Calcium in PDB 8v4t: The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-3

The structure of The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-3, PDB code: 8v4t 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)	25.74 / 1.47
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	38.324, 38.324, 163.022, 90, 90, 120
R / Rfree (%)	19.5 / 21.1

The binding sites of Calcium atom in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-3 (pdb code 8v4t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-3, PDB code: 8v4t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:20.1 occ:0.41 OP1 A:DC2 2.3 17.9 1.0 O A:HOH278 2.4 24.4 1.0 P A:DC2 3.5 17.0 1.0 H5'' A:DC2 3.7 23.2 1.0 OP2 A:DC2 3.9 18.4 1.0 O5' A:DC2 4.2 15.7 1.0 C5' A:DC2 4.4 19.3 1.0 O A:HOH213 4.8 30.2 1.0 O3' A:DG1 4.8 16.5 1.0 H5' A:DC2 4.9 23.2 1.0

Calcium binding site 2 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:19.4 occ:1.00 O A:HOH208 2.3 22.6 1.0 O A:HOH272 2.3 15.7 1.0 O A:HOH287 2.4 25.6 1.0 O A:HOH288 2.5 18.6 1.0 O A:HOH258 2.5 24.8 1.0 O A:HOH283 3.0 26.7 1.0 H4' A:DG4 4.0 19.5 1.0 O A:HOH251 4.0 26.9 1.0 O A:HOH248 4.2 28.9 1.0 O4' A:DG4 4.5 16.1 1.0 O A:HOH292 4.5 25.7 1.0 O2 A:DT3 4.6 17.2 1.0 C4' A:DG4 4.6 16.2 1.0 H5' A:DG4 4.7 21.4 1.0 O A:HOH232 4.7 19.7 1.0

Calcium binding site 3 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:16.4 occ:0.39 O A:HOH276 2.3 22.7 1.0 OP1 A:DG6 2.4 14.4 1.0 H5'' A:DG6 3.4 16.9 1.0 H5'' A:DC5 3.6 20.5 1.0 P A:DG6 3.7 14.2 1.0 C5' A:DG6 4.1 14.2 1.0 O5' A:DG6 4.2 14.9 1.0 H5' A:DG6 4.2 16.9 1.0 H4' A:DC5 4.3 16.8 1.0 OP2 A:DG6 4.4 14.5 1.0 C5' A:DC5 4.5 17.1 1.0 O A:HOH221 4.6 26.4 1.0 C4' A:DC5 4.8 14.0 1.0 O3' A:DC5 4.9 15.4 1.0 H5' A:DC5 4.9 20.5 1.0 H3' A:DC5 5.0 18.3 1.0

Calcium binding site 4 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:15.5 occ:0.39 O A:HOH252 2.3 19.9 1.0 OP2 A:DG6 2.3 14.5 1.0 P A:DG6 3.5 14.2 1.0 O5' A:DG6 3.8 14.9 1.0 O A:HOH214 4.0 23.9 1.0 OP1 A:DG6 4.2 14.4 1.0 H3' A:DG6 4.4 17.7 1.0 H2' A:DG6 4.5 19.6 1.0 O3' A:DC5 4.8 15.4 1.0 O A:HOH267 4.9 33.7 1.0

Calcium binding site 5 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:24.8 occ:1.00 O A:HOH240 2.3 21.2 1.0 O A:HOH263 2.4 24.9 1.0 O A:HOH269 2.4 24.9 1.0 O A:HOH235 2.4 25.2 1.0 O A:HOH289 2.5 31.9 1.0 O A:HOH264 2.6 31.5 1.0 H21 A:DG6 3.8 24.2 1.0 H5' A:DT7 4.3 27.0 1.0 H4' A:DT7 4.4 23.6 1.0 N2 A:DG6 4.5 20.1 1.0 O A:HOH259 4.6 30.7 1.0 N3 A:DG6 4.6 16.6 1.0 O A:HOH291 4.8 39.4 1.0 O A:HOH270 4.8 41.2 1.0 O4' A:DT7 4.9 18.0 1.0 H1' A:DG6 4.9 18.9 1.0 C4' A:DT7 5.0 19.7 1.0 C5' A:DT7 5.0 22.5 1.0

Calcium binding site 6 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:12.4 occ:0.42 OP1 A:DC16 2.3 16.5 1.0 O A:HOH247 2.3 16.9 1.0 H5' A:DC16 3.3 21.9 1.0 P A:DC16 3.6 13.8 1.0 C5' A:DC16 4.2 18.3 1.0 OP2 A:DC16 4.2 17.3 1.0 O5' A:DC16 4.3 16.7 1.0 H4' A:DC16 4.4 22.4 1.0 O A:HOH224 4.6 19.4 1.0 O3' A:DG15 4.7 11.8 1.0 C4' A:DC16 4.9 18.6 1.0 H5'' A:DC16 4.9 21.9 1.0

Calcium binding site 7 out of 7 in the The Native Dna 16-Mer Sequence 5'-Gctgcgttaacgcagc-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'-Gctgcgttaacgcagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca107 b:47.0 occ:1.00 O A:HOH245 2.3 33.2 1.0 O A:HOH275 2.3 32.0 1.0 O A:HOH253 2.4 28.9 1.0 OP1 A:DT7 3.1 27.4 1.0 OP2 A:DT7 3.9 21.3 1.0 P A:DT7 3.9 21.2 1.0 O A:HOH286 4.0 41.4 1.0 O5' A:DT7 4.7 19.8 1.0 H5'' A:DT7 4.9 27.0 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.