Sodium in PDB 4k70: Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein

The structure of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein, PDB code: 4k70 was solved by J.D.Pitts, E.E.Heldwein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.12 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.670, 156.589, 67.381, 90.00, 91.33, 90.00
R / Rfree (%)	17.3 / 22

The structure of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Calcium	(Ca)	6 atoms
Chlorine	(Cl)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein (pdb code 4k70). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 21 binding sites of Sodium where determined in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein, PDB code: 4k70:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


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 N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:38.7 occ:1.00 O A:HIS378 2.5 25.7 1.0 OD1 A:ASP382 2.8 26.9 1.0 NH2 A:ARG343 3.2 29.9 0.4 CB A:ASP382 3.5 20.2 1.0 CG A:ASP382 3.5 26.6 1.0 C A:HIS378 3.6 26.4 1.0 O A:ARG379 3.6 23.1 1.0 N A:ASP382 3.7 20.4 1.0 CG B:GLU82 4.0 30.0 1.0 C A:ARG379 4.0 23.3 1.0 CA A:ARG379 4.0 25.3 1.0 CZ A:ARG343 4.1 29.4 0.4 CA A:ASP382 4.2 21.9 1.0 CD B:GLU82 4.3 30.1 1.0 N A:ARG379 4.3 24.9 1.0 NE A:ARG343 4.3 32.7 0.4 CA A:CA1002 4.4 22.7 1.0 OE1 B:GLU82 4.5 24.6 1.0 N A:LEU381 4.5 20.2 1.0 O A:HOH1389 4.6 33.4 1.0 C A:LEU381 4.7 24.0 1.0 OD2 A:ASP382 4.7 26.8 1.0 CA A:HIS378 4.8 24.2 1.0 OE2 B:GLU82 4.8 30.5 1.0 CB A:LEU381 4.9 22.7 1.0 N A:LEU380 4.9 22.0 1.0 CA A:LEU381 4.9 22.1 1.0 CB B:GLU82 5.0 25.5 1.0

Sodium binding site 2 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


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 N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:45.3 occ:1.00 O A:HOH1313 2.3 37.4 1.0 OD1 A:ASP79 3.2 25.5 1.0 N A:TRP80 3.6 21.9 1.0 OD2 A:ASP81 3.6 28.4 1.0 O B:HOH1301 3.6 32.6 1.0 O B:HOH1290 4.1 40.1 1.0 O A:HOH1217 4.1 31.4 1.0 NH2 B:ARG178 4.2 49.4 1.0 CA A:ASP79 4.2 22.4 1.0 CG A:ASP81 4.3 28.9 1.0 N A:ASP81 4.3 25.3 1.0 C A:ASP79 4.3 23.4 1.0 CG A:ASP79 4.3 26.2 1.0 CA A:CA1003 4.4 27.4 1.0 CA A:TRP80 4.5 21.4 1.0 CB A:TRP80 4.5 26.4 1.0 NH1 B:ARG178 4.7 49.0 1.0 OD1 A:ASP81 4.7 29.6 1.0 NA B:NA1009 4.7 34.8 1.0 O A:HOH1281 4.7 42.1 1.0 O A:HIS78 4.7 24.5 1.0 C A:TRP80 4.8 24.3 1.0 CZ B:ARG178 4.8 45.7 1.0 CB A:ASP79 4.9 24.9 1.0 CD1 A:TYR179 4.9 26.7 1.0

Sodium binding site 3 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


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 N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:41.4 occ:1.00 OD1 A:ASN95 2.3 32.8 1.0 O A:HOH1170 2.6 35.7 1.0 OD1 A:ASP117 2.8 35.9 1.0 CG A:ASN95 3.3 33.9 1.0 CB A:PRO116 3.3 27.7 1.0 N A:ASP117 3.5 26.1 1.0 CA A:ASN95 3.5 28.3 1.0 C A:PRO116 3.5 27.2 1.0 O A:ASN95 3.8 36.9 1.0 O A:PRO116 3.8 26.2 1.0 CB A:ASN95 3.8 29.5 1.0 CA A:ASP117 3.9 27.2 1.0 O A:HOH1309 3.9 42.8 1.0 CG A:PRO116 4.0 30.6 1.0 CG A:ASP117 4.0 38.5 1.0 C A:ASN95 4.0 35.8 1.0 CA A:PRO116 4.1 25.0 1.0 ND2 A:ASN95 4.4 31.0 1.0 O A:VAL94 4.5 25.4 1.0 OG1 A:THR100 4.5 37.4 1.0 CB A:ASP117 4.6 31.6 1.0 N A:ASN95 4.6 26.1 1.0 C A:VAL94 5.0 29.4 1.0

Sodium binding site 4 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:44.0 occ:1.00 O A:HIS311 2.5 33.9 1.0 OE1 A:GLN288 2.9 33.1 1.0 C A:HIS311 3.5 31.1 1.0 CB A:GLN288 3.7 36.0 1.0 CD A:GLN288 3.7 39.9 1.0 CG A:GLN288 4.0 33.1 1.0 O A:HOH1129 4.0 28.9 1.0 CA A:THR312 4.0 29.7 1.0 N A:THR312 4.1 30.0 1.0 O A:HOH1357 4.2 41.6 1.0 N A:GLN313 4.5 27.9 1.0 CA A:HIS311 4.6 28.5 1.0 C A:THR312 4.6 25.9 1.0 CA A:GLN288 4.8 34.5 1.0 NE2 A:GLN288 4.9 38.1 1.0

Sodium binding site 5 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:57.1 occ:1.00 O A:VAL246 2.3 49.0 1.0 OE1 A:GLU248 2.6 61.1 1.0 OE2 A:GLU248 2.9 59.2 1.0 CD A:GLU248 3.0 55.8 1.0 C A:VAL246 3.3 44.7 1.0 N A:GLU248 3.5 47.4 1.0 C A:GLY247 3.5 47.8 1.0 CA A:GLY247 3.5 44.7 1.0 N A:GLY247 3.8 47.4 1.0 O A:GLY247 4.1 48.7 1.0 CB A:PRO245 4.2 42.6 1.0 CG A:GLU248 4.3 49.0 1.0 O A:PRO245 4.3 41.5 1.0 C A:PRO245 4.3 45.1 1.0 CA A:GLU248 4.3 43.2 1.0 N A:VAL246 4.5 43.5 1.0 CA A:VAL246 4.5 44.7 1.0 CB A:GLU248 4.6 45.1 1.0 CA A:PRO245 4.9 43.3 1.0

Sodium binding site 6 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:53.0 occ:1.00 OE2 A:GLU105 2.4 48.8 1.0 CD A:GLU105 3.4 48.1 1.0 CG A:GLU105 3.7 46.9 1.0 CB A:GLU105 4.4 41.0 1.0 OE1 A:GLU105 4.5 46.3 1.0

Sodium binding site 7 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:40.5 occ:1.00 O A:HOH1377 2.4 34.0 1.0 O B:HOH1262 2.4 31.1 1.0 O B:HOH1390 2.6 39.0 1.0 O A:HOH1288 2.7 34.0 1.0 NH1 A:ARG178 3.3 50.1 1.0 CL A:CL1014 3.4 61.0 1.0 OD1 A:ASP383 3.8 25.4 1.0 CA B:CA1003 4.0 25.9 1.0 OD2 B:ASP79 4.3 26.0 1.0 O B:HOH1313 4.3 34.6 1.0 CG B:ASP79 4.4 24.3 1.0 CZ A:ARG178 4.4 50.9 1.0 OD1 B:ASP79 4.5 22.4 1.0 OD1 A:ASP389 4.5 29.6 0.5 O B:HOH1402 4.7 44.1 1.0 OD2 A:ASP389 4.7 27.0 0.5 CG A:ASP383 4.7 26.1 1.0 NH2 A:ARG178 4.8 45.5 1.0 CB A:ALA393 4.9 21.3 1.0

Sodium binding site 8 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:60.8 occ:1.00 O A:GLU200 2.4 38.5 1.0 O A:HOH1158 3.4 41.6 1.0 C A:GLU200 3.4 36.6 1.0 OE1 A:GLU200 3.5 53.0 1.0 CA A:GLU200 3.9 36.4 1.0 CB A:GLU200 4.0 41.0 1.0 NH1 A:ARG207 4.3 35.8 1.0 O A:LEU202 4.5 38.3 1.0 N A:GLY201 4.6 35.8 1.0 CD A:GLU200 4.6 52.9 1.0 CG A:GLU200 4.9 43.9 1.0

Sodium binding site 9 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1015 b:41.2 occ:1.00 O A:HOH1341 2.4 47.1 1.0 OD1 B:ASP347 2.4 43.2 1.0 OE1 A:GLU89 2.5 40.1 1.0 O B:HOH1327 2.5 37.5 1.0 O B:HOH1259 2.7 39.7 1.0 OE2 A:GLU89 2.8 43.2 1.0 O B:HOH1233 2.8 43.0 1.0 CD A:GLU89 3.0 42.7 1.0 CG B:ASP347 3.6 38.9 1.0 CB B:ASP347 4.0 29.1 1.0 CA B:ASP347 4.2 27.7 1.0 O A:HOH1373 4.3 40.9 1.0 NA B:NA1016 4.4 42.6 1.0 OE1 B:GLU350 4.4 36.9 1.0 CG A:GLU89 4.5 37.5 1.0 NH2 A:ARG39 4.5 33.4 1.0 NH2 B:ARG351 4.5 44.2 1.0 OD2 B:ASP347 4.6 46.4 1.0 NH1 A:ARG39 4.7 38.4 1.0 CZ A:ARG39 4.8 35.3 1.0 O B:HOH1395 4.8 32.9 1.0 CD B:GLU350 4.8 37.0 1.0 O B:HOH1326 4.9 35.9 1.0 OE2 B:GLU350 5.0 39.5 1.0

Sodium binding site 10 out of 21 in the Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of N-Terminal Half of Pseudorabiesvirus UL37 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1017 b:54.6 occ:1.00 NH2 A:ARG195 2.4 51.8 1.0 N A:VAL149 2.8 39.1 1.0 CZ A:ARG195 3.4 50.0 1.0 CG A:ARG148 3.4 51.3 1.0 CA A:ARG148 3.5 40.1 1.0 O A:VAL149 3.6 40.4 1.0 C A:ARG148 3.6 39.4 1.0 CA A:VAL149 3.7 37.0 1.0 NH1 A:ARG195 3.8 52.0 1.0 CB A:VAL149 3.9 39.3 1.0 CB A:ARG148 4.1 41.2 1.0 C A:VAL149 4.1 41.5 1.0 CG2 A:VAL149 4.4 35.5 1.0 O A:PRO147 4.4 42.0 1.0 NE A:ARG195 4.5 49.3 1.0 CD A:ARG148 4.6 59.5 1.0 N A:ARG148 4.7 36.8 1.0 O A:ARG148 4.8 37.2 1.0

J.D.Pitts, J.Klabis, A.L.Richards, G.A.Smith, E.E.Heldwein. Crystal Structure of the Herpesvirus Inner Tegument Protein UL37 Supports Its Essential Role in Control of Viral Trafficking. J.Virol. V. 88 5462 2014.
ISSN: ISSN 0022-538X
PubMed: 24599989
DOI: 10.1128/JVI.00163-14