Calcium in PDB 8v5j: The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3

The structure of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3, PDB code: 8v5j was solved by J.R.Terrell, W.D.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.61 / 1.19
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	38.829, 38.829, 159.676, 90, 90, 120
R / Rfree (%)	18.8 / 21

The binding sites of Calcium atom in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 (pdb code 8v5j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3, PDB code: 8v5j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:33.6 occ:1.00 O A:HOH240 2.8 19.2 1.0 H21 A:DG4 3.6 18.6 1.0 O A:HOH203 4.1 24.0 1.0 N2 A:DG4 4.2 15.5 1.0 H22 A:DG4 4.6 18.6 1.0 N3 A:DG4 4.7 15.0 1.0 C2 A:DG4 4.8 16.0 1.0

Calcium binding site 2 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:15.6 occ:0.40 OP1 A:DA6 2.3 13.8 1.0 O A:HOH267 2.4 16.4 1.0 H5'' A:DA6 3.4 17.4 1.0 H5'' A:DG5 3.5 21.2 1.0 P A:DA6 3.6 13.8 1.0 H5' A:DA6 3.9 17.4 1.0 C5' A:DA6 4.0 14.5 1.0 O5' A:DA6 4.1 15.2 1.0 H4' A:DG5 4.1 19.2 1.0 OP2 A:DA6 4.3 15.1 1.0 C5' A:DG5 4.4 17.7 1.0 C4' A:DG5 4.6 16.0 1.0 O A:HOH212 4.7 21.6 1.0 O3' A:DG5 4.8 14.8 1.0 H5' A:DG5 4.8 21.2 1.0 H3' A:DG5 4.9 18.1 1.0 C3' A:DG5 5.0 15.1 1.0

Calcium binding site 3 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:19.1 occ:0.46 OP2 A:DA6 2.3 15.1 1.0 O A:HOH269 2.4 18.9 1.0 P A:DA6 3.5 13.8 1.0 O5' A:DA6 3.8 15.2 1.0 OP1 A:DA6 4.2 13.8 1.0 O A:HOH238 4.2 29.2 1.0 H3' A:DA6 4.5 18.4 1.0 O A:HOH302 4.5 21.7 1.0 O A:HOH210 4.6 24.5 1.0 H2' A:DA6 4.7 19.2 1.0 O3' A:DG5 4.8 14.8 1.0 H5'' A:DA6 4.9 17.4 1.0 C5' A:DA6 5.0 14.5 1.0

Calcium binding site 4 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:23.1 occ:1.00 OP1 A:DG15 2.3 19.3 1.0 O A:HOH271 2.4 20.4 1.0 O A:HOH258 2.6 26.5 1.0 O A:HOH280 2.6 26.8 1.0 H5'' A:DG15 3.5 17.7 1.0 P A:DG15 3.6 17.1 1.0 O A:HOH266 4.0 33.4 1.0 O5' A:DG15 4.2 15.1 1.0 C5' A:DG15 4.3 14.8 1.0 OP2 A:DG15 4.4 20.4 1.0 H5' A:DG15 4.7 17.7 1.0 O3' A:DA14 4.8 17.4 1.0

Calcium binding site 5 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:15.8 occ:0.39 OP1 A:DC16 2.2 18.7 1.0 H5' A:DC16 3.4 28.5 1.0 P A:DC16 3.6 16.2 1.0 OP2 A:DC16 4.2 24.0 1.0 C5' A:DC16 4.3 23.8 1.0 O A:HOH262 4.3 26.2 1.0 O5' A:DC16 4.4 24.4 1.0 CA A:CA107 4.5 36.5 1.0 H4' A:DC16 4.7 29.9 1.0 O3' A:DG15 4.7 14.6 1.0 H5'' A:DC16 4.9 28.5 1.0

Calcium binding site 6 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:20.1 occ:0.23 O A:HOH252 2.4 28.2 1.0 OP1 A:DC2 2.4 21.1 1.0 P A:DC2 3.6 19.8 1.0 H5'' A:DC2 4.0 28.1 1.0 OP2 A:DC2 4.0 24.7 1.0 O A:HOH256 4.2 23.6 1.0 O5' A:DC2 4.3 19.9 1.0 C5' A:DC2 4.7 23.4 1.0 O3' A:DG1 4.9 19.9 1.0 H3' A:DC2 4.9 35.1 1.0

Calcium binding site 7 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca107 b:36.5 occ:1.00 OP2 A:DC16 2.8 24.0 1.0 O A:HOH226 3.7 28.3 1.0 P A:DC16 3.8 16.2 1.0 O5' A:DC16 4.1 24.4 1.0 OP1 A:DC16 4.2 18.7 1.0 CA A:CA105 4.5 15.8 0.4 H5' A:DC16 4.6 28.5 1.0 C5' A:DC16 4.9 23.8 1.0 H5'' A:DC16 5.0 28.5 1.0

Calcium binding site 8 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca108 b:29.4 occ:1.00 O A:HOH219 2.3 24.6 1.0 O A:HOH282 2.7 32.9 1.0 O A:HOH209 3.1 27.9 1.0 H4' A:DC13 4.0 23.9 1.0 O4' A:DC13 4.2 20.4 1.0 O A:HOH279 4.2 42.9 1.0 H5' A:DA14 4.3 23.3 1.0 C4' A:DC13 4.6 19.9 1.0 O A:HOH211 4.6 34.3 1.0 H5' A:DC13 4.7 29.4 1.0 O2 A:DC13 4.8 18.9 1.0 O2 A:DC12 4.8 21.8 1.0 H1' A:DC13 4.9 22.9 1.0

Calcium binding site 9 out of 9 in the The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Native Dna 16-Mer Sequence 5'-Gctggattaatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca109 b:46.8 occ:1.00 O A:HOH228 2.0 40.1 1.0 O A:HOH272 2.1 39.5 1.0 O A:HOH224 2.3 28.2 1.0 O A:HOH249 3.9 31.2 1.0 O A:HOH261 4.2 34.9 1.0 O A:HOH223 4.2 37.6 1.0 H41 A:DC16 4.4 23.5 1.0 O6 A:DG15 4.5 17.3 1.0 O A:HOH304 4.6 51.6 1.0 H42 A:DC16 4.6 23.5 1.0 N7 A:DG15 4.7 16.5 1.0 N7 A:DA14 4.7 19.6 1.0 H2'' A:DC13 4.7 26.8 1.0 N4 A:DC16 4.8 19.6 1.0 H8 A:DA14 4.9 23.5 1.0

J.R.Terrell, A.Paul, E.N.Ogbonna, A.A.Farahat, W.D.Wilson. Structural Examination of Dna Minor Groove Binding By Diamidine Stacked Dimers To Be Published.