Chlorine in PDB 5emf: Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc)

The structure of Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc), PDB code: 5emf was solved by A.Kiliszek, K.Banaszak, Z.Dauter, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.41 / 1.14
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	35.110, 35.110, 69.114, 90.00, 90.00, 120.00
R / Rfree (%)	12.2 / 15.3

The binding sites of Chlorine atom in the Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc) (pdb code 5emf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc), PDB code: 5emf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:21.1 occ:0.50 CL A:CL101 0.0 21.1 0.5 CL A:CL101 0.9 18.4 0.5 O B:HOH316 2.3 25.0 0.5 O B:HOH313 2.9 11.1 1.0 O A:HOH206 2.9 14.4 0.5 O A:HOH206 3.6 13.3 0.3 O B:HOH316 3.9 18.7 0.5 O2 A:C2 4.3 13.3 1.0 O1' B:CPN108 4.7 11.8 1.0 O2' A:C2 4.7 17.7 1.0 N2 A:G1 4.8 10.2 1.0 C1' A:C2 4.9 14.0 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:18.4 occ:0.50 CL A:CL101 0.0 18.4 0.5 CL A:CL101 0.9 21.1 0.5 O A:HOH206 2.2 14.4 0.5 O B:HOH313 2.7 11.1 1.0 O B:HOH316 3.1 25.0 0.5 O A:HOH206 3.2 13.3 0.3 O2 A:C2 3.5 13.3 1.0 O2' A:C2 4.2 17.7 1.0 C1' A:C2 4.2 14.0 1.0 N2 A:G1 4.3 10.2 1.0 C2 A:C2 4.5 11.9 1.0 O B:HOH316 4.5 18.7 0.5 O2 B:CPN108 4.6 9.8 1.0 C2' A:C2 4.7 15.6 1.0 N2 B:GPN107 4.8 10.6 1.0 N1 A:C2 4.9 13.0 1.0 O1' B:CPN108 4.9 11.8 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Rna R(Gcugcugc) with Antisense Pna P(Gcagcagc) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:33.9 occ:0.50 N1' B:GPN107 3.4 14.5 0.5 N1' B:GPN107 3.4 11.8 0.5 C2' B:GPN107 3.5 12.5 0.5 C2' B:GPN107 3.5 12.9 0.5 O B:HOH312 3.7 33.2 1.0 C' B:APN106 3.8 15.9 0.5 C' B:APN106 3.8 15.0 0.5 C3' B:APN106 4.0 12.4 0.5 O1' B:APN106 4.1 16.6 0.5 C3' B:APN106 4.2 17.7 0.5 C5' B:APN106 4.3 15.9 0.5 O1' B:APN106 4.3 17.6 0.5 C5' B:APN106 4.6 16.8 0.5 N4' B:APN106 4.6 18.5 0.5 C2' B:APN106 4.7 14.1 0.5 N4' B:APN106 4.7 13.6 0.5 O B:HOH315 4.8 15.0 1.0 C2' B:APN106 4.8 17.8 0.5 O A:HOH262 4.9 24.5 0.6 C3' B:GPN107 4.9 11.9 0.5

A.Kiliszek, K.Banaszak, Z.Dauter, W.Rypniewski. The First Crystal Structures of Rna-Pna Duplexes and A Pna-Pna Duplex Containing Mismatches-Toward Anti-Sense Therapy Against Treds. Nucleic Acids Res. V. 44 1937 2016.
ISSN: ESSN 1362-4962
PubMed: 26717983
DOI: 10.1093/NAR/GKV1513