104 2.7 31.0 1.0
O6 A:DG3 2.7 21.7 1.0
O B:HOH103 2.9 38.6 1.0
C6 A:DG3 3.7 21.4 1.0
N7 A:DG3 3.9 19.8 1.0
N4 A:DC2 4.1 21.8 1.0
C5 A:DG3 4.1 21.1 1.0
N4 B:DC18 4.5 24.9 1.0
O B:HOH160 4.5 33.6 0.5
N6 B:DA17 4.5 17.8 1.0
O4 A:DT4 4.6 15.6 1.0
O B:HOH129 4.8 30.8 1.0
C4 A:DC2 4.9 22.7 1.0
N1 A:DG3 4.9 17.9 1.0

Reference:

M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the Rna Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. Biochemistry V. 44 9045 2005.
ISSN: ISSN 0006-2960
PubMed: 15966728
DOI: 10.1021/BI050574M
Page generated: Mon Jan 25 16:03:09 2021

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