Sodium in PDB 4osu: Crystal Structure of Hcmv Gb-Neutralizing SM5-1 Fab Fragment

The structure of Crystal Structure of Hcmv Gb-Neutralizing SM5-1 Fab Fragment, PDB code: 4osu was solved by U.Diestel, Y.A.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 1.87
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.645, 92.645, 124.646, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Hcmv Gb-Neutralizing SM5-1 Fab Fragment (pdb code 4osu). 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 Hcmv Gb-Neutralizing SM5-1 Fab Fragment, PDB code: 4osu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hcmv Gb-Neutralizing SM5-1 Fab Fragment


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 Hcmv Gb-Neutralizing SM5-1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Na304 b:23.1 occ:1.00 OE2 H:GLU10 2.3 24.4 1.0 O H:HOH535 2.3 33.4 1.0 O H:HOH444 2.4 19.0 1.0 O H:LYS19 2.4 16.0 1.0 O H:HOH534 2.5 31.0 1.0 CD H:GLU10 3.3 23.4 1.0 C H:LYS19 3.6 15.6 1.0 OE1 H:GLU10 3.6 23.0 1.0 N H:LYS19 3.9 15.2 1.0 O H:HOH443 4.0 18.9 1.0 CB H:LYS19 4.1 18.0 1.0 CA H:LYS19 4.1 15.6 1.0 O H:HOH481 4.2 27.1 1.0 O H:HOH553 4.3 43.2 1.0 CG H:GLU10 4.6 20.6 1.0 N H:VAL20 4.7 14.4 1.0 CG2 H:VAL18 4.8 13.9 1.0 CG H:LYS19 4.9 20.1 1.0 CA H:VAL20 5.0 14.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hcmv Gb-Neutralizing SM5-1 Fab Fragment


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 Hcmv Gb-Neutralizing SM5-1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:34.9 occ:1.00 O H:HOH524 2.2 32.0 1.0 O H:HOH525 2.4 44.2 1.0 OG1 H:THR103 2.4 34.8 1.0 O H:HOH496 2.5 29.1 1.0 O H:THR103 2.6 38.5 1.0 C H:THR103 3.2 37.7 1.0 CB H:THR103 3.4 34.5 1.0 CA H:THR103 3.8 34.0 1.0 N H:VAL104 4.1 41.4 1.0 OD1 H:ASP31 4.1 28.3 1.0 O H:LYS30 4.2 24.1 1.0 N H:THR103 4.2 32.0 1.0 CA H:ASP31 4.3 24.1 1.0 O H:ASP31 4.5 22.4 1.0 CA H:VAL104 4.5 47.5 1.0 NE2 H:GLN54 4.5 34.2 1.0 CG2 H:THR103 4.7 33.2 1.0 C H:ASP31 4.7 22.4 1.0 CB H:GLN54 4.7 27.9 1.0 CG H:GLN54 4.8 31.3 1.0 O H:HOH500 4.9 30.7 1.0 C H:LYS30 4.9 24.4 1.0 CG H:ASP31 5.0 27.6 1.0

N.Spindler, U.Diestel, J.D.Stump, A.K.Wiegers, T.H.Winkler, H.Sticht, M.Mach, Y.A.Muller. Structural Basis For the Recognition of Human Cytomegalovirus Glycoprotein B By A Neutralizing Human Antibody. Plos Pathog. V. 10 04377 2014.
ISSN: ISSN 1553-7366
PubMed: 25299639
DOI: 10.1371/JOURNAL.PPAT.1004377