Sodium in PDB 3jtz: Structure of the Arm-Type Binding Domain of Hpi Integrase

The structure of Structure of the Arm-Type Binding Domain of Hpi Integrase, PDB code: 3jtz was solved by A.Szwagierczak, U.Antonenka, G.M.Popowicz, T.Sitar, T.A.Holak, A.Rakin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.750, 48.750, 74.200, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.9

The binding sites of Sodium atom in the Structure of the Arm-Type Binding Domain of Hpi Integrase (pdb code 3jtz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Arm-Type Binding Domain of Hpi Integrase, PDB code: 3jtz:

Sodium binding site 1 out of 1 in the Structure of the Arm-Type Binding Domain of Hpi Integrase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Arm-Type Binding Domain of Hpi Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na89 b:15.6 occ:1.00 O A:LYS16 2.9 12.4 1.0 O A:VAL30 2.9 8.8 1.0 N A:SER14 3.0 17.9 1.0 C A:LYS31 3.2 10.3 1.0 N A:PRO32 3.2 10.5 1.0 OG A:SER14 3.3 18.1 1.0 CD A:PRO32 3.5 10.7 1.0 CE1 A:PHE18 3.6 10.8 1.0 C A:LYS16 3.6 12.3 1.0 CA A:LYS31 3.6 9.8 1.0 C A:VAL30 3.6 8.9 1.0 CD1 A:PHE18 3.6 10.1 1.0 O A:LYS31 3.6 10.7 1.0 CA A:PRO32 3.7 11.8 1.0 CA A:PRO13 3.7 20.0 1.0 O A:SER14 3.8 17.0 1.0 C A:PRO13 3.8 19.1 1.0 CG A:PRO32 3.9 12.3 1.0 CA A:PRO17 3.9 10.4 1.0 N A:LYS31 3.9 9.1 1.0 CA A:SER14 3.9 17.3 1.0 C A:SER14 4.0 16.5 1.0 N A:PRO17 4.1 11.1 1.0 CB A:SER14 4.1 17.4 1.0 CG1 A:VAL30 4.2 11.0 1.0 N A:PHE18 4.3 9.1 1.0 CB A:PRO13 4.4 20.4 1.0 N A:LYS16 4.4 14.0 1.0 C A:PRO17 4.4 9.8 1.0 CB A:PRO32 4.5 12.3 1.0 CA A:LYS16 4.6 14.1 1.0 CB A:VAL30 4.6 8.9 1.0 CZ A:PHE18 4.7 10.7 1.0 CA A:VAL30 4.8 8.7 1.0 CG A:PHE18 4.8 9.1 1.0 N A:ASP15 4.9 15.5 1.0 O A:LYS12 4.9 21.1 1.0 N A:PRO13 5.0 20.8 1.0 C A:PRO32 5.0 13.3 1.0

A.Szwagierczak, U.Antonenka, G.M.Popowicz, T.Sitar, T.A.Holak, A.Rakin. Structures of the Arm-Type Binding Domains of Hpi and HAI7 Integrases J.Biol.Chem. V. 284 31664 2009.
ISSN: ISSN 0021-9258
PubMed: 19737930
DOI: 10.1074/JBC.M109.059261