Sodium in PDB 2b2b: Structural Distortions in Psoralen Cross-Linked Dna

The structure of Structural Distortions in Psoralen Cross-Linked Dna, PDB code: 2b2b was solved by F.A.Hays, H.Yonggang, B.F.Eichman, W.Kong, J.Hearst, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.89 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.007, 22.496, 44.670, 90.00, 128.80, 90.00
R / Rfree (%)	21 / 26.2

The structure of Structural Distortions in Psoralen Cross-Linked Dna also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structural Distortions in Psoralen Cross-Linked Dna (pdb code 2b2b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Distortions in Psoralen Cross-Linked Dna, PDB code: 2b2b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structural Distortions in Psoralen Cross-Linked Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Distortions in Psoralen Cross-Linked Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na24 b:15.8 occ:1.00 O A:HOH151 1.9 18.5 1.0 O A:HOH166 2.0 33.7 1.0 O A:HOH70 2.6 13.5 1.0 O A:HOH180 2.6 20.1 1.0 O A:HOH33 2.7 15.6 1.0 O A:HOH57 3.1 29.9 1.0 O A:HOH149 3.6 27.4 1.0 N7 A:DA6 3.8 2.4 1.0 C8 A:DA6 4.0 2.3 1.0 O A:HOH190 4.2 35.3 1.0 O A:HOH217 4.2 78.3 1.0 N7 A:DG7 4.3 2.4 1.0 OP2 A:DA6 4.4 16.3 1.0 O6 A:DG7 4.4 3.3 1.0 OP2 A:DT5 4.4 8.2 1.0 OP1 A:DT5 4.6 8.6 1.0 O A:HOH201 4.7 16.9 1.0 P A:DT5 4.9 7.6 1.0

Sodium binding site 2 out of 3 in the Structural Distortions in Psoralen Cross-Linked Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Distortions in Psoralen Cross-Linked Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na27 b:16.8 occ:1.00 O A:HOH29 2.5 42.6 1.0 OP1 A:DC4 2.6 4.8 1.0 O4 B:DT15 2.8 6.6 1.0 O A:HOH141 3.0 22.1 1.0 C12 A:PSO21 3.8 2.5 1.0 P A:DC4 3.8 7.1 1.0 C4 B:DT15 3.8 6.8 1.0 C5' A:DC4 3.8 4.2 1.0 C7 B:DT15 3.8 10.0 1.0 O A:HOH201 3.9 16.9 1.0 C5 A:PSO21 3.9 2.0 1.0 C5 B:DT15 4.2 4.5 1.0 O5' A:DC4 4.2 4.3 1.0 O3' A:DG3 4.2 5.4 1.0 O A:HOH126 4.2 37.4 1.0 O B:HOH196 4.2 52.1 1.0 C5 B:DC14 4.3 3.6 1.0 N4 B:DC14 4.3 4.4 1.0 C13 A:PSO21 4.4 7.1 1.0 N6 A:DA6 4.4 3.2 1.0 C4 B:DC14 4.4 5.3 1.0 C4' A:PSO21 4.5 4.2 1.0 C6 A:PSO21 4.6 5.2 1.0 O A:HOH34 4.7 17.4 1.0 C10 A:PSO21 4.8 4.3 1.0 O A:HOH140 4.8 23.3 1.0 C4 A:PSO21 4.8 4.3 1.0 C6 B:DC14 5.0 7.3 1.0 C3' A:DG3 5.0 4.8 1.0 N3 B:DT15 5.0 5.0 1.0

Sodium binding site 3 out of 3 in the Structural Distortions in Psoralen Cross-Linked Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Distortions in Psoralen Cross-Linked Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na26 b:9.6 occ:1.00 O B:HOH58 3.4 26.6 1.0 N2 B:DG19 4.6 18.1 1.0

F.A.Hays, H.Yonggang, B.F.Eichman, W.Kong, J.Hearst, P.S.Ho. Structural Distortions in Psoralen Cross-Linked Dna To Be Published.