Sodium in PDB 5ulp: Structure of the NS5 Methyltransferase From Zika Bound to MS2042

The structure of Structure of the NS5 Methyltransferase From Zika Bound to MS2042, PDB code: 5ulp was solved by R.Jain, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.72 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.989, 111.231, 77.400, 90.00, 93.87, 90.00
R / Rfree (%)	17.3 / 19.9

The structure of Structure of the NS5 Methyltransferase From Zika Bound to MS2042 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Structure of the NS5 Methyltransferase From Zika Bound to MS2042 (pdb code 5ulp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the NS5 Methyltransferase From Zika Bound to MS2042, PDB code: 5ulp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the NS5 Methyltransferase From Zika Bound to MS2042


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 NS5 Methyltransferase From Zika Bound to MS2042 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:32.6 occ:1.00 O A:HIS110 2.3 26.0 1.0 O A:GLY107 2.4 26.1 1.0 O A:HOH610 2.5 47.9 1.0 OE2 A:GLU112 2.6 32.0 1.0 C A:GLY107 3.2 25.4 1.0 N A:GLY107 3.4 24.2 1.0 C A:HIS110 3.5 27.0 1.0 CD A:GLU112 3.5 31.7 1.0 CG A:GLU112 3.7 27.7 1.0 CA A:GLY107 3.7 26.0 1.0 N A:HIS110 4.0 25.4 1.0 C A:GLY106 4.1 23.5 1.0 N A:PRO108 4.2 21.5 1.0 CA A:HIS110 4.3 24.6 1.0 N A:GLU112 4.4 21.7 1.0 CA A:GLY106 4.4 20.5 1.0 C A:GLU111 4.5 22.0 1.0 CA A:PRO108 4.5 22.9 1.0 N A:GLU111 4.5 22.5 1.0 O A:HOH627 4.5 39.1 1.0 O A:HOH565 4.6 44.4 1.0 N A:GLY109 4.6 25.0 1.0 CA A:GLU111 4.7 24.1 1.0 CB A:HIS110 4.7 24.7 1.0 C A:PRO108 4.7 25.7 1.0 OE1 A:GLU112 4.7 29.4 1.0 O A:HOH611 4.8 43.4 1.0 O A:GLY106 4.9 24.3 1.0 CB A:GLU112 4.9 26.2 1.0

Sodium binding site 2 out of 2 in the Structure of the NS5 Methyltransferase From Zika Bound to MS2042


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the NS5 Methyltransferase From Zika Bound to MS2042 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na308 b:30.1 occ:1.00 O B:HOH691 2.9 48.7 1.0 O B:HOH628 3.1 41.0 1.0 N B:GLY148 3.2 20.1 1.0 CAL B:KB1301 3.4 32.0 1.0 C8 B:KB1301 3.5 24.0 1.0 CAJ B:KB1301 3.6 38.7 1.0 C B:GLY148 3.8 20.9 1.0 N B:GLU149 3.9 24.2 1.0 CA B:GLY148 4.0 22.1 1.0 CA B:ILE147 4.0 17.8 1.0 CG2 B:ILE147 4.1 21.6 1.0 CBD B:KB1301 4.1 22.0 1.0 O B:GLY148 4.1 26.1 1.0 CAQ B:KB1301 4.1 20.0 1.0 C B:ILE147 4.1 20.5 1.0 OAU B:KB1301 4.2 19.6 1.0 CB B:GLU149 4.3 29.8 1.0 CA B:GLU149 4.4 24.4 1.0 N9 B:KB1301 4.4 20.9 1.0 N7 B:KB1301 4.5 24.0 1.0 CAY B:KB1301 4.5 27.1 1.0 CBF B:KB1301 4.5 19.6 1.0 CL B:CL302 4.5 37.0 1.0 CBC B:KB1301 4.5 22.5 1.0 CB B:ILE147 4.5 19.9 1.0 CBE B:KB1301 4.5 19.7 1.0 CAW B:KB1301 4.7 47.8 1.0 O B:ASP146 4.8 24.2 1.0 CG1 B:ILE147 4.9 20.7 1.0

R.Jain, K.V.Butler, J.Coloma, J.Jin, A.K.Aggarwal. Development of A S-Adenosylmethionine Analog That Intrudes the Rna-Cap Binding Site of Zika Methyltransferase. Sci Rep V. 7 1632 2017.
ISSN: ESSN 2045-2322
PubMed: 28487506
DOI: 10.1038/S41598-017-01756-7