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Strontium in PDB 1wv6: X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form

Protein crystallography data

The structure of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form, PDB code: 1wv6 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.Manoharam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.55
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.566, 43.566, 69.944, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.3

Strontium Binding Sites:

The binding sites of Strontium atom in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form (pdb code 1wv6). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 5 binding sites of Strontium where determined in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form, PDB code: 1wv6:
Jump to Strontium binding site number: 1; 2; 3; 4; 5;

Strontium binding site 1 out of 5 in 1wv6

Go back to Strontium Binding Sites List in 1wv6
Strontium binding site 1 out of 5 in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form within 5.0Å range:

Strontium binding site 2 out of 5 in 1wv6

Go back to Strontium Binding Sites List in 1wv6
Strontium binding site 2 out of 5 in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr102

b:93.8
occ:0.50
O4 B:2BT16 3.0 68.0 1.0
C5M B:2BT16 3.8 74.3 1.0
C4 B:2BT16 4.0 68.4 1.0
N6 B:DA17 4.4 68.7 1.0
C5 B:2BT16 4.4 70.2 1.0
N6 B:DA15 4.5 69.2 1.0
N7 B:DA15 4.5 69.0 1.0
N6 A:DA5 4.6 71.2 1.0
O4 A:DT4 4.8 64.5 1.0

Strontium binding site 3 out of 5 in 1wv6

Go back to Strontium Binding Sites List in 1wv6
Strontium binding site 3 out of 5 in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr103

b:80.5
occ:0.25
C5 B:DC18 3.9 64.5 1.0
N4 B:DC18 4.3 64.6 1.0
C4 B:DC18 4.5 63.2 1.0
N7 B:DG19 4.7 60.0 1.0
C6 B:DC18 4.7 64.7 1.0
OP2 B:DC18 5.0 64.1 1.0

Strontium binding site 4 out of 5 in 1wv6

Go back to Strontium Binding Sites List in 1wv6
Strontium binding site 4 out of 5 in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr104

b:63.7
occ:0.25
N7 A:DG9 3.2 63.8 1.0
N4 A:DC8 3.6 65.3 1.0
O6 A:DG9 3.7 64.2 1.0
C5 A:DC8 3.7 64.8 1.0
C4 A:DC8 3.9 64.8 1.0
N4 A:DC10 4.1 65.8 1.0
C5 A:DG9 4.1 63.9 1.0
C6 A:DG9 4.2 64.1 1.0
C8 A:DG9 4.3 63.7 1.0
C6 A:DC8 4.6 65.1 1.0
N3 A:DC8 4.8 63.4 1.0
C4 A:DC10 5.0 65.0 1.0

Strontium binding site 5 out of 5 in 1wv6

Go back to Strontium Binding Sites List in 1wv6
Strontium binding site 5 out of 5 in the X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of X-Ray Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Butyl Thymine in Place of T6, Sr-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr105

b:68.8
occ:0.25
O4 A:2BT6 3.0 68.6 1.0
C5M A:2BT6 3.6 70.9 1.0
C4 A:2BT6 3.9 67.8 1.0
C5 A:2BT6 4.3 67.5 1.0
N6 A:DA7 4.4 68.6 1.0
N6 A:DA5 4.5 71.2 1.0
N7 A:DA5 4.5 70.7 1.0
N6 B:DA15 4.5 69.2 1.0
O4 B:DT14 4.8 67.9 1.0
C5 A:DA5 5.0 69.9 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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