Sodium in PDB 7nqa: Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution

The structure of Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution, PDB code: 7nqa was solved by M.Sola-Colom, S.Trakhanov, D.Goerlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.76, 96.63, 100.87, 90, 90, 90
R / Rfree (%)	17.6 / 22.6

The binding sites of Sodium atom in the Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution (pdb code 7nqa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution, PDB code: 7nqa:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na202 b:23.4 occ:0.63 OD1 D:ASP101 2.7 30.7 1.0 O D:GLY107 2.9 30.4 1.0 NH1 D:ARG30 3.1 34.2 1.0 CD A:GLN845 3.2 30.1 1.0 OE1 A:GLN845 3.2 31.1 1.0 NE2 A:GLN845 3.4 28.0 1.0 OG1 D:THR103 3.5 32.3 1.0 CD D:ARG30 3.5 30.4 1.0 CG D:ASP101 3.5 27.8 1.0 CE A:LYS844 3.5 57.0 1.0 OD2 D:ASP101 3.6 28.7 1.0 CB D:THR103 3.7 36.1 1.0 NZ A:LYS844 3.9 49.9 1.0 CG A:GLN845 3.9 23.2 1.0 C D:GLY107 4.0 33.5 1.0 CZ D:ARG30 4.0 31.4 1.0 CG2 D:THR103 4.1 24.6 1.0 NE D:ARG30 4.2 34.3 1.0 CD1 D:TYR108 4.4 27.9 1.0 CA D:TYR108 4.5 36.2 1.0 N D:TYR108 4.6 31.0 1.0 N D:GLY107 4.7 31.2 1.0 CG D:ARG30 4.7 32.4 1.0 CB A:ALA841 4.9 28.2 1.0 CD A:LYS844 5.0 58.9 1.0 CB D:ASP101 5.0 28.4 1.0 CA D:GLY107 5.0 35.0 1.0

Sodium binding site 2 out of 3 in the Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:25.0 occ:0.63 ND2 C:ASN97 2.4 39.6 1.0 O C:ASP34 2.9 32.0 1.0 CE B:LYS817 3.0 40.4 1.0 O C:HOH321 3.0 42.9 1.0 C C:ASP34 3.3 28.1 1.0 O C:ASN97 3.4 28.6 1.0 CD B:LYS817 3.5 33.9 1.0 CG C:ASN97 3.6 41.4 1.0 CB C:ASP34 3.6 26.9 1.0 N C:VAL35 3.7 34.3 1.0 CA C:VAL35 3.7 33.2 1.0 C C:VAL35 3.9 38.7 1.0 CG C:GLU99 4.0 32.5 1.0 N C:GLY36 4.0 33.2 1.0 CG B:LYS817 4.0 31.3 1.0 C C:ASN97 4.0 29.5 1.0 N C:GLU99 4.1 25.1 1.0 CB C:ASN97 4.1 31.6 1.0 CA C:ASP34 4.1 28.6 1.0 NZ B:LYS817 4.2 42.3 1.0 CD C:GLU99 4.6 33.0 1.0 O C:VAL35 4.6 36.7 1.0 CB C:GLU99 4.6 32.1 1.0 N C:ILE98 4.7 31.3 1.0 OD1 C:ASN97 4.7 47.1 1.0 C C:ILE98 4.7 27.0 1.0 CA C:ASN97 4.7 33.0 1.0 CA C:ILE98 4.8 29.1 1.0 OE2 C:GLU51 4.8 36.4 1.0 OH C:TYR38 4.8 39.0 1.0 CA C:GLY36 4.8 27.7 1.0 CB B:LYS817 4.9 29.0 1.0 OE2 C:GLU99 4.9 41.0 1.0 CA C:GLU99 4.9 33.7 1.0 CG C:ASP34 5.0 35.4 1.0

Sodium binding site 3 out of 3 in the Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of Nucleoporin-98 and Nanobody MS98-27 Solved at 1.85A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:49.9 occ:0.78 O C:LYS57 2.7 46.5 1.0 OE1 C:GLU51 3.0 49.6 1.0 OG1 C:THR59 3.2 52.9 1.0 O C:GLU51 3.3 41.8 1.0 N C:THR59 3.3 53.4 1.0 CB C:THR59 3.3 46.0 1.0 CG2 C:THR53 3.4 36.1 1.0 C C:LYS57 3.5 47.0 1.0 CG C:GLU51 3.5 44.9 1.0 CD C:GLU51 3.7 42.3 1.0 C C:GLU51 3.7 42.5 1.0 CB C:GLU51 3.7 39.0 1.0 C C:VAL58 3.8 51.8 1.0 CE C:LYS57 3.8 61.5 1.0 CA C:THR59 3.9 50.8 1.0 CA C:VAL58 3.9 51.4 1.0 N C:THR53 4.0 46.5 1.0 N C:VAL58 4.0 50.2 1.0 CB C:LYS57 4.2 50.6 1.0 CG C:LYS57 4.2 57.2 1.0 N C:ILE52 4.2 41.5 1.0 CA C:GLU51 4.3 39.6 1.0 CA C:ILE52 4.3 46.7 1.0 CA C:LYS57 4.4 48.5 1.0 C C:ILE52 4.5 40.6 1.0 O C:VAL58 4.6 50.9 1.0 CB C:THR53 4.6 39.0 1.0 CD C:LYS57 4.7 60.7 1.0 CG2 C:THR59 4.7 60.1 1.0 CA C:THR53 4.8 41.9 1.0 OE2 C:GLU51 4.9 36.4 1.0 NZ C:LYS57 4.9 69.1 1.0 N C:GLU51 4.9 38.0 1.0

M.Sola-Colom, S.Trakhanov, D.Goerlich. Crystal Structure of Nucleoporin-98 Nanobody MS98-6 Complex Solved at 2.2A Resolution To Be Published.