Sodium in PDB 4o1r: Crystal Structure of Npudnab Intein

The structure of Crystal Structure of Npudnab Intein, PDB code: 4o1r was solved by A.S.Aranko, J.S.Oeemig, D.Zhou, T.Kajander, A.Wlodawer, H.Iwai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.05 / 1.40
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.054, 61.054, 122.179, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.9

The structure of Crystal Structure of Npudnab Intein also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Npudnab Intein (pdb code 4o1r). 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 Npudnab Intein, PDB code: 4o1r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Npudnab Intein


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 Npudnab Intein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:14.5 occ:1.00 O A:PRO89 2.3 13.0 1.0 O A:HOH332 2.4 22.7 1.0 O A:HOH343 2.4 26.3 1.0 OG1 A:THR88 2.4 13.7 1.0 CB A:THR88 3.3 13.0 1.0 C A:PRO89 3.5 13.0 1.0 C A:THR88 3.9 13.1 1.0 N A:GLU91 4.0 11.9 1.0 N A:PRO89 4.0 13.0 1.0 O A:THR88 4.2 12.0 1.0 CA A:THR88 4.2 12.9 1.0 CA A:PRO89 4.4 13.3 1.0 C A:LYS90 4.4 12.9 1.0 CB A:LYS90 4.4 14.1 1.0 N A:LYS90 4.4 13.2 1.0 CG2 A:THR88 4.4 13.4 1.0 CD A:PRO89 4.5 13.3 1.0 CB A:GLU91 4.6 11.9 1.0 CA A:LYS90 4.6 13.7 1.0 CA A:GLU91 4.6 12.1 1.0 O A:HOH571 4.6 58.6 1.0 O A:HOH346 4.9 25.2 1.0 CB A:PRO89 4.9 14.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Npudnab Intein


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 Npudnab Intein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:23.5 occ:1.00 O A:HOH412 2.4 41.8 1.0 O A:HOH358 2.4 29.3 1.0 O A:ASP12 2.4 24.2 1.0 O A:HOH318 2.4 19.9 1.0 O A:HOH411 2.5 35.5 1.0 C A:ASP12 3.6 23.8 1.0 O A:SER13 4.2 19.2 1.0 C A:SER13 4.2 19.0 1.0 O A:HOH453 4.3 39.6 1.0 CA A:SER13 4.4 19.6 1.0 N A:SER13 4.5 21.0 1.0 CA A:ASP12 4.6 24.9 1.0 O A:VAL11 4.6 23.3 1.0 N A:GLY14 4.7 17.9 1.0 O A:HOH444 4.8 40.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Npudnab Intein


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 Npudnab Intein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:32.5 occ:1.00 O A:HOH487 2.1 54.1 1.0 O A:HOH322 2.2 22.8 1.0 O A:ILE78 2.3 15.9 1.0 O A:HOH384 2.4 49.3 1.0 O A:HOH347 2.5 30.4 1.0 C A:ILE78 3.6 14.5 1.0 O A:HOH438 4.0 43.3 1.0 OD1 A:ASN79 4.2 21.1 1.0 CG1 A:ILE78 4.3 16.2 1.0 O A:HOH327 4.3 23.4 1.0 CA A:ASN79 4.4 15.9 1.0 N A:ASN79 4.5 14.9 1.0 O A:HOH402 4.5 46.5 1.0 CA A:ILE78 4.6 14.2 1.0 O A:HOH560 4.7 60.2 1.0 O A:HOH465 4.7 41.5 1.0 CD1 A:ILE78 4.7 17.9 1.0 CB A:ILE78 4.9 14.0 1.0 CG A:ASN79 5.0 18.0 1.0

A.S.Aranko, J.S.Oeemig, D.Zhou, T.Kajander, A.Wlodawer, H.Iwai. Structure-Based Engineering and Comparison of Novel Split Inteins For Protein Ligation. Mol Biosyst V. 10 1023 2014.
ISSN: ISSN 1742-206X
PubMed: 24574026
DOI: 10.1039/C4MB00021H