Calcium in PDB 6gh8: Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2

The structure of Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2, PDB code: 6gh8 was solved by H.Cohen-Dvashi, I.Kilimnik, R.Diskin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.00 / 2.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.808, 59.294, 83.567, 90.00, 90.00, 90.00
R / Rfree (%)	26.6 / 31.2

The binding sites of Calcium atom in the Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2 (pdb code 6gh8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2, PDB code: 6gh8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:47.0 occ:1.00 OD2 A:ASP86 2.3 56.1 1.0 O A:HOH301 2.3 23.9 1.0 O A:ARG130 2.3 35.9 1.0 OD1 A:ASP127 2.3 47.1 1.0 OD1 A:ASP86 2.4 51.2 1.0 OE2 A:GLU79 2.4 68.0 1.0 CG A:ASP86 2.5 50.5 1.0 O A:HOH305 2.7 40.4 1.0 C A:ARG130 3.5 47.8 1.0 CD A:GLU79 3.6 67.3 1.0 CG A:ASP127 3.6 49.4 1.0 CB A:ASP86 3.8 47.5 1.0 N A:ARG130 4.0 56.2 1.0 CB A:GLU79 4.1 55.6 1.0 N A:ASP127 4.1 48.6 1.0 OH A:TYR49 4.1 61.3 1.0 OG A:SER126 4.3 64.7 1.0 CA A:ARG130 4.4 53.5 1.0 CG A:GLU79 4.4 60.3 1.0 OD2 A:ASP127 4.4 42.9 1.0 N A:ASP86 4.5 50.0 1.0 OE1 A:GLU79 4.5 70.5 1.0 N A:GLN131 4.5 36.7 1.0 CE1 A:TYR49 4.5 53.2 1.0 CB A:ASP127 4.5 53.4 1.0 OE1 A:GLN131 4.6 38.9 1.0 CA A:ASP86 4.6 47.3 1.0 CG A:ARG130 4.6 40.4 1.0 CB A:TYR85 4.6 43.8 1.0 CA A:GLN131 4.7 44.2 1.0 CA A:ASP127 4.7 46.9 1.0 O A:ASP127 4.8 46.7 1.0 C A:ALA129 4.8 62.9 1.0 C A:ASP127 4.8 43.1 1.0 NZ D:LYS110 4.8 55.4 1.0 CZ A:TYR49 4.8 58.5 1.0 N A:ALA129 4.9 62.5 1.0 CG A:GLN131 5.0 36.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of GP1 Domain of Lujo Virus in Complex with the First Cub Domain of Neuropilin-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:51.7 occ:1.00 OD2 C:ASP127 2.0 74.3 1.0 O C:ARG130 2.3 41.9 1.0 OE1 C:GLU79 2.5 58.6 1.0 OD2 C:ASP86 2.5 47.6 1.0 OD1 C:ASP86 2.8 47.1 1.0 CG C:ASP127 2.9 64.0 1.0 CG C:ASP86 2.9 48.3 1.0 N C:ARG130 3.1 69.3 1.0 C C:ARG130 3.2 42.9 1.0 OD1 C:ASP127 3.4 63.5 1.0 CD C:GLU79 3.7 58.5 1.0 CA C:ARG130 3.7 55.8 1.0 C C:ALA129 3.8 95.4 1.0 N C:ASP127 4.0 50.3 1.0 N C:ALA129 4.0 99.3 1.0 NE2 C:GLN131 4.0 42.3 1.0 CB C:ASP127 4.0 59.3 1.0 C C:ASP127 4.2 49.5 1.0 NZ B:LYS110 4.2 80.3 1.0 O C:ASP127 4.3 46.8 1.0 CA C:ALA129 4.3 99.2 1.0 CA C:ASP127 4.3 50.4 1.0 CB C:ASP86 4.3 41.0 1.0 OE2 C:GLU79 4.4 63.7 1.0 CB C:ARG130 4.4 58.2 1.0 N C:GLN131 4.4 42.1 1.0 OG C:SER126 4.5 72.5 1.0 O C:ALA129 4.5 0.8 1.0 CB C:ALA129 4.5 0.1 1.0 CB C:GLU79 4.6 48.4 1.0 CG C:GLU79 4.7 50.3 1.0 N C:TYR128 4.7 54.7 1.0 OH C:TYR49 4.8 40.2 1.0 CB C:TYR85 4.9 47.1 1.0 CD C:GLN131 4.9 41.8 1.0 C C:TYR128 4.9 77.4 1.0 CE1 C:TYR49 4.9 41.7 1.0 CA C:GLN131 4.9 40.0 1.0 N C:ASP86 4.9 45.8 1.0

H.Cohen-Dvashi, I.Kilimnik, R.Diskin. Structural Basis For Receptor Recognition By Lujo Virus. Nat Microbiol V. 3 1153 2018.
ISSN: ESSN 2058-5276
PubMed: 30150732
DOI: 10.1038/S41564-018-0224-5