Sodium in PDB 7aqx: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9)

The structure of Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9), PDB code: 7aqx was solved by C.E.Stebbins, A.Hempelmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.088, 95.565, 123.721, 90, 90, 90
R / Rfree (%)	16.4 / 19.2

The binding sites of Sodium atom in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9) (pdb code 7aqx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9), PDB code: 7aqx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:30.0 occ:1.00 O C:GLU109 2.2 32.8 1.0 OD1 C:ASP99 2.3 29.4 1.0 O C:HOH329 2.3 26.1 1.0 OE2 C:GLU111 2.4 34.6 1.0 O A:HOH528 2.6 35.8 1.0 OE1 C:GLU111 2.8 29.6 1.0 CD C:GLU111 3.0 31.2 1.0 HB2 C:GLU109 3.3 42.4 1.0 H C:LEU100 3.4 27.6 1.0 C C:GLU109 3.4 31.4 1.0 CG C:ASP99 3.4 29.1 1.0 HA C:ASP99 3.5 28.6 1.0 H C:GLU109 3.7 38.6 1.0 O C:HOH331 3.8 31.1 1.0 N C:LEU100 3.9 23.0 1.0 CB C:GLU109 4.0 35.4 1.0 CA C:GLU109 4.1 32.6 1.0 HA C:TYR110 4.1 32.7 1.0 HB3 C:SER108 4.1 43.2 1.0 CA C:ASP99 4.1 23.9 1.0 N C:GLU109 4.2 32.2 1.0 HB3 C:LEU100 4.2 27.7 1.0 HB3 C:GLU109 4.2 42.4 1.0 CB C:ASP99 4.2 26.5 1.0 O A:GLY296 4.2 26.8 1.0 OD2 C:ASP99 4.3 31.0 1.0 C C:ASP99 4.3 24.2 1.0 HB2 C:ASP99 4.4 31.7 1.0 O C:HOH337 4.4 44.3 1.0 N C:TYR110 4.4 29.7 1.0 O C:HOH324 4.4 39.3 1.0 O C:LEU100 4.5 24.2 1.0 H C:GLU111 4.5 30.0 1.0 CG C:GLU111 4.5 30.0 1.0 HG1 A:THR298 4.7 30.9 1.0 CA C:TYR110 4.7 27.3 1.0 HG3 C:GLU111 4.8 36.0 1.0 OG1 A:THR298 4.8 25.8 1.0 HA A:THR298 4.8 29.0 1.0 CA C:LEU100 4.8 23.9 1.0 N C:GLU111 4.9 25.0 1.0 HG2 C:GLU111 4.9 36.0 1.0 CB C:LEU100 4.9 23.1 1.0 O A:HOH542 5.0 31.3 1.0 HA C:GLU109 5.0 39.1 1.0

Sodium binding site 2 out of 2 in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:30.0 occ:1.00 O D:GLU109 2.3 39.7 1.0 OD1 D:ASP99 2.3 37.1 1.0 O D:HOH304 2.3 31.0 1.0 OE2 D:GLU111 2.4 41.9 1.0 O B:HOH541 2.7 38.3 1.0 OE1 D:GLU111 2.9 38.3 1.0 CD D:GLU111 3.0 40.4 1.0 HB2 D:GLU109 3.2 53.7 1.0 H D:LEU100 3.3 31.4 1.0 CG D:ASP99 3.4 36.3 1.0 C D:GLU109 3.4 39.5 1.0 HA D:ASP99 3.5 37.6 1.0 O D:HOH316 3.7 36.0 1.0 H D:GLU109 3.7 48.5 1.0 N D:LEU100 3.8 26.2 1.0 CB D:GLU109 3.9 44.8 1.0 CA D:GLU109 4.0 41.8 1.0 CA D:ASP99 4.1 31.4 1.0 HB3 D:GLU109 4.1 53.7 1.0 HB3 D:LEU100 4.1 30.7 1.0 CB D:ASP99 4.2 33.2 1.0 N D:GLU109 4.2 40.4 1.0 HA D:TYR110 4.2 44.8 1.0 O D:HOH323 4.2 42.9 1.0 C D:ASP99 4.3 28.8 1.0 OD2 D:ASP99 4.3 37.3 1.0 HB2 D:ASP99 4.3 39.8 1.0 HB3 D:SER108 4.3 61.4 1.0 O B:GLY296 4.4 29.1 1.0 O D:LEU100 4.4 27.3 1.0 N D:TYR110 4.5 37.3 1.0 H D:GLU111 4.5 41.8 1.0 CG D:GLU111 4.5 39.3 1.0 O D:HOH327 4.6 49.3 1.0 HG1 B:THR298 4.7 34.7 1.0 CA D:LEU100 4.8 25.2 1.0 CA D:TYR110 4.8 37.3 1.0 HG3 D:GLU111 4.8 47.2 1.0 CB D:LEU100 4.8 25.6 1.0 OG1 B:THR298 4.9 29.0 1.0 N D:GLU111 4.9 34.9 1.0 HA B:THR298 4.9 30.2 1.0 HG2 D:GLU111 4.9 47.2 1.0 HA D:GLU109 5.0 50.1 1.0

C.E.Stebbins, A.Hempelmann. Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB9) To Be Published.