Calcium in PDB 7een: Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna

The structure of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna, PDB code: 7een was solved by J.Kondo, S.Sekiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.28 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.867, 68.867, 116.016, 90, 90, 90
R / Rfree (%)	18.9 / 23.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Calcium atom in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna (pdb code 7een). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 33 binding sites of Calcium where determined in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna, PDB code: 7een:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:12.3 occ:1.00 OP1 C:A24 2.3 13.7 1.0 O6 A:G15 2.4 13.1 1.0 O C:HOH288 2.4 19.4 1.0 O B:HOH227 2.4 21.3 1.0 O B:HOH278 2.5 17.7 1.0 O A:HOH278 2.5 18.9 1.0 O A:HOH281 2.5 16.9 1.0 O B:HOH311 2.7 27.9 1.0 C6 A:G15 3.4 14.7 1.0 P C:A24 3.8 14.3 1.0 N1 A:G15 3.8 15.1 1.0 N1 A:A16 4.1 14.2 1.0 C5' C:A24 4.2 17.5 1.0 O5' C:A24 4.2 17.6 1.0 O B:HOH314 4.3 22.3 1.0 O B:HOH326 4.5 16.6 1.0 O2' A:G13 4.5 14.7 1.0 O3' C:G23 4.6 11.9 1.0 N3 B:C20 4.6 11.2 1.0 N6 A:A14 4.6 23.0 1.0 C5 A:G15 4.7 13.8 1.0 O2 B:C20 4.7 13.9 1.0 N6 A:A16 4.7 13.9 1.0 C2 A:A16 4.8 14.4 1.0 C6 A:A16 4.8 14.3 1.0 OP2 C:G25 4.8 19.6 1.0 OP2 C:A24 4.8 16.0 1.0 O B:HOH286 4.9 23.1 1.0 O2 B:C21 5.0 12.8 1.0

Calcium binding site 2 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:20.9 occ:1.00 OP1 A:OMU10 2.3 13.8 1.0 O A:HOH325 2.3 25.2 1.0 P A:OMU10 3.8 13.9 1.0 O A:HOH316 4.3 17.6 1.0 C5' A:OMU10 4.3 14.3 1.0 O5' A:OMU10 4.4 15.0 1.0 OP2 A:OMU10 4.6 13.7 1.0 O3' A:DG9 4.7 12.4 1.0 O A:HOH324 4.8 28.3 1.0 C3' A:DG9 4.9 13.7 1.0

Calcium binding site 3 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:18.8 occ:1.00 O A:HOH316 2.3 17.6 1.0 O A:HOH276 2.5 14.7 1.0 O A:HOH225 2.5 21.2 1.0 O6 A:G18 2.7 14.3 1.0 O A:HOH253 3.2 26.0 1.0 C6 A:G18 3.7 12.9 1.0 N1 A:G18 4.4 12.3 1.0 O A:HOH256 4.5 22.0 1.0 N7 A:G17 4.5 15.0 1.0 O A:HOH240 4.6 14.4 1.0 O A:HOH244 4.6 22.3 1.0 C5 A:G18 4.7 13.4 1.0 OP2 A:OMU10 4.8 13.7 1.0 O A:HOH210 4.8 27.5 1.0 O6 A:G17 4.8 13.7 1.0 C2' A:DG9 4.8 13.5 1.0 C8 A:DG9 4.9 17.5 1.0

Calcium binding site 4 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:25.0 occ:1.00 O A:HOH210 2.3 27.5 1.0 O A:HOH333 2.4 31.9 1.0 O A:HOH306 2.4 24.8 1.0 O A:HOH284 2.5 24.5 1.0 O A:HOH253 3.0 26.0 1.0 CA A:CA108 3.2 29.9 1.0 OP2 A:G17 4.4 18.1 1.0 O A:HOH328 4.5 30.4 1.0 O A:HOH326 4.5 29.5 1.0 C5' A:G17 4.5 19.2 1.0 N7 A:DG9 4.5 16.9 1.0 OP1 A:G17 4.6 21.9 1.0 O A:HOH225 4.7 21.2 1.0 OP2 A:G18 4.8 18.9 1.0 O6 A:DG9 4.9 15.8 1.0 P A:G17 4.9 19.3 1.0 N7 A:G18 5.0 15.5 1.0

Calcium binding site 5 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:22.8 occ:1.00 O A:HOH251 2.5 21.2 1.0 O A:HOH346 2.5 28.6 1.0 O A:HOH329 2.5 24.6 1.0 O A:HOH342 2.5 17.4 1.0 O A:HOH274 3.9 26.8 1.0 C5' A:G15 4.1 17.0 1.0 O A:HOH339 4.3 34.4 1.0 O A:HOH293 4.5 24.5 1.0 OP1 A:G15 4.7 14.4 1.0 O A:HOH226 4.8 19.8 1.0 C4' A:G15 4.9 18.5 1.0

Calcium binding site 6 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:19.6 occ:1.00 O A:HOH219 2.4 24.6 1.0 O A:HOH338 2.6 23.5 1.0 OP1 A:A16 4.4 19.5 1.0 O A:HOH256 4.8 22.0 1.0 O A:HOH293 4.9 24.5 1.0 O A:HOH326 5.0 29.5 1.0

Calcium binding site 7 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca107 b:21.6 occ:1.00 OP1 A:OMC12 2.3 16.6 1.0 OP1 B:G13 2.4 16.2 1.0 O B:HOH229 2.4 27.4 1.0 O A:HOH323 2.5 27.3 1.0 O A:HOH254 2.6 20.4 1.0 P A:OMC12 3.6 15.2 1.0 O3' A:A2M11 3.8 13.9 1.0 P B:G13 3.8 13.9 1.0 C5' A:OMC12 4.1 13.2 1.0 O5' A:OMC12 4.4 12.9 1.0 C5' B:G13 4.5 17.0 1.0 O5' B:G13 4.5 13.1 1.0 OP2 B:A14 4.6 20.9 1.0 O3' B:OMC12 4.7 13.6 1.0 OP2 B:G13 4.8 16.9 1.0 O2' A:A2M11 4.8 16.4 1.0 OP2 A:OMC12 4.8 15.1 1.0

Calcium binding site 8 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca108 b:29.9 occ:1.00 O6 A:DG9 2.4 15.8 1.0 OP2 A:G18 2.4 18.9 1.0 O A:HOH284 2.4 24.5 1.0 O A:HOH333 2.5 31.9 1.0 O A:HOH236 2.6 38.0 1.0 O A:HOH306 2.6 24.8 1.0 CA A:CA104 3.2 25.0 1.0 C6 A:DG9 3.4 17.4 1.0 O A:HOH328 3.7 30.4 1.0 P A:G18 3.9 16.3 1.0 N7 A:DG9 4.1 16.9 1.0 C5 A:DG9 4.1 17.0 1.0 N7 A:G18 4.3 15.5 1.0 O5' A:G18 4.4 13.2 1.0 O A:HOH253 4.5 26.0 1.0 O A:HOH252 4.5 27.7 1.0 N1 A:DG9 4.5 13.2 1.0 C8 A:G18 4.6 12.4 1.0 OP1 A:G18 4.8 18.2 1.0 O3' A:G17 4.8 14.9 1.0 C5' A:G17 4.8 19.2 1.0 O A:HOH210 4.9 27.5 1.0 C3' A:G17 4.9 16.6 1.0

Calcium binding site 9 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca109 b:42.0 occ:1.00 OP1 A:DG9 2.5 18.0 1.0 O A:HOH291 2.7 24.5 1.0 O A:HOH286 3.0 29.4 1.0 O A:HOH287 3.3 32.2 1.0 P A:DG9 3.9 16.6 1.0 O A:HOH324 4.4 28.3 1.0 O A:HOH343 4.6 27.3 1.0 OP2 A:DG9 4.6 22.4 1.0 C5' A:DA8 4.6 14.0 1.0 OP1 A:OMU7 4.6 13.2 1.0 O A:HOH242 4.6 21.8 1.0 C3' A:DA8 4.7 12.3 1.0 CA A:CA110 4.8 41.9 1.0 O3' A:DA8 4.8 15.0 1.0 C4' A:DA8 4.8 15.5 1.0 O5' A:DG9 4.9 17.0 1.0

Calcium binding site 10 out of 33 in the Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca110 b:41.9 occ:1.00 O A:HOH287 4.5 32.2 1.0 CA A:CA109 4.8 42.0 1.0

J.Kondo, S.Sekiguchi. Bulged-G Motif Composed of Rna, Dna and 2'-O-Methyl Rna To Be Published.