Sodium in PDB 6nyp: Crystal Structure of UL144/Btla Complex

The structure of Crystal Structure of UL144/Btla Complex, PDB code: 6nyp was solved by B.Aruna, D.M.Zajonc, T.Doukov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.93 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.990, 77.200, 101.720, 90.00, 91.67, 90.00
R / Rfree (%)	23 / 27.7

The binding sites of Sodium atom in the Crystal Structure of UL144/Btla Complex (pdb code 6nyp). 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 UL144/Btla Complex, PDB code: 6nyp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of UL144/Btla Complex


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 UL144/Btla Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:77.0 occ:1.00 O A:LEU38 2.7 63.4 1.0 O A:ILE40 2.9 61.9 1.0 C F:THR52 3.2 64.2 1.0 N F:SER53 3.2 64.2 1.0 N A:HIS127 3.3 68.8 1.0 N A:ILE40 3.5 57.7 1.0 O F:THR52 3.6 66.8 1.0 CA A:SER126 3.6 58.6 1.0 CA F:SER53 3.6 62.9 1.0 C A:LEU38 3.7 64.0 1.0 CA F:THR52 3.8 65.1 1.0 CD2 A:HIS127 3.8 56.9 1.0 C A:ILE40 3.8 59.7 1.0 CB A:SER126 3.9 57.5 1.0 C A:SER126 4.0 63.1 1.0 CB F:SER53 4.0 61.1 1.0 CA A:ILE40 4.0 58.3 1.0 O F:TYR51 4.1 63.0 1.0 CB A:ILE40 4.1 60.8 1.0 N F:THR52 4.2 63.6 1.0 CB A:HIS127 4.2 60.5 1.0 CG A:HIS127 4.2 58.5 1.0 C F:TYR51 4.4 63.4 1.0 CA A:HIS127 4.4 64.3 1.0 CB A:LEU38 4.4 67.1 1.0 OG F:SER53 4.5 59.5 1.0 C A:TYR39 4.5 62.0 1.0 N A:TYR39 4.5 65.8 1.0 CA A:TYR39 4.6 66.1 1.0 CA A:LEU38 4.7 65.4 1.0 NE2 A:HIS127 4.8 56.6 1.0 N A:SER126 4.8 58.8 1.0 OG A:SER126 4.9 53.5 1.0 O A:GLU125 4.9 64.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of UL144/Btla Complex


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 UL144/Btla Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:53.9 occ:1.00 O D:ILE40 2.5 50.2 1.0 O D:LEU38 2.9 57.1 1.0 N D:HIS127 3.1 53.7 1.0 N D:ILE40 3.3 49.0 1.0 C E:THR52 3.4 49.1 1.0 C D:ILE40 3.5 49.3 1.0 N E:SER53 3.5 52.4 1.0 CA D:SER126 3.6 51.0 1.0 ND1 D:HIS127 3.6 59.7 1.0 O E:THR52 3.7 52.8 1.0 CA D:ILE40 3.7 50.0 1.0 CB D:ILE40 3.8 53.4 1.0 CB D:SER126 3.8 52.1 1.0 C D:SER126 3.8 53.0 1.0 CA E:SER53 3.9 53.5 1.0 C D:LEU38 3.9 52.9 1.0 CB D:HIS127 3.9 56.1 1.0 CA E:THR52 4.0 47.6 1.0 CG D:HIS127 4.0 58.4 1.0 CA D:HIS127 4.1 54.8 1.0 O E:TYR51 4.2 47.8 1.0 CB E:SER53 4.3 55.1 1.0 N E:THR52 4.3 46.8 1.0 C E:TYR51 4.4 46.9 1.0 C D:TYR39 4.4 54.6 1.0 CE1 D:HIS127 4.5 57.9 1.0 CB D:LEU38 4.5 52.2 1.0 CG2 D:ILE40 4.6 55.5 1.0 N D:TYR39 4.6 53.7 1.0 CA D:TYR39 4.6 54.7 1.0 OG D:SER126 4.7 54.0 1.0 O D:HIS127 4.7 56.0 1.0 N D:LYS41 4.7 45.9 1.0 CA D:LEU38 4.8 54.7 1.0 OG E:SER53 4.9 57.2 1.0 CG1 D:ILE40 4.9 54.0 1.0 N D:SER126 4.9 52.0 1.0 C D:HIS127 5.0 56.5 1.0

A.Bitra, I.Nemcovicova, G.Picarda, T.Doukov, J.Wang, C.A.Benedict, D.M.Zajonc. Structure of Human Cytomegalovirus UL144, An Hvem Orthologue, Bound to the B and T Cell Lymphocyte Attenuator. J.Biol.Chem. V. 294 10519 2019.
ISSN: ESSN 1083-351X
PubMed: 31126984
DOI: 10.1074/JBC.RA119.009199