Sodium in PDB 2gxb: Crystal Structure of the Za Domain Bound to Z-Rna

The structure of Crystal Structure of the Za Domain Bound to Z-Rna, PDB code: 2gxb was solved by A.Athanasiadis, D.Placido, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.603, 92.776, 50.229, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.4

The binding sites of Sodium atom in the Crystal Structure of the Za Domain Bound to Z-Rna (pdb code 2gxb). 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 the Za Domain Bound to Z-Rna, PDB code: 2gxb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Za Domain Bound to Z-Rna


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 the Za Domain Bound to Z-Rna within 5.0Å range: probe atom residue distance (Å) B Occ E:Na162 b:26.4 occ:1.00 O E:HOH61 2.2 25.8 1.0 O2' E:C5 2.4 19.1 1.0 O2' F:C3 2.5 15.6 1.0 O2 F:C3 2.6 12.2 1.0 O2 E:C5 2.6 23.3 1.0 C2' E:C5 3.5 20.8 1.0 C2 F:C3 3.5 13.5 1.0 C2' F:C3 3.6 13.9 1.0 C2 E:C5 3.6 19.5 1.0 O F:HOH172 3.6 24.8 1.0 C1' E:C5 3.7 19.3 1.0 C1' F:C3 3.7 13.4 1.0 N2 E:G4 3.8 15.2 1.0 N2 F:G2 4.0 17.1 1.0 N1 F:C3 4.0 13.6 1.0 N1 E:C5 4.1 19.6 1.0 O3' F:C3 4.1 12.1 1.0 O3' E:C5 4.1 28.6 1.0 C3' E:C5 4.4 21.4 1.0 C3' F:C3 4.4 14.0 1.0 N3 F:C3 4.5 12.8 1.0 N3 E:C5 4.6 18.7 1.0 O F:HOH164 4.6 9.7 1.0 C2 E:G4 4.9 14.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Za Domain Bound to Z-Rna


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 the Za Domain Bound to Z-Rna within 5.0Å range: probe atom residue distance (Å) B Occ F:Na163 b:27.9 occ:1.00 O2' E:C3 2.4 13.4 1.0 O2' F:C5 2.4 14.3 1.0 O2 F:C5 2.5 15.1 1.0 O F:HOH189 2.7 30.6 1.0 O2 E:C3 2.8 15.1 1.0 C2 F:C5 3.4 17.1 1.0 C2' F:C5 3.5 16.6 1.0 C2' E:C3 3.5 15.8 1.0 C2 E:C3 3.6 15.9 1.0 O F:HOH166 3.6 20.7 1.0 C1' F:C5 3.7 16.6 1.0 C1' E:C3 3.7 14.4 1.0 N2 E:G2 3.8 19.2 1.0 N2 F:G4 3.9 16.5 1.0 N1 F:C5 4.0 16.8 1.0 O3' F:C5 4.0 20.9 1.0 N1 E:C3 4.0 15.7 1.0 O3' E:C3 4.2 17.9 1.0 O F:HOH172 4.2 24.8 1.0 C3' F:C5 4.4 18.2 1.0 O F:HOH167 4.4 18.8 1.0 N3 F:C5 4.4 17.4 1.0 O F:HOH190 4.5 22.3 1.0 O E:HOH78 4.5 9.0 1.0 C3' E:C3 4.5 15.8 1.0 N3 E:C3 4.6 14.4 1.0 C2 E:G2 4.9 18.2 1.0 C2 F:G4 5.0 16.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Za Domain Bound to Z-Rna


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 the Za Domain Bound to Z-Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:15.4 occ:1.00 OP1 F:C3 2.6 11.8 1.0 O B:HOH211 2.8 12.2 1.0 OD1 B:ASN173 2.9 10.7 1.0 NE1 B:TRP195 3.2 15.7 1.0 P F:C3 3.7 15.6 1.0 CB B:ALA158 3.7 15.5 1.0 CG B:PRO193 3.7 18.6 1.0 CG B:ASN173 3.8 12.9 1.0 O F:HOH165 3.8 12.0 1.0 CB B:PRO193 3.8 18.7 1.0 CZ2 B:TRP195 3.9 15.8 1.0 CE2 B:TRP195 3.9 15.4 1.0 CD B:PRO193 3.9 18.6 1.0 ND2 B:ASN173 3.9 12.1 1.0 OP2 F:C3 4.0 11.0 1.0 OH B:TYR177 4.2 11.9 1.0 O B:HOH216 4.3 24.2 1.0 CE1 B:TYR177 4.3 14.8 1.0 O B:PRO193 4.3 18.4 1.0 CD1 B:TRP195 4.4 15.4 1.0 O3' F:G2 4.4 16.2 1.0 N B:ALA158 4.6 16.1 1.0 N B:PRO193 4.6 19.0 1.0 CZ B:TYR177 4.7 15.8 1.0 CA B:PRO193 4.7 19.1 1.0 CA B:ALA158 4.8 16.6 1.0 C B:PRO193 4.9 19.0 1.0 CD1 B:LEU176 4.9 13.8 1.0 O5' F:C3 5.0 13.5 1.0

D.Placido, B.A.Brown, K.Lowenhaupt, A.Rich, A.Athanasiadis. A Left-Handed Rna Double Helix Bound By the Zalpha Domain of the Rna-Editing Enzyme ADAR1. Structure V. 15 395 2007.
ISSN: ISSN 0969-2126
PubMed: 17437712
DOI: 10.1016/J.STR.2007.03.001