Calcium in PDB 8d5l: Crystal Structure of Theophylline Aptamer in Complex with TAL1

The structure of Crystal Structure of Theophylline Aptamer in Complex with TAL1, PDB code: 8d5l was solved by E.Menichelli, G.Spraggon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.06 / 1.64
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.606, 50.271, 79.845, 94.28, 91.53, 90.13
R / Rfree (%)	19.3 / 22.1

The structure of Crystal Structure of Theophylline Aptamer in Complex with TAL1 also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Sodium	(Na)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of Theophylline Aptamer in Complex with TAL1 (pdb code 8d5l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Theophylline Aptamer in Complex with TAL1, PDB code: 8d5l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Theophylline Aptamer in Complex with TAL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Theophylline Aptamer in Complex with TAL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:18.9 occ:1.00 O C:HOH327 2.4 19.0 1.0 O C:HOH244 2.4 16.0 1.0 O A:HOH319 2.4 26.4 1.0 O A:HOH204 2.5 16.1 1.0 O C:HOH318 2.5 18.9 1.0 O C:HOH270 2.5 16.4 1.0 O A:HOH303 2.6 25.2 1.0 O A:HOH242 2.7 25.9 1.0 H22 C:G26 3.7 17.4 1.0 H5'' A:U24 4.0 25.7 1.0 H4' A:C27 4.2 17.5 1.0 O C:HOH283 4.2 26.7 1.0 N2 C:G26 4.2 14.6 1.0 O04 C:QIJ101 4.2 15.4 1.0 OP1 A:G26 4.3 15.2 1.0 OP2 A:A28 4.3 16.8 1.0 H21 C:G26 4.4 17.4 1.0 OP2 A:G26 4.4 14.5 1.0 O C:HOH205 4.5 19.2 1.0 H5' A:U24 4.6 25.7 1.0 H5' A:C27 4.6 17.8 1.0 O C:HOH249 4.6 25.1 1.0 C5' A:U24 4.7 21.4 1.0 O A:HOH308 4.7 35.5 1.0 P A:G26 4.8 16.6 1.0 H051 C:QIJ101 4.9 13.4 1.0 O C:HOH306 5.0 25.1 1.0 H5'' A:C27 5.0 17.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Theophylline Aptamer in Complex with TAL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Theophylline Aptamer in Complex with TAL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:18.9 occ:1.00 O B:HOH252 2.2 20.1 1.0 OP2 B:G25 2.3 19.4 1.0 O A:HOH261 2.3 26.5 1.0 O A:HOH263 2.4 17.4 1.0 O A:HOH291 2.7 30.7 1.0 O A:HOH307 2.7 26.4 1.0 H5'' B:G25 3.3 18.3 1.0 H5' B:U24 3.7 29.2 1.0 P B:G25 3.7 20.7 1.0 H3' B:U24 4.1 21.0 1.0 H5'' A:G4 4.2 28.6 1.0 C5' B:G25 4.2 15.3 1.0 O5' B:G25 4.4 18.0 1.0 H5' B:G25 4.4 18.3 1.0 OP1 A:G4 4.5 31.1 1.0 OP1 B:G25 4.5 20.3 1.0 OP1 A:A5 4.6 22.8 1.0 C5' B:U24 4.6 24.4 1.0 OP2 B:G26 4.7 19.9 1.0 O3' B:U24 4.7 18.4 1.0 C3' B:U24 4.7 17.6 1.0 H5'' B:U24 4.8 29.2 1.0 H5' A:G4 5.0 28.6 1.0 C5' A:G4 5.0 23.9 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Theophylline Aptamer in Complex with TAL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Theophylline Aptamer in Complex with TAL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca103 b:26.6 occ:1.00 O C:HOH243 2.2 28.5 1.0 O C:HOH267 2.3 21.9 1.0 O2 C:C27 2.4 18.2 1.0 O C:HOH321 2.4 29.5 1.0 O C:HOH256 2.5 22.9 1.0 O C:HOH343 2.8 33.6 1.0 O C:HOH325 3.2 31.9 1.0 C2 C:C27 3.5 20.9 1.0 HO2' C:C27 3.7 21.2 1.0 O C:HOH309 3.9 28.7 1.0 O A:HOH311 4.0 30.6 1.0 N3 C:C27 4.1 18.3 1.0 H1' C:C27 4.1 20.9 1.0 OP1 C:G29 4.3 18.3 1.0 O2' C:C27 4.5 17.7 1.0 O A:HOH275 4.6 20.7 1.0 N1 C:C27 4.6 17.6 1.0 C1' C:C27 4.8 17.4 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Theophylline Aptamer in Complex with TAL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Theophylline Aptamer in Complex with TAL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca103 b:19.7 occ:1.00 O D:HOH211 2.2 26.5 1.0 OP2 D:G4 2.2 14.7 1.0 OP2 D:U23 2.3 22.1 1.0 O D:HOH262 2.4 26.7 1.0 O D:HOH319 2.4 28.1 1.0 O D:HOH228 2.4 22.6 1.0 P D:U23 3.6 20.3 1.0 P D:G4 3.7 17.8 1.0 H3' D:C3 4.1 17.2 1.0 O D:HOH244 4.2 27.6 1.0 OP1 D:U23 4.2 20.1 1.0 O5' D:G4 4.3 12.9 1.0 H8 D:G4 4.4 18.2 1.0 OP1 D:G4 4.4 18.8 1.0 O D:HOH270 4.4 20.9 1.0 O3' D:C22 4.4 22.6 1.0 N7 D:G4 4.6 13.4 1.0 O5' D:U23 4.7 19.7 1.0 O3' D:C3 4.7 15.4 1.0 O2' D:C22 4.7 19.9 1.0 C8 D:G4 4.8 15.2 1.0 H3' D:C22 4.8 25.0 1.0 C3' D:C3 4.8 14.4 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Theophylline Aptamer in Complex with TAL1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Theophylline Aptamer in Complex with TAL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca104 b:19.7 occ:1.00 O C:HOH217 2.3 28.5 1.0 O D:HOH280 2.4 21.8 1.0 OP2 D:G25 2.4 15.7 1.0 O C:HOH234 2.5 18.1 1.0 O C:HOH317 2.5 29.2 1.0 O C:HOH314 2.6 26.0 1.0 H5'' D:G25 3.3 19.2 1.0 H5' D:U24 3.7 26.9 1.0 P D:G25 3.8 18.0 1.0 H3' D:U24 4.1 19.1 1.0 H5'' C:G4 4.1 30.9 1.0 C5' D:G25 4.2 16.1 1.0 H5' D:G25 4.4 19.2 1.0 O5' D:G25 4.4 19.2 1.0 OP1 C:G4 4.5 28.6 1.0 OP1 C:A5 4.5 24.1 1.0 C5' D:U24 4.6 22.4 1.0 O C:HOH226 4.6 28.5 1.0 OP1 D:G25 4.7 23.2 1.0 H5'' D:U24 4.7 26.9 1.0 O3' D:U24 4.8 16.4 1.0 C3' D:U24 4.8 15.9 1.0 OP2 D:G26 4.8 15.9 1.0 C5' C:G4 5.0 25.8 1.0 H5' C:G4 5.0 30.9 1.0

E.Menichelli, B.J.Lam, Y.Wang, V.S.Wang, J.Shaffer, K.F.Tjhung, B.Bursulaya, T.N.Nguyen, T.Vo, P.B.Alper, C.S.Mcallister, D.H.Jones, G.Spraggon, P.Y.Michellys, J.Joslin, G.F.Joyce, J.Rogers. Discovery of Small Molecules That Target A Tertiary-Structured Rna. Proc.Natl.Acad.Sci.Usa V. 119 17119 2022.
ISSN: ESSN 1091-6490
PubMed: 36413497
DOI: 10.1073/PNAS.2213117119