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Sodium 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:

Chlorine (Cl) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches, PDB code: 5emg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5emg

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Sodium binding site 1 out of 7 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na104

b:12.4
occ:0.40
 O A:HOH224 1.7 21.7 0.5
O A:HOH224 2.0 15.4 0.5
O B:HOH221 2.4 10.8 0.5
O1' A:TPN3 2.4 9.3 0.5
O B:HOH221 2.5 17.1 0.5
O B:HOH233 2.7 28.8 0.8
O1' A:TPN3 2.7 10.7 0.5
C' A:TPN3 3.6 8.0 0.5
O A:HOH225 3.8 12.3 0.5
C3' A:GPN4 4.0 9.2 0.5
C' A:TPN3 4.0 9.0 0.5
O B:HOH203 4.0 17.1 0.6
C3' A:GPN4 4.1 10.6 0.5
C3' A:TPN3 4.3 8.3 0.5
N4' A:TPN3 4.3 8.7 0.5
C2' A:GPN4 4.4 8.8 0.5
C3' A:TPN3 4.4 7.5 0.5
N1' A:GPN4 4.4 8.2 0.5
C8' A:GPN4 4.4 7.1 0.5
O B:HOH203 4.5 13.4 0.4
N4' A:TPN3 4.5 7.5 0.5
C7' A:TPN3 4.6 8.9 0.5
C5' A:TPN3 4.6 9.2 0.5
C2' A:GPN4 4.7 11.4 0.5
C5' A:TPN3 4.7 7.5 0.5
O2 A:TPN3 4.7 9.2 0.5
O A:HOH225 4.7 11.7 0.5
C8' A:GPN4 4.8 8.4 0.5
N1' A:GPN4 4.8 10.4 0.5
C8' A:TPN3 4.8 9.8 0.5
O2 B:TPN6 4.9 9.8 1.0
C7' A:TPN3 4.9 8.0 0.5
O2 A:TPN3 4.9 8.3 0.5
O B:HOH218 4.9 23.5 1.0

Sodium binding site 2 out of 7 in 5emg

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na105

b:12.8
occ:0.30
 O A:HOH233 1.8 21.0 0.3
O4 A:TPN6 2.3 13.3 0.5
O4 B:TPN3 2.3 12.3 0.5
O4 A:TPN6 2.4 6.4 0.5
O A:HOH222 2.4 31.9 0.7
O A:HOH233 2.4 24.6 0.7
O6 A:GPN7 2.5 11.3 0.5
O B:HOH231 2.5 14.6 0.5
O4 B:TPN3 2.6 15.5 0.5
O6 A:GPN7 2.7 11.4 0.5
C4 B:TPN3 3.0 10.8 0.5
N3 B:TPN3 3.0 7.9 0.5
O B:HOH231 3.0 22.9 0.5
C6 A:GPN7 3.3 8.6 0.5
C4 B:TPN3 3.3 12.2 0.5
O B:HOH201 3.4 15.6 0.9
C4 A:TPN6 3.4 6.9 0.5
N3 B:TPN3 3.5 10.4 0.5
C4 A:TPN6 3.5 10.5 0.5
C6 A:GPN7 3.6 10.1 0.5
C5M A:TPN6 3.7 8.3 0.5
N4 B:CPN2 3.7 10.4 0.5
N4 B:CPN2 3.9 21.2 0.5
C5 A:TPN6 4.0 7.7 0.5
C5 A:GPN7 4.0 8.8 0.5
N7 A:GPN7 4.1 10.7 0.5
N7 A:GPN7 4.2 9.7 0.5
C5M A:TPN6 4.2 12.8 0.5
C5 A:GPN7 4.2 10.1 0.5
C2 B:TPN3 4.3 7.6 0.5
N1 A:GPN7 4.3 7.3 0.5
O6 B:GPN4 4.3 10.2 1.0
C5 B:TPN3 4.3 10.4 0.5
O A:HOH244 4.3 29.8 1.0
C5 A:TPN6 4.4 9.6 0.5
O A:HOH205 4.5 17.0 0.7
N3 A:TPN6 4.5 8.9 0.5
N3 A:TPN6 4.6 7.3 0.5
N1 A:GPN7 4.6 10.0 0.5
C5 B:TPN3 4.6 11.0 0.5
C2 B:TPN3 4.7 10.0 0.5
C6 B:GPN4 4.7 8.5 1.0
C4 B:CPN2 4.8 7.5 0.5
O2 B:TPN3 4.8 8.1 0.5
C4 B:CPN2 5.0 14.7 0.5
C5M B:TPN3 5.0 12.0 0.5

Sodium binding site 3 out of 7 in 5emg

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Sodium binding site 3 out of 7 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
B:Na103

b:31.5
occ:0.50
 NA B:NA103 0.0 31.5 0.5
NA B:NA103 1.6 26.2 0.5
O6 B:GPN1 1.9 16.5 0.5
O6 B:GPN1 2.2 8.6 0.5
O B:HOH215 2.2 20.7 1.0
C6 B:GPN1 3.0 11.4 0.5
C6 B:GPN1 3.2 9.4 0.5
N4 A:CPN8 3.6 12.5 1.0
N7 B:GPN1 3.7 11.9 0.5
C5 B:GPN1 3.7 11.4 0.5
N7 B:GPN1 3.8 15.1 0.5
C5 B:GPN1 3.8 10.7 0.5
N1 B:GPN1 4.2 11.0 0.5
O A:HOH226 4.4 33.6 1.0
N1 B:GPN1 4.4 9.0 0.5
N4 B:CPN2 4.5 10.4 0.5
C4 A:CPN8 4.8 10.2 1.0
N4 B:CPN2 4.8 21.2 0.5
C5 B:CPN2 4.9 9.2 0.5
C4 B:CPN2 4.9 7.5 0.5
C8 B:GPN1 4.9 12.6 0.5

Sodium binding site 4 out of 7 in 5emg

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Sodium binding site 4 out of 7 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na103

b:26.2
occ:0.50
 NA B:NA103 0.0 26.2 0.5
NA B:NA103 1.6 31.5 0.5
O6 B:GPN1 3.1 16.5 0.5
O6 B:GPN1 3.2 8.6 0.5
O A:HOH226 3.3 33.6 1.0
N4 A:CPN8 3.3 12.5 1.0
O B:HOH215 3.5 20.7 1.0
C6 B:GPN1 4.3 11.4 0.5
C6 B:GPN1 4.4 9.4 0.5
C4 A:CPN8 4.6 10.2 1.0

Sodium binding site 5 out of 7 in 5emg

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Sodium binding site 5 out of 7 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na105

b:20.4
occ:0.60
 O C:HOH239 1.9 32.4 1.0
O4 C:TPN6 2.2 9.1 0.5
O D:HOH204 2.5 15.7 0.6
O6 C:GPN7 2.6 12.0 1.0
O4 D:TPN3 2.7 14.4 1.0
O4 C:TPN6 2.9 8.3 0.5
C4 C:TPN6 3.3 7.8 0.5
C4 D:TPN3 3.5 12.6 1.0
C6 C:GPN7 3.5 10.0 1.0
O D:HOH204 3.5 9.4 0.4
N3 D:TPN3 3.6 10.9 1.0
O C:HOH248 3.6 35.0 1.0
O D:HOH223 3.7 26.8 1.0
N4 D:CPN2 3.7 11.1 0.5
C5M C:TPN6 3.7 10.1 0.5
O D:HOH218 3.7 30.5 1.0
N4 D:CPN2 3.9 16.9 0.5
C4 C:TPN6 4.0 7.0 0.5
C5 C:TPN6 4.0 8.3 0.5
C5M C:TPN6 4.1 8.2 0.5
C5 C:GPN7 4.2 8.8 1.0
N7 C:GPN7 4.2 10.2 1.0
O C:HOH210 4.2 20.3 1.0
N3 C:TPN6 4.4 6.7 0.5
N1 C:GPN7 4.5 10.1 1.0
C5 C:TPN6 4.5 7.9 0.5
O6 D:GPN4 4.5 9.6 1.0
C5 D:TPN3 4.7 12.8 1.0
C2 D:TPN3 4.8 11.2 1.0
C4 D:CPN2 4.9 11.1 0.5
C4 D:CPN2 4.9 11.0 0.5

Sodium binding site 6 out of 7 in 5emg

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Sodium binding site 6 out of 7 in the Crystal Structures of Pna P(Gctgctgc)2 Duplex Containing T-T Mismatches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na106

b:13.8
occ:0.50
 O C:HOH231 2.4 12.8 0.5
O1' C:TPN3 2.5 10.2 1.0
O D:HOH239 2.6 25.2 1.0
O D:HOH201 2.7 20.5 0.8
O C:HOH244 3.0 32.4 1.0
C' C:TPN3 3.7 8.7 1.0
C3' C:GPN4 3.9 9.2 0.5
O C:HOH216 4.0 14.5 0.5
O D:HOH225 4.1 14.4 0.5
C3' C:GPN4 4.2 10.2 0.5
C3' C:TPN3 4.3 9.0 1.0
C2' C:GPN4 4.3 9.4 0.5
O D:HOH225 4.4 13.5 0.5
N4' C:TPN3 4.4 8.4 1.0
N1' C:GPN4 4.5 9.2 1.0
O C:HOH216 4.5 18.8 0.5
C8' C:GPN4 4.6 9.8 1.0
C2' C:GPN4 4.6 10.5 0.5
O D:HOH205 4.6 25.6 1.0
C5' C:TPN3 4.7 8.2 1.0
C7' C:TPN3 4.7 8.4 1.0
O2 C:TPN3 4.8 9.2 1.0
O2 D:TPN6 4.9 10.0 1.0
O D:HOH240 4.9 33.2 1.0

Sodium binding site 7 out of 7 in 5emg

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
D:Na104

b:31.6
occ:1.00
 O D:HOH220 2.2 27.4 1.0
O D:HOH223 2.7 26.8 1.0
O D:HOH203 2.8 18.2 1.0
O6 D:GPN1 2.8 11.6 0.5
O6 D:GPN1 3.1 10.4 0.5
N4 C:CPN8 3.7 12.2 1.0
C6 D:GPN1 3.9 11.4 0.5
O C:HOH238 4.0 31.4 0.6
N4 D:CPN2 4.0 16.9 0.5
C6 D:GPN1 4.2 10.2 0.5
N4 D:CPN2 4.4 11.1 0.5
O C:HOH238 4.4 17.3 0.4
N7 D:GPN1 4.5 11.3 0.5
C5 D:GPN1 4.6 10.7 0.5
C4 D:CPN2 4.8 11.0 0.5
N7 D:GPN1 4.8 12.4 0.5
C5 D:CPN2 4.9 12.7 0.5
C5 D:GPN1 5.0 11.1 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: Mon Oct 7 20:49:02 2024

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