Calcium in PDB 8fb4: Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3

The structure of Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3, PDB code: 8fb4 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)	28.41 / 1.49
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	38.73, 38.73, 160.394, 90, 90, 120
R / Rfree (%)	25.8 / 29.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 (pdb code 8fb4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3, PDB code: 8fb4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:36.9 occ:1.00 O A:HOH213 2.3 40.3 1.0 OP1 A:DC3 2.4 31.9 1.0 P A:DC3 3.7 31.9 1.0 H5'' A:DC3 4.0 39.4 1.0 O A:HOH228 4.2 36.6 1.0 OP2 A:DC3 4.2 31.8 1.0 O5' A:DC3 4.4 32.8 1.0 C5' A:DC3 4.7 32.8 1.0 O3' A:DG2 4.9 31.4 1.0

Calcium binding site 2 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:20.9 occ:1.00 OP1 C:DA7 2.3 18.6 1.0 OP1 A:DA7 2.3 18.0 1.0 O C:HOH238 2.3 24.2 1.0 O A:HOH240 2.3 26.0 1.0 H5'' C:DA7 3.3 24.9 1.0 H5'' A:DA7 3.4 24.9 1.0 H5'' C:DG6 3.5 28.8 1.0 H5'' A:DG6 3.6 24.6 1.0 P C:DA7 3.6 20.2 1.0 P A:DA7 3.7 19.7 1.0 H5' C:DA7 3.8 24.9 1.0 C5' C:DA7 3.9 20.8 1.0 H5' A:DA7 3.9 24.9 1.0 C5' A:DA7 4.0 20.7 1.0 O5' C:DA7 4.1 23.1 1.0 H4' C:DG6 4.1 27.2 1.0 O5' A:DA7 4.2 21.7 1.0 H4' A:DG6 4.2 25.9 1.0 OP2 A:DA7 4.4 19.8 1.0 OP2 C:DA7 4.4 20.6 1.0 C5' C:DG6 4.4 24.0 1.0 C5' A:DG6 4.5 20.5 1.0 C4' C:DG6 4.7 22.6 1.0 O C:HOH209 4.7 29.4 1.0 C4' A:DG6 4.7 21.6 1.0 O3' C:DG6 4.8 21.1 1.0 O3' A:DG6 4.8 21.8 1.0 H3' A:DG6 4.8 26.2 1.0 H5' C:DG6 4.8 28.8 1.0 O A:HOH205 4.9 30.1 1.0 H5' A:DG6 4.9 24.6 1.0 H3' C:DG6 4.9 25.1 1.0

Calcium binding site 3 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:20.4 occ:1.00 OP2 C:DA7 2.3 20.6 1.0 O C:HOH242 2.4 26.0 1.0 O C:HOH240 2.4 27.5 1.0 OP2 A:DA7 2.4 19.8 1.0 P C:DA7 3.5 20.2 1.0 P A:DA7 3.6 19.7 1.0 O5' C:DA7 3.8 23.1 1.0 O5' A:DA7 3.8 21.7 1.0 OP1 A:DA7 4.1 18.0 1.0 O C:HOH221 4.1 30.5 1.0 OP1 C:DA7 4.2 18.6 1.0 O A:HOH206 4.4 29.8 1.0 O C:HOH208 4.4 33.1 1.0 H3' C:DA7 4.6 24.8 1.0 H3' A:DA7 4.7 24.2 1.0 O3' C:DG6 4.8 21.1 1.0 O3' A:DG6 4.9 21.8 1.0 H5'' C:DA7 4.9 24.9 1.0 H5'' A:DA7 4.9 24.9 1.0 H2' C:DA7 4.9 24.8 1.0 C5' C:DA7 5.0 20.8 1.0 C5' A:DA7 5.0 20.7 1.0

Calcium binding site 4 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:61.6 occ:1.00 OP1 A:DT8 2.7 24.1 1.0 P A:DT8 3.8 22.3 1.0 OP2 A:DT8 4.0 24.4 1.0 O5' A:DT8 4.8 21.7 1.0 O A:HOH206 4.9 29.8 1.0 O3' A:DA7 4.9 21.5 1.0

Calcium binding site 5 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca106 b:26.1 occ:1.00 O C:HOH220 2.2 25.8 1.0 O C:HOH239 2.3 29.0 1.0 O A:HOH242 2.4 25.5 1.0 OP1 A:DG16 2.4 21.6 1.0 O B:HOH204 2.5 25.3 1.0 O A:HOH239 2.5 25.1 1.0 O A:HOH236 2.6 42.3 1.0 H5'' A:DG16 3.6 23.1 1.0 P A:DG16 3.8 21.7 1.0 O A:HOH233 4.0 37.6 1.0 H21 C:DG16 4.0 27.0 1.0 O C:HOH217 4.1 29.9 1.0 H4' B:DG5 4.1 30.2 1.0 O B:HOH233 4.3 39.9 1.0 O C:HOH250 4.3 34.8 1.0 O5' A:DG16 4.3 20.6 1.0 C5' A:DG16 4.3 19.3 1.0 OP2 A:DG16 4.4 25.5 1.0 O4' B:DG5 4.5 24.7 1.0 H4' C:DG16 4.5 21.5 1.0 H2 C:DA15 4.6 25.8 1.0 O2 B:DT4 4.6 26.5 1.0 O B:HOH220 4.6 23.1 1.0 N3 C:DG16 4.7 22.4 1.0 H5' A:DG16 4.7 23.1 1.0 H1' C:DG16 4.7 26.0 1.0 N2 C:DG16 4.7 22.5 1.0 C4' B:DG5 4.8 25.1 1.0 O3' A:DA15 4.9 21.4 1.0 H5' B:DG5 4.9 32.7 1.0

Calcium binding site 6 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca107 b:64.1 occ:1.00 OP1 C:DT8 2.5 25.9 1.0 O A:HOH243 2.5 44.8 1.0 H8 A:DG6 2.8 26.2 1.0 H2'' A:DG6 3.1 25.5 1.0 H2' A:DG6 3.2 25.5 1.0 C8 A:DG6 3.4 21.8 1.0 O C:HOH237 3.4 44.7 1.0 C2' A:DG6 3.6 21.2 1.0 P C:DT8 3.6 25.4 1.0 OP2 C:DT8 4.0 26.0 1.0 N7 A:DG6 4.0 21.8 1.0 O A:HOH209 4.1 33.1 1.0 N9 A:DG6 4.2 22.6 1.0 C1' A:DG6 4.5 21.7 1.0 H62 A:DA7 4.6 25.2 1.0 O5' C:DT8 4.6 25.0 1.0 O3' C:DA7 4.7 23.2 1.0 H5'' C:DT8 4.7 28.7 1.0 O C:HOH208 4.9 33.1 1.0 C3' A:DG6 4.9 21.8 1.0 H1' A:DG6 5.0 26.1 1.0

Calcium binding site 7 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca108 b:54.0 occ:1.00 O B:HOH243 2.2 22.4 1.0 O A:HOH249 2.6 41.8 1.0 O A:HOH204 2.9 34.9 1.0 H5' A:DC14 4.2 39.3 1.0 H4' A:DC14 4.4 35.6 1.0 H1' A:DC13 4.6 38.5 1.0 O4' A:DC14 4.7 29.5 1.0 C4' A:DC14 4.8 29.6 1.0 C5' A:DC14 4.9 32.8 1.0

Calcium binding site 8 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca109 b:69.3 occ:1.00 OP1 A:DT12 2.2 42.0 1.0 H5'' A:DT12 3.2 44.7 1.0 P A:DT12 3.5 40.1 1.0 C5' A:DT12 3.9 37.3 1.0 O5' A:DT12 4.0 39.4 1.0 O3' A:DA11 4.0 38.6 1.0 H5' A:DT12 4.0 44.7 1.0 OP2 A:DT12 4.7 40.3 1.0 H9 A:WFB101 4.7 37.0 0.4

Calcium binding site 9 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 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 Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:50.5 occ:1.00 O A:HOH229 2.2 39.4 1.0 O B:HOH214 2.3 36.3 1.0 O C:HOH224 2.4 38.7 1.0 O A:HOH245 2.6 34.4 1.0 O A:HOH208 2.7 36.7 1.0 O C:HOH219 3.7 31.6 1.0 H4' B:DC14 4.0 35.2 1.0 H21 C:DG6 4.0 25.5 1.0 O4' B:DC14 4.1 27.2 1.0 OP2 A:DG6 4.1 24.6 1.0 O B:HOH237 4.3 35.9 1.0 H5' C:DT8 4.3 28.7 1.0 H5' B:DA15 4.3 30.3 1.0 H1' C:DA7 4.5 24.8 1.0 C4' B:DC14 4.5 29.4 1.0 H22 C:DG6 4.7 25.5 1.0 N2 C:DG6 4.7 21.2 1.0 O2 B:DC14 4.7 24.6 1.0 H5' B:DC14 4.7 38.9 1.0 N3 C:DA7 4.7 19.8 1.0 O2 B:DC13 4.8 29.6 1.0 H1' B:DC14 4.9 31.0 1.0 O4' C:DA7 4.9 21.3 1.0 O A:HOH221 4.9 37.1 1.0 H4' C:DT8 5.0 32.7 1.0

Calcium binding site 10 out of 15 in the Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of An Alternating at 16-Mer Bound By Diamidine DB1476: 5'- Gctggatatatccagc-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:26.0 occ:1.00 OP1 B:DG16 2.4 23.6 1.0 O A:HOH203 2.5 28.9 1.0 O B:HOH240 2.5 28.7 1.0 O B:HOH230 2.5 32.8 1.0 H5'' B:DG16 3.5 26.2 1.0 P B:DG16 3.7 23.9 1.0 H4' A:DG5 4.1 28.1 1.0 O B:HOH229 4.2 41.6 1.0 C5' B:DG16 4.2 21.9 1.0 O5' B:DG16 4.3 23.4 1.0 O4' A:DG5 4.5 22.1 1.0 OP2 B:DG16 4.5 28.4 1.0 O A:HOH235 4.6 32.6 1.0 H5' B:DG16 4.6 26.2 1.0 O A:HOH225 4.6 23.4 1.0 O2 A:DT4 4.7 26.8 1.0 C4' A:DG5 4.7 23.4 1.0 O3' B:DA15 4.8 22.4 1.0 H5' A:DG5 4.9 30.8 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