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

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

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 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 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 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 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 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 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 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 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 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 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

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