Sodium in PDB 191d: Crystal Structure of Intercalated Four-Stranded D(C3T)

The structure of Crystal Structure of Intercalated Four-Stranded D(C3T), PDB code: 191d was solved by C.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	28.281, 44.341, 50.472, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.5

The binding sites of Sodium atom in the Crystal Structure of Intercalated Four-Stranded D(C3T) (pdb code 191d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Intercalated Four-Stranded D(C3T), PDB code: 191d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Intercalated Four-Stranded D(C3T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na19 b:28.2 occ:1.00 OP2 A:DC2 2.7 8.8 1.0 O A:HOH44 3.4 8.6 1.0 P A:DC2 3.6 11.4 1.0 C3' A:DC1 3.6 12.6 1.0 O3' A:DC1 3.7 11.2 1.0 C5' A:DC1 3.7 13.2 1.0 OP1 A:DC2 4.1 11.2 1.0 C4' A:DC1 4.3 13.6 1.0 O A:HOH64 4.5 22.1 1.0 C2' A:DC1 4.8 13.5 1.0 C6 A:DC1 4.8 8.8 1.0 O5' A:DC2 5.0 9.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Intercalated Four-Stranded D(C3T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na17 b:28.7 occ:1.00 O D:HOH69 2.8 10.7 1.0 OP1 B:DT8 2.9 13.6 1.0 O5' B:DT8 3.4 11.7 1.0 C2' B:DT8 3.6 14.5 1.0 P B:DT8 3.7 12.7 1.0 C3' B:DC7 3.9 13.4 1.0 H41 D:DC13 4.0 0.0 0.0 C2' B:DC7 4.0 12.7 1.0 C3' B:DT8 4.2 13.0 1.0 O3' B:DC7 4.4 13.0 1.0 C6 B:DT8 4.4 13.9 1.0 C6 B:DC7 4.5 13.5 1.0 O D:HOH46 4.6 11.8 1.0 C5' B:DT8 4.7 12.5 1.0 C1' B:DT8 4.7 13.0 1.0 N1 B:DT8 4.7 13.5 1.0 N4 D:DC13 4.9 8.4 1.0 C4' B:DT8 4.9 14.0 1.0 OP2 B:DT8 5.0 14.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Intercalated Four-Stranded D(C3T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Intercalated Four-Stranded D(C3T) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na18 b:37.2 occ:1.00 O C:HOH35 3.1 44.2 1.0 O C:HOH42 3.1 34.6 1.0 O C:HOH23 3.5 15.3 1.0 OP2 C:DC11 3.6 12.4 1.0 OP2 C:DC10 3.9 29.2 1.0 HO3' C:DT12 4.2 0.0 0.0 O3' C:DT12 4.3 11.1 1.0 OP1 C:DC10 4.3 30.4 1.0 O A:HOH75 4.3 15.4 1.0 P C:DC10 4.5 28.6 1.0 O5' C:DC10 4.8 26.0 1.0

C.H.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich. Crystal Structure of Intercalated Four-Stranded D(C3T) at 1.4 Angstroms Resolution. Proc.Natl.Acad.Sci.Usa V. 91 11636 1994.
ISSN: ISSN 0027-8424
PubMed: 7972115
DOI: 10.1073/PNAS.91.24.11636