Magnesium in PDB 9ftf: Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein

All present enzymatic activity of Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein:
2.1.1.375; 2.7.7.48; 2.7.7.88;

The structure of Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein, PDB code: 9ftf was solved by E.Balikci, F.Gunl, L.Carrique, J.R.Keown, E.Fodor, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.80 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.76, 50.54, 61.1, 90, 95.71, 90
R / Rfree (%)	19.3 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein (pdb code 9ftf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein, PDB code: 9ftf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1801 b:46.7 occ:1.00 OG A:SER1529 2.0 39.3 1.0 O A:HOH2048 2.2 38.6 1.0 O A:SER1523 2.3 36.3 1.0 OD1 A:ASN1526 2.5 44.1 1.0 O A:HOH1994 2.7 48.0 1.0 CG A:ASN1526 3.2 43.6 1.0 CB A:SER1529 3.3 37.7 1.0 C A:SER1523 3.4 42.3 1.0 ND2 A:ASN1526 3.4 40.4 1.0 N A:SER1529 3.6 38.5 1.0 CA A:SER1529 3.8 42.7 1.0 N A:SER1523 4.1 43.4 1.0 CA A:ASP1524 4.1 43.4 1.0 N A:ASP1524 4.1 36.7 1.0 CA A:SER1523 4.4 38.9 1.0 CB A:ASN1528 4.5 43.3 1.0 C A:ASN1528 4.5 44.0 1.0 C A:ASP1524 4.5 44.5 1.0 CB A:ASN1526 4.6 35.9 1.0 N A:ASN1526 4.6 37.9 1.0 OD1 A:ASP1524 4.8 62.1 1.0 O A:ASN1526 4.8 34.2 1.0 O A:HOH2003 4.9 45.4 1.0 OD2 A:ASP1522 4.9 75.3 1.0 N A:ASP1525 4.9 35.7 1.0 CA A:ASN1528 4.9 40.6 1.0 O A:ASP1524 5.0 35.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1802 b:45.9 occ:1.00 OD2 A:ASP1513 2.3 48.5 1.0 O A:HOH1905 2.4 38.7 1.0 O A:ASP1511 3.1 35.1 1.0 CG A:ASP1513 3.3 40.0 1.0 OD1 A:ASP1513 3.7 39.2 1.0 C A:ASP1511 4.2 34.8 1.0 O A:HOH2077 4.2 39.7 1.0 CB A:ASP1513 4.5 37.5 1.0 O A:HOH1931 4.6 42.7 1.0 O A:HOH2073 4.8 50.8 1.0 C A:LYS1512 4.8 35.5 1.0 N A:ASP1513 4.8 35.5 1.0 CA A:LYS1512 4.9 39.7 1.0 N A:LYS1512 5.0 33.8 1.0 O A:HOH1967 5.0 38.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Connecting Domain of the Nipah Virus Large Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:41.4 occ:1.00 O A:GLN1652 2.1 35.6 1.0 O A:HOH2011 2.4 39.6 1.0 OE1 A:GLU1654 2.4 43.7 1.0 C A:GLN1652 3.2 32.0 1.0 CD A:GLU1654 3.5 31.7 1.0 OE2 A:GLU1654 3.9 37.8 1.0 CA A:GLN1652 4.1 30.4 1.0 N A:ASP1653 4.1 35.1 1.0 N A:GLU1654 4.2 29.5 1.0 CA A:ASP1653 4.2 31.5 1.0 CB A:GLN1652 4.3 40.7 1.0 C A:ASP1653 4.7 33.6 1.0 CG A:GLU1654 4.8 33.5 1.0 O A:HOH2078 4.8 43.2 1.0 CB A:GLU1654 5.0 33.3 1.0

E.Balikci, F.Gunl, L.Carrique, J.R.Keown, E.Fodor, J.M.Grimes. Structure of the Nipah Virus Polymerase Complex. Embo J. 2024.
ISSN: ESSN 1460-2075
PubMed: 39739115
DOI: 10.1038/S44318-024-00321-Z