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Strontium in PDB 7sb8: D(Ga(Cga)5) Parallel-Stranded Homo-Duplex

Protein crystallography data

The structure of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex, PDB code: 7sb8 was solved by E.M.Luteran, P.J.Paukstelis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.41 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 19.677, 30.422, 180.822, 90, 90.41, 90
R / Rfree (%) 17.1 / 21.4

Other elements in 7sb8:

The structure of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex also contains other interesting chemical elements:

Sodium (Na) 1 atom
Cobalt (Co) 11 atoms

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Strontium atom in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex (pdb code 7sb8). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 23 binding sites of Strontium where determined in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex, PDB code: 7sb8:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 23 in 7sb8

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Strontium binding site 1 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:13.7
occ:0.33
SR A:SR101 0.0 13.7 0.3
SR A:SR101 0.6 14.5 0.4
SR A:SR101 2.3 26.8 0.3
O B:HOH248 2.7 24.3 1.0
N7 A:DG7 2.8 12.5 1.0
O A:HOH274 2.9 20.5 1.0
O6 A:DG7 3.8 12.8 1.0
C8 A:DG7 3.8 11.0 1.0
C5 A:DG7 3.8 9.4 1.0
C6 A:DG7 4.2 11.1 1.0
O A:HOH214 4.4 20.6 1.0
O A:HOH278 4.7 34.2 1.0
N3 B:DA8 4.9 12.8 1.0
OP2 A:DC6 4.9 16.3 1.0

Strontium binding site 2 out of 23 in 7sb8

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Strontium binding site 2 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:26.8
occ:0.27
SR A:SR101 0.0 26.8 0.3
SR A:SR101 2.3 13.7 0.3
SR A:SR101 2.6 14.5 0.4
OP2 A:DC6 2.7 16.3 1.0
O6 A:DG7 3.0 12.8 1.0
N7 A:DG7 3.0 12.5 1.0
O A:HOH274 3.3 20.5 1.0
C6 A:DG7 3.5 11.1 1.0
C5 A:DG7 3.5 9.4 1.0
O A:HOH225 3.7 23.2 1.0
C5' A:DC6 3.7 15.3 1.0
P A:DC6 3.8 15.3 1.0
O A:HOH214 3.8 20.6 1.0
C6 A:DC6 3.9 11.1 1.0
OP1 A:DC6 4.1 15.6 1.0
C8 A:DG7 4.1 11.0 1.0
O5' A:DC6 4.2 16.0 1.0
O A:HOH257 4.3 24.8 1.0
C5 A:DC6 4.4 12.1 1.0
C2' A:DC6 4.4 12.1 1.0
O B:HOH248 4.5 24.3 1.0
C4' A:DC6 4.7 13.0 1.0
O4' A:DC6 4.7 12.2 1.0
N1 A:DC6 4.7 10.1 1.0
C4 A:DG7 4.8 9.2 1.0
N1 A:DG7 4.8 10.6 1.0
O A:HOH278 4.8 34.2 1.0
C1' A:DC6 4.9 11.5 1.0
C3' A:DC6 4.9 12.1 1.0

Strontium binding site 3 out of 23 in 7sb8

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Strontium binding site 3 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:14.5
occ:0.40
SR A:SR101 0.0 14.5 0.4
SR A:SR101 0.6 13.7 0.3
O A:HOH274 2.4 20.5 1.0
SR A:SR101 2.6 26.8 0.3
N7 A:DG7 2.8 12.5 1.0
O B:HOH248 2.9 24.3 1.0
C8 A:DG7 3.6 11.0 1.0
C5 A:DG7 4.0 9.4 1.0
O6 A:DG7 4.2 12.8 1.0
O A:HOH278 4.4 34.2 1.0
O A:HOH214 4.5 20.6 1.0
C6 A:DG7 4.5 11.1 1.0
O A:HOH258 4.6 21.6 1.0
O B:HOH258 4.8 22.8 1.0
N9 A:DG7 4.9 9.3 1.0
C5' A:DC6 5.0 15.3 1.0

Strontium binding site 4 out of 23 in 7sb8

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Strontium binding site 4 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr102

b:12.7
occ:0.31
SR A:SR102 0.0 12.7 0.3
SR A:SR102 0.7 14.6 0.5
O A:HOH269 2.3 29.6 1.0
O6 A:DG1 2.5 20.6 1.0
O A:HOH211 3.0 27.0 1.0
C6 A:DG1 3.6 18.6 1.0
N7 A:DG1 4.2 20.4 1.0
C5 A:DG1 4.3 16.6 1.0
N1 A:DG1 4.8 15.3 1.0
C1' B:DA2 4.8 18.9 1.0
C2' B:DA2 5.0 20.2 1.0

Strontium binding site 5 out of 23 in 7sb8

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Strontium binding site 5 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr102

b:14.6
occ:0.48
SR A:SR102 0.0 14.6 0.5
SR A:SR102 0.7 12.7 0.3
O A:HOH211 2.4 27.0 1.0
O6 A:DG1 2.7 20.6 1.0
O A:HOH269 3.0 29.6 1.0
C6 A:DG1 3.6 18.6 1.0
N7 A:DG1 3.8 20.4 1.0
C5 A:DG1 4.1 16.6 1.0
N1 A:DG1 4.9 15.3 1.0
N3 B:DA2 5.0 15.7 1.0

Strontium binding site 6 out of 23 in 7sb8

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Strontium binding site 6 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr103

b:23.7
occ:0.34
O B:HOH243 2.5 24.4 1.0
O A:HOH238 3.8 26.7 1.0
O B:HOH231 4.4 36.1 1.0
O A:HOH270 4.7 28.8 1.0
OP2 A:DA14 4.8 18.6 1.0
OP1 A:DA14 4.9 20.6 1.0

Strontium binding site 7 out of 23 in 7sb8

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Strontium binding site 7 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr101

b:18.6
occ:0.36
OP2 B:DC12 2.5 19.4 1.0
O6 B:DG13 2.5 15.9 1.0
O B:HOH228 2.8 34.5 1.0
O B:HOH265 3.6 14.5 1.0
C6 B:DG13 3.6 14.1 1.0
P B:DC12 3.8 18.1 1.0
N7 B:DG13 4.3 14.7 1.0
C5 B:DG13 4.4 13.2 1.0
OP1 B:DC12 4.4 18.7 1.0
O5' B:DC12 4.7 16.6 1.0
N1 B:DG13 4.7 13.5 1.0
O5' B:DA11 4.8 18.8 1.0
O3' B:DA11 4.8 17.3 1.0

Strontium binding site 8 out of 23 in 7sb8

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Strontium binding site 8 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr102

b:19.1
occ:0.34
O B:HOH256 2.5 62.3 1.0
OP1 B:DA2 2.6 19.2 1.0
O B:HOH235 2.7 26.6 1.0
P B:DA2 3.7 18.6 1.0
OP2 B:DA2 3.8 23.3 1.0
O B:HOH233 4.2 21.8 1.0
O B:HOH245 4.5 40.7 1.0
O5' B:DA2 4.7 20.8 1.0
O3' B:DG1 4.8 19.1 1.0
C3' B:DG1 4.9 18.9 1.0

Strontium binding site 9 out of 23 in 7sb8

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Strontium binding site 9 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr101

b:17.5
occ:0.36
OP2 D:DC6 2.5 23.2 1.0
O6 D:DG7 2.6 16.8 1.0
O D:HOH263 3.2 17.1 1.0
C6 D:DG7 3.7 13.2 1.0
P D:DC6 3.9 18.9 1.0
N7 D:DG7 4.3 13.8 1.0
C5 D:DG7 4.3 11.5 1.0
OP1 D:DC6 4.5 21.7 1.0
O5' D:DC6 4.8 15.8 1.0
N1 D:DG7 4.8 14.0 1.0
O3' D:DA5 4.8 18.8 1.0
O5' D:DA5 4.9 17.5 1.0

Strontium binding site 10 out of 23 in 7sb8

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Strontium binding site 10 out of 23 in the D(Ga(Cga)5) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of D(Ga(Cga)5) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr102

b:17.9
occ:0.36
O D:HOH230 2.7 34.5 1.0
O D:HOH207 4.3 34.3 1.0
OP2 D:DG10 4.5 22.4 1.0
O D:HOH208 4.8 24.8 1.0

Reference:

E.M.Luteran, P.J.Paukstelis. The Parallel-Stranded D(Cga) Duplex Is A Highly Predictable Structural Motif with Two Conformationally Distinct Strands To Be Published.
Page generated: Fri Nov 5 16:14:31 2021

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