Calcium in PDB 8f94: Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3

The structure of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3, PDB code: 8f94 was solved by J.R.Terrell, E.N.Ogbonna, W.D.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.63 / 1.08
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	38.769, 38.769, 159.771, 90, 90, 120
R / Rfree (%)	20.1 / 22.5

The binding sites of Calcium atom in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 (pdb code 8f94). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3, PDB code: 8f94:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:20.4 occ:0.31 O A:HOH252 2.4 24.1 1.0 OP1 A:DC3 2.4 16.6 1.0 P A:DC3 3.6 16.9 1.0 H5'' A:DC3 3.9 22.3 1.0 OP2 A:DC3 4.1 21.3 1.0 O A:HOH256 4.1 22.0 1.0 O5' A:DC3 4.3 18.2 1.0 C5' A:DC3 4.6 18.6 1.0 O A:HOH204 4.6 34.2 1.0 O3' A:DG2 4.8 16.7 1.0 O A:HOH211 4.9 41.7 1.0

Calcium binding site 2 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:17.2 occ:0.33 OP1 A:DA7 2.3 14.2 1.0 O A:HOH266 2.4 16.8 1.0 H5'' A:DA7 3.4 16.6 1.0 H5'' A:DG6 3.5 18.4 1.0 P A:DA7 3.6 13.4 1.0 H5' A:DA7 4.0 16.6 1.0 C5' A:DA7 4.0 13.8 1.0 O5' A:DA7 4.1 14.7 1.0 H4' A:DG6 4.1 17.9 1.0 OP2 A:DA7 4.4 15.3 1.0 C5' A:DG6 4.4 15.4 1.0 C4' A:DG6 4.6 14.9 1.0 O A:HOH207 4.7 21.6 1.0 O3' A:DG6 4.8 13.8 1.0 H5' A:DG6 4.8 18.4 1.0 H3' A:DG6 4.9 16.4 1.0

Calcium binding site 3 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:14.3 occ:0.33 OP2 A:DA7 2.2 15.3 1.0 O A:HOH267 2.4 19.8 1.0 P A:DA7 3.5 13.4 1.0 O5' A:DA7 3.8 14.7 1.0 OP1 A:DA7 4.2 14.2 1.0 O A:HOH236 4.4 21.6 1.0 H3' A:DA7 4.5 16.8 1.0 O A:HOH214 4.7 28.8 1.0 O3' A:DG6 4.7 13.8 1.0 O A:HOH288 4.8 40.9 1.0 H2' A:DA7 4.8 17.1 1.0 H5'' A:DA7 5.0 16.6 1.0

Calcium binding site 4 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:15.7 occ:0.33 OP1 A:DC17 2.3 16.8 1.0 H5' A:DC17 3.6 25.6 1.0 P A:DC17 3.6 14.3 1.0 O A:HOH255 4.2 23.2 1.0 OP2 A:DC17 4.3 20.8 1.0 C5' A:DC17 4.4 21.3 1.0 O5' A:DC17 4.4 19.8 1.0 O A:HOH219 4.6 17.3 1.0 H4' A:DC17 4.7 26.8 1.0 O3' A:DG16 4.7 13.3 1.0

Calcium binding site 5 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:20.0 occ:1.00 OP1 A:DG16 2.3 17.6 1.0 O A:HOH269 2.4 18.3 1.0 O A:HOH259 2.5 23.4 1.0 O A:HOH274 2.6 22.1 1.0 H5'' A:DG16 3.5 16.6 1.0 O A:HOH262 3.5 41.5 1.0 P A:DG16 3.6 14.9 1.0 O5' A:DG16 4.2 13.9 1.0 C5' A:DG16 4.2 13.8 1.0 OP2 A:DG16 4.3 19.0 1.0 H5' A:DG16 4.6 16.6 1.0 O3' A:DA15 4.8 14.0 1.0

Calcium binding site 6 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:34.1 occ:1.00 O A:HOH272 2.2 26.2 1.0 O A:HOH223 2.3 19.7 1.0 O A:HOH208 3.1 22.1 1.0 H4' A:DC14 4.0 20.8 1.0 O4' A:DC14 4.3 16.3 1.0 H5' A:DA15 4.5 18.3 1.0 O A:HOH240 4.6 28.2 1.0 C4' A:DC14 4.6 17.3 1.0 O2 A:DC13 4.7 16.9 1.0 H5' A:DC14 4.7 22.8 1.0 O2 A:DC14 4.9 14.5 1.0

Calcium binding site 7 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca107 b:63.3 occ:1.00 O A:HOH220 2.2 30.6 1.0 O A:HOH232 2.2 24.4 1.0 O A:HOH254 2.8 36.6 1.0 O A:HOH247 3.7 28.7 1.0 O A:HOH283 3.7 50.5 1.0 H41 A:DC17 4.1 21.1 1.0 H42 A:DC17 4.3 21.1 1.0 O6 A:DG16 4.4 15.3 1.0 N4 A:DC17 4.5 17.6 1.0 O A:HOH261 4.5 33.7 1.0 N7 A:DG16 4.6 14.9 1.0 N7 A:DA15 5.0 15.9 1.0

Calcium binding site 8 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca108 b:26.7 occ:1.00 OP1 A:DT12 2.2 29.1 1.0 O A:HOH258 2.6 42.0 1.0 O A:HOH281 3.2 50.6 1.0 P A:DT12 3.4 27.2 1.0 OP2 A:DT12 3.9 29.0 1.0 H5'' A:DT12 3.9 29.7 1.0 O5' A:DT12 4.1 25.5 1.0 O A:HOH257 4.5 24.6 1.0 C5' A:DT12 4.5 24.8 1.0 O3' A:DA11 4.5 24.8 1.0 H5' A:DT12 4.9 29.7 1.0

Calcium binding site 9 out of 9 in the Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of An Alternating at 16-Mer: 5'-Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca109 b:54.9 occ:1.00 O A:HOH291 2.3 27.9 1.0 O A:HOH290 2.4 32.7 1.0 O6 A:DG6 2.8 17.5 1.0 O A:HOH238 3.1 31.5 1.0 O A:HOH217 3.1 28.4 1.0 O A:HOH243 3.3 42.9 1.0 C6 A:DG6 3.8 15.1 1.0 N7 A:DG6 4.1 16.1 1.0 C5 A:DG6 4.3 14.6 1.0 O6 A:DG5 4.8 14.9 1.0 N7 A:DG5 4.8 15.6 1.0 H61 A:DA7 5.0 18.8 1.0

E.N.Ogbonna, A.P.Paul, A.Farahat, J.R.Terrell, V.Ogbonna, D.W.Boykin, W.D.Wilson. X-Ray Structure Characterization of the Selective Recognition of at Base Pair Sequences Acs Bio Med Chem Au 2023.
ISSN: ESSN 2694-2437