Atomistry » Barium » PDB 4x1a-5wkx » 5ebi
Atomistry »
  Barium »
    PDB 4x1a-5wkx »
      5ebi »

Barium in PDB 5ebi: Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning

Protein crystallography data

The structure of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning, PDB code: 5ebi was solved by M.Gilski, P.Drozdzal, R.Kierzek, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.94 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.720, 44.100, 35.720, 90.00, 119.98, 90.00
R / Rfree (%) 11.5 / 16.9

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning (pdb code 5ebi). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 16 binding sites of Barium where determined in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning, PDB code: 5ebi:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 1 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:18.8
occ:0.20
O A:HOH223 3.0 33.6 1.0
O A:HOH228 3.1 19.1 0.9
O F:HOH208 4.3 18.4 0.9
OP1 A:G2 4.5 13.2 1.0
OP2 A:G2 4.7 19.6 1.0

Barium binding site 2 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 2 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:8.9
occ:0.46
OP1 E:DC5 2.8 13.1 1.0
O A:HOH203 2.8 15.8 0.9
O A:HOH209 2.8 10.7 1.0
O A:HOH202 2.9 15.7 1.0
OP2 A:DC3 2.9 9.9 0.5
O E:HOH208 2.9 13.8 1.0
O A:HOH211 3.9 22.5 1.0
P A:DC3 4.0 6.4 0.5
O A:HOH213 4.0 14.0 1.0
P E:DC5 4.1 9.9 1.0
OP1 A:DC3 4.1 6.5 0.5
O E:HOH204 4.2 19.7 1.0
OP2 E:DC5 4.4 13.8 1.0
OP1 A:G4 4.4 11.7 1.0
C5' E:DC5 4.6 12.4 1.0
O E:HOH231 4.6 13.9 1.0
OP2 A:G2 4.6 19.6 1.0
O A:HOH201 4.7 15.9 1.0
O5' E:DC5 4.8 15.8 1.0
O5' E:G6 4.9 15.0 1.0
C5' A:G2 4.9 11.6 1.0
OP1 E:G6 4.9 12.3 1.0

Barium binding site 3 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 3 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:11.8
occ:0.29
BA F:BA101 2.2 10.2 0.3
O6 A:G6 2.7 10.5 1.0
N7 A:G6 3.2 14.5 1.0
C6 A:G6 3.4 9.7 1.0
C5 A:G6 3.6 11.5 1.0
C8 A:G6 4.4 16.8 1.0
N4 B:DC7 4.7 10.2 1.0
N1 A:G6 4.8 8.7 1.0
C6 A:DC5 5.0 9.1 1.0
C4 A:G6 5.0 10.3 1.0

Barium binding site 4 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 4 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:8.3
occ:0.26
BA A:BA105 1.7 20.9 0.3
O A:HOH216 2.3 18.0 0.9
BA A:BA106 2.3 13.4 0.2
O A:HOH220 2.6 24.7 1.0
O6 A:G4 2.7 13.2 1.0
OP1 A:DC3 3.0 13.3 0.5
N7 A:G4 3.2 13.9 1.0
C6 A:G4 3.5 11.8 1.0
C5 A:G4 3.7 11.3 1.0
P A:DC3 4.2 8.6 0.5
OP2 A:DC3 4.4 9.6 0.5
C8 A:G4 4.4 11.5 1.0
N4 B:DC9 4.7 11.8 1.0
N1 A:G4 4.8 10.8 1.0
C6 A:DC3 4.8 8.4 1.0
O6 B:G8 4.8 10.6 1.0
C4 A:G4 5.0 10.7 1.0
C5 A:DC3 5.0 6.9 1.0

Barium binding site 5 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 5 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:20.9
occ:0.26
BA A:BA106 1.0 13.4 0.2
BA A:BA104 1.7 8.3 0.3
O A:HOH216 1.9 18.0 0.9
O A:HOH220 3.0 24.7 1.0
OP1 A:DC3 3.9 13.3 0.5
N7 A:G4 4.0 13.9 1.0
O6 A:G4 4.3 13.2 1.0
OP2 A:DC3 4.6 9.6 0.5
P A:DC3 4.9 8.6 0.5
C5 A:G4 4.9 11.3 1.0
C6 A:G4 5.0 11.8 1.0

Barium binding site 6 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 6 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba106

b:13.4
occ:0.20
BA A:BA105 1.0 20.9 0.3
BA A:BA104 2.3 8.3 0.3
O A:HOH216 2.9 18.0 0.9
O A:HOH220 3.0 24.7 1.0
O6 A:G4 4.8 13.2 1.0
N7 A:G4 4.8 13.9 1.0
OP1 A:DC3 4.8 13.3 0.5

Barium binding site 7 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 7 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:9.8
occ:0.51
O B:HOH210 1.7 16.3 0.6
O B:HOH210 2.6 27.3 0.4
OP1 B:DC11 3.1 16.9 1.0
OP1 B:G12 3.9 30.2 1.0
P B:DC11 4.2 12.6 1.0
O5' B:G12 4.4 23.2 1.0
OP2 B:DC11 4.4 14.2 1.0
C5' B:DC11 4.6 10.7 1.0
P B:G12 4.8 29.3 1.0
O B:HOH218 5.0 17.7 1.0
O5' B:DC11 5.0 11.0 1.0

Barium binding site 8 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 8 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba101

b:7.3
occ:0.24
BA F:BA103 1.6 14.6 0.2
O G:HOH228 2.3 18.6 0.9
BA F:BA102 2.3 10.9 0.3
O G:HOH235 2.5 27.3 1.0
O F:HOH216 3.5 15.9 1.0
O E:HOH215 3.7 13.2 1.0

Barium binding site 9 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 9 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba102

b:11.6
occ:0.28
BA H:BA101 2.2 10.0 0.3
O G:HOH208 3.8 16.3 1.0
N7 H:G10 4.4 10.6 1.0
OP1 H:DC9 4.7 26.3 0.4
O6 H:G10 4.7 9.6 1.0

Barium binding site 10 out of 16 in 5ebi

Go back to Barium Binding Sites List in 5ebi
Barium binding site 10 out of 16 in the Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of A Dna-Rna Chimera in Complex with BA2+ Ions: A Case of Unusual Multi-Domain Twinning within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba101

b:9.7
occ:0.52
O D:HOH215 2.2 27.9 1.0
OP1 D:DC11 3.1 17.0 1.0
OP1 D:G12 3.8 30.5 1.0
P D:DC11 4.2 12.5 1.0
O5' D:G12 4.4 25.7 1.0
OP2 D:DC11 4.5 13.4 1.0
C5' D:DC11 4.7 10.8 1.0
P D:G12 4.8 28.9 1.0
O D:HOH223 5.0 16.8 1.0

Reference:

M.Gilski, P.Drozdzal, R.Kierzek, M.Jaskolski. Atomic Resolution Structure of A Chimeric Dna-Rna Z-Type Duplex in Complex with Ba(2+) Ions: A Case of Complicated Multi-Domain Twinning. Acta Crystallogr D Struct V. 72 211 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894669
DOI: 10.1107/S2059798315024365
Page generated: Sat Dec 12 01:57:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy