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

Barium in PDB 7ecm: Rna Duplex Containing C-A Base Pair

Protein crystallography data

The structure of Rna Duplex Containing C-A Base Pair, PDB code: 7ecm was solved by J.Kondo, A.Tsudura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.54 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.475, 27.909, 46.665, 100.08, 93.54, 110.47
R / Rfree (%) 15.7 / 19.6

Barium Binding Sites:

The binding sites of Barium atom in the Rna Duplex Containing C-A Base Pair (pdb code 7ecm). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Rna Duplex Containing C-A Base Pair, PDB code: 7ecm:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 1 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:18.5
occ:0.34
 O A:HOH242 2.1 28.8 1.0
O B:HOH247 2.6 28.8 1.0
O A:HOH261 2.7 31.8 1.0
O A:HOH224 2.8 24.1 1.0
O A:HOH219 2.9 21.1 1.0
N7 A:G8 2.9 13.6 1.0
O6 A:G8 2.9 10.9 1.0
O A:HOH239 3.0 26.4 1.0
C5 A:G8 3.6 10.8 1.0
C6 A:G8 3.6 9.2 1.0
O B:HOH256 3.7 15.1 1.0
C8 A:G8 4.1 13.1 1.0
O6 A:G7 4.2 12.3 1.0
O B:HOH239 4.4 8.6 1.0
N7 A:G7 4.5 15.1 1.0
C6 A:G7 4.7 10.3 1.0
C5 A:G7 4.9 12.9 1.0
C4 A:G8 4.9 10.7 1.0
N1 A:G8 4.9 10.7 1.0

Barium binding site 2 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 2 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:14.7
occ:0.44
 O A:HOH234 2.7 25.0 1.0
O A:HOH215 2.8 20.1 1.0
O A:HOH212 2.8 32.9 1.0
OP2 A:G2 2.8 20.0 1.0
O A:HOH210 2.9 23.1 1.0
O A:HOH254 3.8 29.7 1.0
O B:HOH259 3.9 21.9 1.0
P A:G2 4.3 17.7 1.0
N4 A:C4 4.4 11.8 1.0
O A:HOH255 4.5 26.5 1.0
N7 A:G2 4.5 12.9 1.0
O A:HOH232 4.7 21.1 1.0
O5' A:G2 4.8 17.2 1.0
O A:HOH206 4.8 29.0 1.0
O5' A:G1 4.9 23.2 1.0
C8 A:G2 4.9 10.0 1.0
O B:HOH244 4.9 26.8 1.0
BA B:BA101 5.0 39.0 0.4

Barium binding site 3 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 3 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:25.4
occ:0.34
 O A:HOH232 2.5 21.1 1.0
O B:HOH258 2.7 35.1 1.0
O A:HOH252 2.9 31.1 1.0
O6 A:G1 3.2 15.9 1.0
O B:HOH241 3.2 24.9 1.0
O A:HOH254 3.3 29.7 1.0
N7 A:G1 3.7 14.1 1.0
C6 A:G1 4.0 9.9 1.0
C5 A:G1 4.2 11.8 1.0
O B:HOH242 4.4 19.5 1.0
O6 A:G2 4.8 12.4 1.0
O A:HOH215 4.8 20.1 1.0
C8 A:G1 4.9 13.3 1.0

Barium binding site 4 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 4 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:39.0
occ:0.44
 O B:HOH259 2.6 21.9 1.0
O6 B:G8 2.6 14.1 1.0
O B:HOH225 2.7 23.1 1.0
O B:HOH224 2.9 16.4 1.0
O6 B:G7 3.0 12.1 1.0
N7 B:G8 3.3 12.6 1.0
C6 B:G8 3.4 8.4 1.0
O B:HOH244 3.5 26.8 1.0
C5 B:G8 3.7 11.5 1.0
C6 B:G7 3.7 10.9 1.0
O B:HOH248 4.0 22.4 1.0
N7 B:G7 4.1 11.8 1.0
C5 B:G7 4.2 10.2 1.0
N4 A:C5 4.4 12.3 1.0
C8 B:G8 4.5 12.4 1.0
N4 A:C6 4.8 13.9 1.0
N1 B:G8 4.8 10.2 1.0
O B:HOH258 4.8 35.1 1.0
N1 B:G7 4.8 10.9 1.0
BA A:BA102 5.0 14.7 0.4

Barium binding site 5 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 5 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba101

b:29.7
occ:0.44
 N7 C:G8 2.7 19.0 1.0
O C:HOH247 2.7 31.3 1.0
O C:HOH237 2.8 27.6 1.0
O C:HOH229 2.9 26.2 1.0
O D:HOH257 2.9 23.1 1.0
O6 C:G8 3.2 15.9 1.0
O C:HOH252 3.3 20.9 1.0
O D:HOH262 3.5 24.4 1.0
C5 C:G8 3.5 14.4 1.0
O C:HOH215 3.5 18.1 1.0
C6 C:G8 3.7 11.4 1.0
N7 C:G7 3.7 17.2 1.0
C8 C:G8 3.8 17.6 1.0
C5 C:G7 4.1 13.9 1.0
O C:HOH223 4.3 26.9 1.0
C8 C:G7 4.3 20.4 1.0
O6 C:G7 4.4 12.7 1.0
C6 C:G7 4.4 11.4 1.0
C4 C:G8 4.8 14.2 1.0
O D:HOH260 4.8 13.2 1.0
O D:HOH210 4.9 24.5 1.0
O C:HOH218 4.9 24.3 1.0
N9 C:G8 4.9 18.5 1.0
OP2 C:G8 4.9 25.8 1.0
C4 C:G7 4.9 15.4 1.0
O D:HOH261 4.9 27.6 1.0

Barium binding site 6 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 6 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba102

b:50.1
occ:0.42
 O C:HOH207 2.3 28.7 1.0
O C:HOH227 2.7 27.6 1.0
N7 C:G2 2.8 14.9 1.0
O C:HOH201 2.8 31.7 1.0
O6 C:G2 2.9 13.4 1.0
O C:HOH234 3.2 22.6 1.0
C5 C:G2 3.4 9.7 1.0
C6 C:G2 3.5 8.2 1.0
N7 C:G1 3.6 19.2 1.0
C5 C:G1 3.7 13.4 1.0
O6 C:G1 3.8 16.8 1.0
C6 C:G1 3.8 12.0 1.0
C8 C:G2 3.9 13.5 1.0
O C:HOH249 3.9 26.1 1.0
O C:HOH253 4.2 40.4 1.0
C8 C:G1 4.2 15.0 1.0
C4 C:G1 4.5 11.2 1.0
N1 C:G1 4.7 14.8 1.0
O6 C:G3 4.7 11.6 1.0
N9 C:G1 4.8 15.8 1.0
C4 C:G2 4.8 12.4 1.0
O C:HOH222 4.8 25.8 1.0
N7 C:G3 4.8 14.1 1.0
N1 C:G2 4.9 11.9 1.0
N9 C:G2 5.0 15.1 1.0

Barium binding site 7 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 7 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba101

b:12.4
occ:0.88
 O D:HOH232 2.6 15.4 1.0
O D:HOH241 2.8 13.5 1.0
O C:HOH249 2.8 26.1 1.0
O C:HOH230 2.8 21.7 1.0
O D:HOH217 2.8 13.2 1.0
O C:HOH210 2.8 15.3 1.0
O D:HOH234 2.9 13.9 1.0
O6 D:G8 2.9 10.9 1.0
C6 D:G8 3.9 8.5 1.0
N7 D:G8 4.1 10.6 1.0
O C:HOH201 4.2 31.7 1.0
O6 D:G7 4.4 12.3 1.0
C5 D:G8 4.4 8.4 1.0
N4 C:C5 4.5 10.2 1.0
N7 D:G7 4.7 11.9 1.0
N4 C:C4 4.7 17.7 1.0
O D:HOH258 4.8 24.0 1.0
N6 D:A9 4.9 10.1 1.0
O D:HOH231 5.0 19.6 1.0
C6 D:G7 5.0 12.8 1.0
O C:HOH234 5.0 22.6 1.0
O6 C:G3 5.0 11.6 1.0

Barium binding site 8 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 8 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba102

b:11.6
occ:0.75
 O D:HOH253 2.8 22.2 1.0
O D:HOH252 2.9 20.0 1.0
O D:HOH226 2.9 15.0 1.0
O D:HOH213 3.0 15.7 1.0
OP1 D:C11 4.6 16.9 1.0
OP1 D:C12 4.8 12.1 1.0

Barium binding site 9 out of 9 in 7ecm

Go back to Barium Binding Sites List in 7ecm
Barium binding site 9 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba103

b:123.7
occ:1.00
 O D:HOH246 2.2 30.9 1.0
O D:HOH261 2.8 27.6 1.0
N7 D:G1 2.9 15.1 1.0
O6 D:G1 3.1 14.7 1.0
O D:HOH214 3.3 30.8 1.0
C5 D:G1 3.6 9.7 1.0
C6 D:G1 3.7 10.9 1.0
C8 D:G1 4.1 13.5 1.0
O6 D:G2 4.6 14.2 1.0
O C:HOH217 4.8 28.6 1.0
C4 D:G1 4.9 10.5 1.0
N7 D:G2 4.9 13.7 1.0

Reference:

J.Kondo, A.Tsudura. Rna Duplex Containing C-A Base Pair To Be Published.
Page generated: Wed Jul 10 16:06:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy