Sodium in PDB 2ilz: Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+

All present enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+:
2.7.7.48;

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+, PDB code: 2ilz was solved by A.A.Thompson, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.30 / 2.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	128.159, 128.159, 112.610, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 25.5

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+ also contains other interesting chemical elements:

Arsenic	(As)	4 atoms
Manganese	(Mn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+ (pdb code 2ilz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+, PDB code: 2ilz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+


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 Poliovirus Polymerase Complexed with Gtp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3001 b:43.5 occ:1.00 O A:GLY285 2.5 40.3 1.0 O A:GLY284 2.6 43.5 1.0 O A:LEU268 2.7 42.9 1.0 OG A:SER271 2.7 50.4 1.0 O A:ASN269 2.9 45.6 1.0 C A:GLY284 3.5 42.9 1.0 C A:GLY285 3.5 40.7 1.0 C A:ASN269 3.7 46.3 1.0 CB A:SER271 3.8 50.2 1.0 C A:LEU268 3.8 44.0 1.0 O A:HOH663 3.9 52.6 1.0 CG A:PRO287 4.0 45.6 1.0 CA A:GLY285 4.0 41.6 1.0 CG1 A:VAL282 4.0 46.0 1.0 CD A:PRO287 4.1 44.5 1.0 N A:GLY285 4.1 42.9 1.0 N A:SER271 4.1 49.9 1.0 O A:VAL282 4.2 44.5 1.0 CA A:ASN269 4.3 45.4 1.0 CB A:VAL282 4.3 47.0 1.0 N A:GLY284 4.4 42.9 1.0 CA A:GLY284 4.5 43.1 1.0 NE2 A:HIS273 4.5 56.2 1.0 N A:ASN269 4.5 44.1 1.0 CA A:SER271 4.6 50.3 1.0 N A:MET286 4.6 40.1 1.0 N A:HIS270 4.7 47.3 1.0 N A:PRO287 4.7 45.3 1.0 C A:VAL282 4.7 45.6 1.0 C A:HIS270 4.8 50.2 1.0 O A:TYR267 4.9 50.2 1.0 CA A:MET286 5.0 39.8 1.0 CA A:LEU268 5.0 44.9 1.0 CA A:HIS270 5.0 48.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Poliovirus Polymerase Complexed with Gtp and MN2+


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 Poliovirus Polymerase Complexed with Gtp and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3002 b:42.5 occ:1.00 O A:TYR350 2.6 36.5 1.0 OG A:SER242 2.8 35.4 1.0 N A:SER242 3.0 30.9 1.0 O A:SER240 3.1 35.9 1.0 CB A:SER242 3.2 32.6 1.0 O A:HOH582 3.3 29.6 1.0 CA A:GLY351 3.5 36.1 1.0 C A:TYR350 3.6 38.1 1.0 CD1 A:TRP245 3.6 26.0 1.0 CA A:SER242 3.7 31.2 1.0 O A:GLY351 3.8 37.4 1.0 NE1 A:TRP245 3.8 27.1 1.0 C A:LEU241 3.8 31.7 1.0 C A:GLY351 3.8 36.8 1.0 CA A:LEU241 4.0 31.4 1.0 C A:SER240 4.0 34.6 1.0 N A:GLY351 4.0 36.7 1.0 N A:LEU241 4.4 33.3 1.0 N A:LEU352 4.7 36.5 1.0 N A:LYS66 4.7 47.9 1.0 CD2 A:LEU352 4.7 37.3 1.0 CG1 A:ILE67 4.8 47.1 1.0 CG A:LEU352 4.8 36.0 1.0 CB A:LYS66 4.8 49.5 1.0 O A:LEU241 4.8 33.8 1.0 CA A:TYR350 4.9 38.7 1.0 N A:ILE67 4.9 49.5 1.0 C A:SER242 4.9 31.4 1.0 CG A:TRP245 4.9 26.2 1.0

A.A.Thompson, R.A.Albertini, O.B.Peersen. Stabilization of Poliovirus Polymerase By Ntp Binding and Fingers-Thumb Interactions. J.Mol.Biol. V. 366 1459 2007.
ISSN: ISSN 0022-2836
PubMed: 17223130
DOI: 10.1016/J.JMB.2006.11.070