Atomistry » Barium » PDB 7awn-9b3g » 7t6y
Atomistry »
  Barium »
    PDB 7awn-9b3g »
      7t6y »

Barium in PDB 7t6y: D((Cga)5TGA) Parallel-Stranded Homo-Duplex

Protein crystallography data

The structure of D((Cga)5TGA) Parallel-Stranded Homo-Duplex, PDB code: 7t6y 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) 32.26 / 2.30
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 (%) 20.4 / 24.2

Barium Binding Sites:

The binding sites of Barium atom in the D((Cga)5TGA) Parallel-Stranded Homo-Duplex (pdb code 7t6y). 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: 7t6y:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 10 in 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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 7t6y

Go back to Barium Binding Sites List in 7t6y
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: Wed Jul 10 16:08:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy