Barium in PDB 7sb9: D((Cga)5TGA) Parallel-Stranded Homo-Duplex

Protein crystallography data

The structure of D((Cga)5TGA) Parallel-Stranded Homo-Duplex, PDB code: 7sb9 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) 32.25 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.499, 32.35, 32.26, 90, 91.03, 90
R / Rfree (%) 20 / 25.2

Barium Binding Sites:

The binding sites of Barium atom in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex (pdb code 7sb9). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 10 binding sites of Barium where determined in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex, PDB code: 7sb9:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 10 in 7sb9

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Barium binding site 1 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:15.6
occ:0.50
 BA A:BA101 0.0 15.6 0.5
BA A:BA101 1.2 6.8 0.5
O A:HOH243 2.6 19.9 1.0
N7 A:DG2 2.8 3.3 1.0
O A:HOH229 3.0 11.0 1.0
O B:HOH224 3.2 7.8 1.0
O A:HOH239 3.6 24.4 1.0
C8 A:DG2 3.8 6.8 1.0
C5 A:DG2 3.9 7.3 1.0
O6 A:DG2 3.9 8.1 1.0
C6 A:DG2 4.3 5.7 1.0
O A:HOH212 4.5 9.5 1.0

Barium binding site 2 out of 10 in 7sb9

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Barium binding site 2 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:6.8
occ:0.50
 BA A:BA101 0.0 6.8 0.5
BA A:BA101 1.2 15.6 0.5
O A:HOH239 2.5 24.4 1.0
O A:HOH229 2.6 11.0 1.0
O B:HOH224 2.9 7.8 1.0
O6 A:DG2 3.0 8.1 1.0
N7 A:DG2 3.0 3.3 1.0
C6 A:DG2 3.6 5.7 1.0
C5 A:DG2 3.7 7.3 1.0
O A:HOH243 3.7 19.9 1.0
C8 A:DG2 4.2 6.8 1.0
N3 B:DA3 4.9 6.2 1.0
C4 A:DG2 5.0 7.5 1.0

Barium binding site 3 out of 10 in 7sb9

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Barium binding site 3 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:6.8
occ:0.37
 BA A:BA102 0.0 6.8 0.4
BA A:BA102 1.1 12.6 0.6
O A:HOH218 2.9 11.2 1.0
O A:HOH206 3.0 7.7 1.0
O A:HOH224 3.0 5.9 1.0
O A:HOH204 3.4 11.9 1.0
BA A:BA104 4.1 15.9 0.3
OP1 A:DC4 4.8 8.0 1.0
OP2 A:DC4 4.8 2.3 1.0
O6 A:DG5 4.9 10.2 1.0

Barium binding site 4 out of 10 in 7sb9

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Barium binding site 4 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:12.6
occ:0.63
 BA A:BA102 0.0 12.6 0.6
BA A:BA102 1.1 6.8 0.4
O A:HOH224 2.6 5.9 1.0
O A:HOH204 2.6 11.9 1.0
O A:HOH206 2.9 7.7 1.0
O A:HOH218 3.1 11.2 1.0
OP1 A:DC4 4.5 8.0 1.0
OP2 A:DC4 4.7 2.3 1.0
BA A:BA104 4.9 15.9 0.3
N7 A:DG5 5.0 8.5 1.0

Barium binding site 5 out of 10 in 7sb9

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Barium binding site 5 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:16.4
occ:0.34
 O A:HOH251 2.7 29.3 1.0
O6 A:DG8 2.7 11.8 1.0
O A:HOH235 3.0 24.4 1.0
O A:HOH231 3.5 29.4 1.0
C6 A:DG8 3.9 11.4 1.0
C5 A:DG8 4.7 8.0 1.0
N7 A:DG8 4.8 9.1 1.0
OP2 A:DC7 4.9 21.2 1.0
N1 A:DG8 5.0 9.0 1.0

Barium binding site 6 out of 10 in 7sb9

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Barium binding site 6 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:15.9
occ:0.35
 O6 A:DG5 2.7 10.2 1.0
O A:HOH257 2.7 28.1 1.0
O A:HOH219 3.2 7.7 1.0
O A:HOH206 3.5 7.7 1.0
C6 A:DG5 3.9 10.4 1.0
BA A:BA102 4.1 6.8 0.4
N1 A:DG5 4.6 3.8 1.0
OP2 A:DC4 4.7 2.3 1.0
O A:HOH218 4.8 11.2 1.0
BA A:BA102 4.9 12.6 0.6
C5 A:DG5 4.9 7.4 1.0

Barium binding site 7 out of 10 in 7sb9

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Barium binding site 7 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:5.9
occ:0.27
 O6 A:DG14 2.8 10.6 1.0
O A:HOH227 2.9 8.2 1.0
O A:HOH222 3.3 5.1 1.0
C6 A:DG14 4.0 10.5 1.0
N1 A:DG14 4.6 8.4 1.0
C5 A:DC13 4.7 5.4 1.0
OP2 A:DC13 4.9 6.9 1.0

Barium binding site 8 out of 10 in 7sb9

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Barium binding site 8 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:20.7
occ:0.36
 O B:HOH249 2.2 31.0 1.0
O6 B:DG11 2.5 4.1 1.0
O B:HOH215 2.5 29.4 1.0
O B:HOH252 2.9 19.4 1.0
O A:HOH213 3.1 13.7 1.0
OP2 B:DC10 3.4 17.0 1.0
C6 B:DG11 3.7 11.5 1.0
O B:HOH227 3.8 29.6 1.0
C5 B:DG11 4.5 9.6 1.0
N7 B:DG11 4.5 9.6 1.0
N1 B:DG11 4.7 6.0 1.0
P B:DC10 4.8 17.6 0.2
N3 A:DA12 4.8 6.9 1.0

Barium binding site 9 out of 10 in 7sb9

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Barium binding site 9 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:25.4
occ:0.64
 BA B:BA102 0.0 25.4 0.6
BA B:BA102 1.5 21.9 0.4
O B:HOH223 2.6 14.0 1.0
O B:HOH226 2.8 19.5 1.0
O B:HOH260 2.9 18.2 1.0
N7 B:DG14 2.9 19.1 1.0
O6 B:DG14 3.5 11.1 1.0
C5 B:DG14 3.8 18.4 1.0
C8 B:DG14 3.9 15.7 1.0
O B:HOH235 3.9 18.5 1.0
O B:HOH241 4.0 22.4 1.0
C6 B:DG14 4.0 17.2 1.0
OP2 B:DC13 4.5 14.1 1.0
N3 A:DA15 5.0 19.4 1.0
C2' B:DC13 5.0 7.0 1.0

Barium binding site 10 out of 10 in 7sb9

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Barium binding site 10 out of 10 in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of D((Cga)5TGA) Parallel-Stranded Homo-Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:21.9
occ:0.36
 BA B:BA102 0.0 21.9 0.4
BA B:BA102 1.5 25.4 0.6
O B:HOH241 2.6 22.4 1.0
O6 B:DG14 2.7 11.1 1.0
O B:HOH260 2.9 18.2 1.0
O B:HOH226 2.9 19.5 1.0
O B:HOH235 3.0 18.5 1.0
O B:HOH223 3.3 14.0 1.0
N7 B:DG14 3.4 19.1 1.0
C6 B:DG14 3.5 17.2 1.0
C5 B:DG14 3.8 18.4 1.0
C8 B:DG14 4.6 15.7 1.0
N3 A:DA15 4.7 19.4 1.0
O A:HOH241 4.8 27.2 1.0
N1 B:DG14 4.9 13.1 1.0
OP2 B:DC13 5.0 14.1 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 11:09:13 2021

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