Sodium in PDB 7aqz: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB14)

The structure of Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB14), PDB code: 7aqz was solved by C.E.Stebbins, A.Hempelmann, M.Vanstraaten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.24 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.542, 95.95, 124.337, 90, 90, 90
R / Rfree (%)	15.1 / 17.2

The binding sites of Sodium atom in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB14) (pdb code 7aqz). 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(NB14), PDB code: 7aqz:
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(NB14)


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(NB14) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:14.5 occ:1.00 O C:VAL110 2.2 19.6 1.0 OD1 C:ASP99 2.3 18.2 1.0 O C:HOH332 2.3 16.5 1.0 O B:HOH536 2.4 26.6 1.0 OE2 C:GLU112 2.4 22.7 1.0 O B:HOH572 2.5 20.0 1.0 OE1 C:GLU112 2.8 21.2 1.0 CD C:GLU112 3.0 20.8 1.0 CG C:ASP99 3.4 16.4 1.0 C C:VAL110 3.4 18.4 1.0 H C:LEU100 3.4 18.3 1.0 H C:VAL110 3.5 25.2 1.0 HB C:VAL110 3.5 27.4 1.0 HA C:ASP99 3.6 19.0 1.0 O C:HOH367 3.9 25.9 1.0 N C:LEU100 3.9 15.2 1.0 HB3 C:LEU100 4.1 17.9 1.0 N C:VAL110 4.1 21.0 1.0 CA C:VAL110 4.1 20.1 1.0 HA C:TYR111 4.1 21.7 1.0 CA C:ASP99 4.2 15.8 1.0 CB C:VAL110 4.2 22.8 1.0 OD2 C:ASP99 4.3 18.7 1.0 O B:GLY296 4.3 19.5 1.0 CB C:ASP99 4.3 15.6 1.0 O C:HOH320 4.3 35.1 1.0 HG12 C:VAL110 4.3 30.2 1.0 O C:LEU100 4.4 16.3 1.0 H C:GLU112 4.4 22.2 1.0 C C:ASP99 4.4 15.8 1.0 O C:HOH335 4.4 29.9 1.0 CG C:GLU112 4.4 22.2 1.0 HB2 C:ASP99 4.5 18.7 1.0 HG1 B:THR298 4.5 19.7 1.0 N C:TYR111 4.5 17.9 1.0 HG3 C:GLU112 4.7 26.7 1.0 CA C:TYR111 4.7 18.1 1.0 OG1 B:THR298 4.8 16.4 1.0 N C:GLU112 4.8 18.5 1.0 CA C:LEU100 4.8 14.6 1.0 CB C:LEU100 4.8 14.9 1.0 CG1 C:VAL110 4.9 25.2 1.0 HG2 C:GLU112 4.9 26.7 1.0 HA B:THR298 4.9 19.6 1.0 O B:HOH586 5.0 25.1 1.0

Sodium binding site 2 out of 2 in the Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in Complex with Nanobody VSG2(NB14)


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(NB14) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:21.9 occ:1.00 O A:HOH587 2.2 36.0 1.0 OE2 D:GLU112 2.2 37.2 1.0 OD1 D:ASP99 2.2 33.8 1.0 O A:HOH569 2.4 23.4 1.0 O D:VAL110 2.5 36.9 1.0 O A:HOH535 2.5 28.2 1.0 CD D:GLU112 2.9 35.7 1.0 OE1 D:GLU112 2.9 36.9 1.0 HB D:VAL110 3.2 48.0 1.0 H D:VAL110 3.3 46.2 1.0 CG D:ASP99 3.4 32.5 1.0 C D:VAL110 3.5 35.2 1.0 H D:LEU100 3.6 31.1 1.0 HA D:ASP99 3.8 34.6 1.0 HG12 D:VAL110 3.9 50.0 1.0 CB D:VAL110 3.9 40.0 1.0 N D:VAL110 4.0 38.5 1.0 CA D:VAL110 4.0 37.6 1.0 N D:LEU100 4.1 25.9 1.0 HB3 D:LEU100 4.1 26.6 1.0 O D:HOH619 4.2 38.9 1.0 OD2 D:ASP99 4.2 34.6 1.0 O A:GLY296 4.2 28.8 1.0 O D:HOH618 4.3 36.7 1.0 CB D:ASP99 4.3 30.7 1.0 CG D:GLU112 4.3 34.3 1.0 HA D:TYR111 4.4 42.8 1.0 CA D:ASP99 4.4 28.9 1.0 H D:GLU112 4.4 40.7 1.0 CG1 D:VAL110 4.5 41.7 1.0 HG3 D:GLU112 4.5 41.1 1.0 O D:LEU100 4.5 23.2 1.0 HG1 A:THR298 4.5 27.2 1.0 C D:ASP99 4.6 27.9 1.0 N D:TYR111 4.6 35.3 1.0 OG1 A:THR298 4.7 22.7 1.0 HB3 D:SER109 4.8 56.4 1.0 N D:GLU112 4.8 34.0 1.0 HG2 D:GLU112 4.8 41.1 1.0 CA D:TYR111 4.9 35.6 1.0 HA A:THR298 4.9 25.9 1.0 CB D:LEU100 4.9 22.1 1.0 CA D:LEU100 5.0 23.7 1.0 OE2 A:GLU290 5.0 26.1 1.0

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