Chlorine in PDB 363d: High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex

The structure of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex, PDB code: 363d was solved by V.Tereshko, S.Gryaznov, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	H 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	40.150, 40.150, 304.210, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex (pdb code 363d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex, PDB code: 363d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl255 b:10.3 occ:0.00 HN1 A:A435 2.3 20.0 0.0 N A:NH4239 3.2 13.9 0.0 N A:A435 3.3 6.6 0.5 C5' A:A436 3.8 2.8 0.5 C2' A:A435 3.8 11.1 0.5 C3' A:A435 4.0 14.2 0.5 O1P A:A436 4.0 7.6 0.5 P A:A436 4.1 11.1 0.5 O5' A:A436 4.2 14.6 0.5 C4' A:A435 4.2 5.7 0.5 N A:NH4237 4.4 16.2 0.0 O A:HOH419 4.9 50.0 0.0 C1' A:A435 5.0 12.5 0.5 C4' A:A436 5.0 7.3 0.5

Chlorine binding site 2 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl250 b:9.2 occ:0.33 HN1 A:C429 2.2 20.0 0.0 N A:C429 3.2 15.6 0.5 N A:NH4228 3.2 13.3 0.3 C5' A:G3810 3.8 8.7 0.5 O2A A:G3810 3.8 11.6 0.5 N A:NH4226 4.0 17.2 0.3 C2' A:C429 4.0 15.9 0.5 C3' A:C429 4.0 16.7 0.5 PA A:G3810 4.1 12.9 0.5 C4' A:C429 4.2 10.6 0.5 O5' A:G3810 4.3 12.1 0.5 C4' A:G3810 4.9 12.0 0.5 O A:HOH318 5.0 42.2 1.0

Chlorine binding site 3 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl256 b:9.2 occ:0.00 HN1 B:G3822 2.4 20.0 0.0 N B:NH4240 3.2 13.3 0.0 N B:G3822 3.3 10.3 0.5 C5' B:C4223 3.9 8.9 0.5 C2' B:G3822 3.9 8.8 0.5 N B:NH4238 4.0 17.2 0.0 C3' B:G3822 4.0 9.9 0.5 C4' B:G3822 4.2 5.1 0.5 P B:C4223 4.4 11.3 0.5 O1P B:C4223 4.4 7.4 0.5 O5' B:C4223 4.4 10.1 0.5 C4' B:C4223 4.7 10.4 0.5 O4' B:C4223 4.7 12.1 0.5 C1' B:G3822 5.0 8.7 0.5 O B:HOH420 5.0 42.2 0.0

Chlorine binding site 4 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl249 b:10.3 occ:0.33 HN1 B:A4318 2.3 20.0 0.0 N B:A4318 3.2 12.2 0.5 N B:NH4227 3.2 13.9 0.3 C5' B:NYM19 3.8 12.1 0.5 C2' B:A4318 3.9 13.4 0.5 C3' B:A4318 3.9 16.6 0.5 C4' B:A4318 4.2 8.5 0.5 P1 B:NYM19 4.3 15.0 0.5 OP1 B:NYM19 4.3 13.7 0.5 N B:NH4225 4.4 16.2 0.3 O5' B:NYM19 4.5 22.3 1.0 C4' B:NYM19 4.7 9.5 0.5 O B:HOH317 4.9 50.0 1.0 O4' B:NYM19 5.0 11.3 0.5

Chlorine binding site 5 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl259 b:12.2 occ:0.00 HN1 C:A43106 2.2 20.0 0.0 N C:A43106 3.2 11.6 0.5 N C:NH4245 3.3 15.2 0.0 C5' C:NYM107 3.8 12.4 0.5 C2' C:A43106 3.9 7.2 0.5 C3' C:A43106 4.0 11.7 0.5 N C:NH4243 4.1 15.2 0.0 OP1 C:NYM107 4.1 17.2 0.5 P1 C:NYM107 4.2 14.6 0.5 C4' C:A43106 4.2 8.0 0.5 O5' C:NYM107 4.4 16.5 0.5 O C:HOH459 4.8 50.0 0.0 C4' C:NYM107 4.8 11.9 0.5

Chlorine binding site 6 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl260 b:12.2 occ:0.00 HN1 C:G38110 2.5 20.0 0.0 N C:NH4248 3.3 15.2 0.0 N C:G38110 3.4 15.4 0.5 N C:NH4244 3.8 15.2 0.0 C5' C:C42111 3.9 9.8 0.5 C2' C:G38110 4.0 10.6 0.5 C3' C:G38110 4.1 14.4 0.5 C4' C:G38110 4.3 12.1 0.5 P C:C42111 4.5 18.8 0.5 O1P C:C42111 4.5 5.7 0.5 O C:HOH462 4.5 43.1 0.0 O5' C:C42111 4.6 12.3 0.5 C4' C:C42111 4.8 12.3 0.5

Chlorine binding site 7 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl258 b:15.2 occ:0.00 N D:NH4246 2.4 15.0 0.0 HN1 D:C42121 2.6 20.0 0.0 N D:C42121 3.5 8.7 0.5 C2' D:C42121 3.8 11.3 0.5 C5' D:G38122 4.0 4.0 0.5 C3' D:C42121 4.1 7.7 0.5 C4' D:C42121 4.1 10.5 0.5 N D:NH4242 4.5 15.5 0.0 O2A D:G38122 4.5 13.4 0.5 O D:HOH460 4.6 50.0 0.0 PA D:G38122 4.6 11.2 0.5 O5' D:G38122 4.7 11.7 0.5 C1' D:C42121 4.9 13.6 0.5 C4' D:G38122 4.9 10.1 0.5 O4' D:C42121 4.9 13.7 0.5

Chlorine binding site 8 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl257 b:14.4 occ:0.00 HN1 D:A43117 2.5 20.0 0.0 N D:NH4247 3.2 14.5 0.0 N D:A43117 3.5 11.3 0.5 C5' D:A43118 3.9 13.5 0.5 C2' D:A43117 4.2 5.0 0.5 C3' D:A43117 4.2 11.0 0.5 O1P D:A43118 4.3 15.7 0.5 C4' D:A43117 4.4 9.7 0.5 N D:NH4241 4.4 16.1 0.0 P D:A43118 4.5 14.0 0.5 O5' D:A43118 4.6 16.5 0.5 C4' D:A43118 4.9 10.4 0.5 O D:HOH461 4.9 45.9 0.0

Chlorine binding site 9 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl251 b:14.4 occ:0.33 HN1 E:G38204 2.3 20.0 0.0 N E:NH4235 3.2 14.5 0.3 N E:G38204 3.3 12.7 0.5 C2' E:G38204 3.7 5.6 0.5 C5' E:A43205 3.8 11.0 0.5 C3' E:G38204 3.9 13.9 0.5 O1P E:A43205 4.0 17.9 0.5 P E:A43205 4.2 16.1 0.5 C4' E:G38204 4.2 8.6 0.5 O5' E:A43205 4.2 18.9 0.5 N E:NH4229 4.4 16.1 0.3 C1' E:G38204 4.8 10.2 0.5 C4' E:A43205 4.8 8.2 0.5 O4' E:G38204 4.9 13.5 0.5 O E:HOH361 4.9 45.9 1.0

Chlorine binding site 10 out of 12 in the High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of High-Resolution Crystal Structure of A Fully Modified N3'-> P5' Phosphoramidate Dna Dodecamer Duplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl252 b:15.2 occ:0.33 H3'2 E:NYM208 2.4 20.0 0.0 N E:NH4234 2.4 15.0 0.3 N3' E:NYM208 3.3 12.2 0.5 C2' E:NYM208 3.8 12.1 0.5 C5' E:C42209 4.0 9.1 0.5 C3' E:NYM208 4.0 9.3 0.5 C4' E:NYM208 4.2 12.1 0.5 O1P E:C42209 4.2 17.9 0.5 P E:C42209 4.4 14.5 0.5 N E:NH4230 4.5 15.5 0.3 O5' E:C42209 4.5 16.3 0.5 O E:HOH360 4.6 50.0 1.0 C1' E:NYM208 4.8 14.4 0.5 C4' E:C42209 4.9 14.3 0.5 O4' E:NYM208 4.9 14.5 0.5

V.Tereshko, S.Gryaznov, M.Egli. Consequences of Replacing the Dna 3'-Oxygen By An Amino Group: High-Resolution Crystal Structure of A Fully Modified N3'--> P5' Phosphoramidate Dna Dodecamer Duplex J.Am.Chem.Soc. V. 120 269 1998.
ISSN: ISSN 0002-7863