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Chlorine in PDB 5emg: Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches

Protein crystallography data

The structure of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches, PDB code: 5emg 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) 20.00 / 1.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.771, 42.896, 64.253, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.3

Other elements in 5emg:

The structure of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches also contains other interesting chemical elements:

Sodium (Na) 7 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches (pdb code 5emg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches, PDB code: 5emg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 5emg

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Chlorine binding site 1 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:9.6
occ:0.60
 O1' A:TPN6 2.5 12.4 0.5
C' A:TPN6 3.0 12.1 0.5
C5' A:TPN6 3.1 10.3 0.5
O D:HOH202 3.1 15.1 1.0
O C:HOH217 3.1 13.2 1.0
N2 C:GPN7 3.2 10.9 1.0
O D:HOH237 3.2 19.7 1.0
C' A:TPN6 3.4 7.8 0.5
C3' A:TPN6 3.5 10.0 0.5
O1' A:TPN6 3.5 6.2 0.5
C5' A:TPN6 3.7 7.8 0.5
N1' A:GPN7 3.7 7.8 0.5
N4' A:TPN6 3.8 9.3 0.5
C3' A:TPN6 3.9 9.2 0.5
C3' D:TPN3 3.9 12.2 1.0
N1' A:GPN7 3.9 10.2 0.5
O2 D:CPN2 4.1 9.7 0.5
C2' A:GPN7 4.1 9.3 0.5
C3' C:CPN8 4.1 8.9 1.0
C2' D:TPN3 4.2 12.9 1.0
O A:HOH202 4.2 9.6 1.0
C2' A:GPN7 4.3 8.7 0.5
N4' A:TPN6 4.3 7.8 0.5
C2' A:TPN6 4.4 10.7 0.5
C2 C:GPN7 4.4 9.5 1.0
C8' C:CPN8 4.4 8.9 1.0
O2 C:CPN8 4.4 10.6 1.0
C2' A:TPN6 4.5 10.1 0.5
O2 D:CPN2 4.5 11.0 0.5
N1' D:TPN3 4.5 13.7 0.5
C8' D:TPN3 4.6 9.9 1.0
O D:HOH212 4.7 21.3 1.0
N1' D:TPN3 4.7 13.3 0.5
N3 C:GPN7 4.8 9.3 1.0
O A:HOH221 4.9 26.6 1.0
C7' A:TPN6 5.0 9.2 0.5

Chlorine binding site 2 out of 14 in 5emg

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Chlorine binding site 2 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:15.3
occ:0.70
 O A:HOH249 3.1 16.8 1.0
C2' A:CPN2 3.6 9.6 0.5
C5' A:CPN2 3.6 11.6 0.5
O1' A:GPN1 3.9 16.2 0.5
C5' A:CPN2 3.9 8.9 0.5
N1' A:CPN2 4.2 10.2 0.5
O A:HOH235 4.3 38.1 1.0
O A:HOH227 4.4 20.9 0.5
C2' A:CPN2 4.4 12.7 0.5
O1' A:CPN2 4.6 9.7 0.5
C3' A:CPN2 4.6 8.3 0.5
C' A:CPN2 4.6 10.3 0.5
N4' A:CPN2 4.6 11.0 0.5
O A:HOH204 4.7 23.2 1.0
C' A:CPN2 4.8 7.7 0.5
O A:HOH240 4.8 26.4 1.0
N4' A:CPN2 4.8 8.9 0.5
O1' A:CPN2 4.9 7.0 0.5
C3' A:CPN2 4.9 11.9 0.5
C' A:GPN1 4.9 14.8 0.5

Chlorine binding site 3 out of 14 in 5emg

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Chlorine binding site 3 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:41.2
occ:1.00
 O A:HOH253 3.2 24.1 1.0
C3' A:CPN5 3.4 11.2 0.5
C' A:CPN5 3.5 11.3 0.5
C5' A:CPN5 3.5 14.9 0.5
C' A:CPN5 3.6 11.8 0.5
C2' A:CPN5 3.6 11.8 0.5
C5' A:CPN5 3.6 12.2 0.5
N1' A:TPN6 3.7 10.3 0.5
O1' A:CPN5 3.7 10.7 0.5
C3' A:CPN5 3.8 10.9 0.5
O1' A:CPN5 3.9 17.0 0.5
C2' A:TPN6 3.9 10.7 0.5
N1' A:TPN6 3.9 10.5 0.5
C2' A:CPN5 3.9 12.4 0.5
C2' A:TPN6 4.0 10.1 0.5
N4' A:CPN5 4.2 10.8 0.5
N4' A:CPN5 4.2 12.6 0.5
O D:HOH237 4.6 19.7 1.0
O A:HOH221 4.6 26.6 1.0

Chlorine binding site 4 out of 14 in 5emg

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Chlorine binding site 4 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:16.6
occ:0.80
 O B:HOH219 3.1 14.1 1.0
N4 B:CPN5 3.2 9.1 1.0
C5 B:CPN5 3.7 8.2 1.0
O B:HOH234 3.9 22.2 0.4
C4 B:CPN5 4.0 8.0 1.0
O6 B:GPN4 4.2 10.2 1.0
N7 B:GPN4 4.7 9.2 1.0
C6 B:GPN4 4.8 8.5 1.0
C6 B:CPN5 5.0 7.7 1.0

Chlorine binding site 5 out of 14 in 5emg

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Chlorine binding site 5 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:10.3
occ:1.00
 O B:HOH211 3.1 9.8 1.0
O A:HOH201 3.2 12.2 1.0
O C:HOH243 3.2 25.7 1.0
N2 B:GPN4 3.4 9.0 1.0
C2' C:CPN8 3.6 8.5 1.0
C3' C:CPN8 3.6 8.9 1.0
C5' C:CPN8 3.7 10.5 1.0
C8' A:TPN6 3.7 10.0 0.5
C3' A:TPN6 3.8 9.2 0.5
C' C:CPN8 3.9 12.7 1.0
C3' A:TPN6 3.9 10.0 0.5
C8' A:TPN6 3.9 8.6 0.5
O C:HOH208 4.0 9.5 1.0
C3' B:CPN5 4.1 8.9 1.0
N4' C:CPN8 4.2 9.2 1.0
O2 A:CPN5 4.2 9.3 0.5
O1' C:CPN8 4.2 14.6 1.0
OXT C:CPN8 4.3 17.4 1.0
C2' A:TPN6 4.4 10.7 0.5
C8' B:CPN5 4.4 7.8 1.0
C2' A:TPN6 4.4 10.1 0.5
O2 A:CPN5 4.6 9.0 0.5
C2 B:GPN4 4.6 8.4 1.0
N1' A:TPN6 4.6 10.3 0.5
N1 A:TPN6 4.7 10.2 0.5
O2 A:TPN6 4.7 9.3 0.5
O2 B:CPN5 4.7 8.0 1.0
N4' A:TPN6 4.7 9.3 0.5
N4' A:TPN6 4.8 7.8 0.5
N1 A:TPN6 4.8 8.3 0.5
C7' A:TPN6 4.8 9.2 0.5
N1' A:TPN6 4.8 10.5 0.5
O2 A:TPN6 4.8 10.6 0.5
N3 B:GPN4 4.9 8.7 1.0
N4' B:CPN5 4.9 8.6 1.0
N1' C:CPN8 4.9 8.7 1.0
C7' A:TPN6 5.0 7.9 0.5
O A:HOH234 5.0 16.1 0.5

Chlorine binding site 6 out of 14 in 5emg

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Chlorine binding site 6 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl101

b:13.0
occ:0.90
 O C:HOH215 3.2 10.1 1.0
O D:HOH207 3.2 15.8 1.0
N2 C:GPN1 3.5 9.7 0.5
N2 C:GPN1 3.6 15.8 0.5
O C:HOH220 3.9 16.1 0.5
O C:HOH220 4.0 12.7 0.5
C3' C:CPN2 4.0 11.8 0.5
C3' C:CPN2 4.1 10.5 0.5
O2 D:CPN8 4.5 9.8 0.5
C2 C:GPN1 4.7 9.8 0.5
C2 C:GPN1 4.7 14.7 0.5
C2' C:CPN2 4.8 16.2 0.5
C8' C:CPN2 4.8 10.6 1.0
O D:HOH219 4.9 23.8 1.0
O1' C:GPN1 4.9 14.5 0.5
N3 C:GPN1 4.9 14.0 0.5
O2 D:CPN8 4.9 13.3 0.5
N3 C:GPN1 5.0 10.7 0.5

Chlorine binding site 7 out of 14 in 5emg

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Chlorine binding site 7 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl102

b:11.9
occ:0.80
 O B:HOH214 2.1 8.3 0.2
C' C:TPN6 3.0 7.9 0.5
N2 A:GPN7 3.0 10.8 0.5
O B:HOH214 3.0 12.8 0.8
O A:HOH218 3.1 14.2 1.0
O1' C:TPN6 3.1 8.1 0.5
C5' C:TPN6 3.2 7.8 0.5
N2 A:GPN7 3.4 7.1 0.5
N1' C:GPN7 3.6 7.2 0.5
C' C:TPN6 3.6 8.4 0.5
C3' C:TPN6 3.6 9.9 0.5
O2 B:CPN2 3.6 14.8 0.5
N4' C:TPN6 3.7 8.8 0.5
O1' C:TPN6 3.8 10.2 0.5
C3' B:TPN3 3.9 8.3 0.5
C5' C:TPN6 3.9 8.0 0.5
C3' B:TPN3 3.9 8.5 0.5
N1' C:GPN7 4.0 8.5 0.5
C3' C:TPN6 4.1 8.8 0.5
C2' B:TPN3 4.1 9.8 0.5
C3' A:CPN8 4.1 8.6 1.0
C2' C:GPN7 4.1 8.1 0.5
C2' C:TPN6 4.2 10.3 0.5
C2 A:GPN7 4.2 9.5 0.5
C2' C:GPN7 4.2 8.5 0.5
O A:HOH206 4.3 9.8 1.0
C2' B:TPN3 4.3 9.7 0.5
O2 A:CPN8 4.4 10.4 1.0
N4' C:TPN6 4.4 7.8 0.5
C8' A:CPN8 4.5 10.0 1.0
O2 B:CPN2 4.5 7.3 0.5
C8' B:TPN3 4.5 7.9 0.5
C2 A:GPN7 4.5 7.0 0.5
C2' C:TPN6 4.5 9.3 0.5
N1' B:TPN3 4.5 9.7 0.5
N3 A:GPN7 4.7 8.8 0.5
N1' B:TPN3 4.7 9.9 0.5
C8' B:TPN3 4.8 8.1 0.5
N3 A:GPN7 4.8 8.0 0.5
O B:HOH220 4.8 20.2 1.0
O A:HOH247 4.9 31.1 1.0
C2 B:CPN2 4.9 14.5 0.5
O C:HOH202 4.9 25.0 1.0
C7' C:TPN6 4.9 8.4 0.5

Chlorine binding site 8 out of 14 in 5emg

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Chlorine binding site 8 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl103

b:31.1
occ:0.50
 CL C:CL103 0.0 31.1 0.5
CL C:CL103 1.4 38.3 0.5
O C:HOH248 2.9 35.0 1.0
O C:HOH246 2.9 33.7 1.0
O C:HOH211 3.0 21.1 1.0
C5M C:TPN6 3.4 10.1 0.5
C5 C:CPN5 3.6 7.4 0.5
C5M C:TPN6 3.8 8.2 0.5
C5 C:CPN5 3.9 8.6 0.5
C6 C:CPN5 4.1 7.5 0.5
C4 C:CPN5 4.1 7.9 0.5
N4 C:CPN5 4.3 8.1 0.5
C4 C:CPN5 4.3 7.3 0.5
N4 C:CPN5 4.4 9.0 0.5
C6 C:CPN5 4.5 8.5 0.5
O C:HOH239 4.7 32.4 1.0
O C:HOH214 4.8 23.1 1.0
C5 C:TPN6 4.8 8.3 0.5
N3 C:CPN5 4.9 6.7 0.5
O7' C:CPN5 4.9 7.3 0.5
N1 C:CPN5 4.9 6.2 0.5

Chlorine binding site 9 out of 14 in 5emg

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Chlorine binding site 9 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl103

b:38.3
occ:0.50
 CL C:CL103 0.0 38.3 0.5
CL C:CL103 1.4 31.1 0.5
O C:HOH248 2.8 35.0 1.0
O C:HOH246 3.1 33.7 1.0
C5 C:CPN5 3.7 7.4 0.5
C5 C:CPN5 4.1 8.6 0.5
O C:HOH214 4.2 23.1 1.0
O C:HOH221 4.3 17.4 0.4
N4 C:CPN5 4.3 8.1 0.5
C4 C:CPN5 4.3 7.9 0.5
O C:HOH211 4.3 21.1 1.0
C6 C:CPN5 4.4 7.5 0.5
C5M C:TPN6 4.4 10.1 0.5
N4 C:CPN5 4.5 9.0 0.5
C4 C:CPN5 4.7 7.3 0.5
C5M C:TPN6 4.9 8.2 0.5
C6 C:CPN5 4.9 8.5 0.5

Chlorine binding site 10 out of 14 in 5emg

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Chlorine binding site 10 out of 14 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl104

b:18.9
occ:0.80
 O C:HOH241 3.1 31.6 1.0
C' C:GPN4 3.3 11.9 0.5
N1' C:CPN5 3.5 12.8 0.5
C' C:GPN4 3.5 12.4 0.5
N1' C:CPN5 3.5 11.3 0.5
O1' C:GPN4 3.6 11.0 0.5
C5' C:GPN4 3.6 11.1 0.5
O1' C:GPN4 3.7 18.1 0.5
C3' C:GPN4 3.7 10.2 0.5
C2' C:CPN5 3.8 12.1 0.5
C2' C:CPN5 3.8 13.9 0.5
C3' C:GPN4 3.9 9.2 0.5
C5' C:GPN4 4.1 10.3 0.5
C2' C:GPN4 4.1 9.4 0.5
C2' C:GPN4 4.1 10.5 0.5
N4' C:GPN4 4.3 9.6 0.5
N4' C:GPN4 4.4 10.7 0.5
O C:HOH244 4.9 32.4 1.0
O C:HOH216 4.9 18.8 0.5

Reference:

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
Page generated: Fri Jul 26 07:24:05 2024

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