Magnesium in PDB 4miw: High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase

All present enzymatic activity of High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase:
2.7.7.48;

The structure of High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase, PDB code: 4miw was solved by G.D.Wallat, Q.Huang, W.Wang, H.Dong, H.Ly, Y.Liang, C.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.81 / 1.72
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.720, 57.720, 134.510, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 17.8

The binding sites of Magnesium atom in the High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase (pdb code 4miw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase, PDB code: 4miw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:15.4 occ:1.00 OD2 A:ASP89 2.3 10.9 1.0 O A:CYS103 2.3 8.7 1.0 O A:HOH407 2.4 19.6 1.0 O A:HOH438 2.5 18.7 1.0 O A:HOH408 2.5 23.0 1.0 H A:CYS103 3.1 8.6 1.0 CG A:ASP89 3.2 9.0 1.0 OD1 A:ASP89 3.3 9.2 1.0 C A:CYS103 3.5 6.5 1.0 O A:HOH334 3.5 25.4 1.0 HG A:CYS103 3.7 23.6 1.0 O A:HOH450 3.7 32.5 1.0 N A:CYS103 3.8 7.2 1.0 MG A:MG202 3.8 12.7 1.0 OE1 A:GLU102 4.0 16.2 1.0 O A:HOH412 4.1 26.6 1.0 CA A:CYS103 4.2 6.6 1.0 SG A:CYS103 4.2 19.7 1.0 HA A:PHE104 4.2 8.5 1.0 O A:HOH405 4.3 11.8 1.0 HA A:GLU102 4.4 8.2 1.0 HB3 A:PHE104 4.4 12.1 1.0 HG2 A:GLU51 4.4 13.7 1.0 OE2 A:GLU51 4.4 14.5 1.0 HB3 A:GLU102 4.5 10.4 1.0 O A:HOH399 4.5 42.2 1.0 CB A:ASP89 4.5 8.8 1.0 N A:PHE104 4.6 8.4 1.0 O A:HOH404 4.6 18.9 1.0 HB2 A:ASP89 4.7 10.5 1.0 C A:GLU102 4.8 8.3 1.0 CA A:PHE104 4.8 7.1 1.0 CB A:CYS103 4.8 14.9 1.0 HB3 A:ASP89 4.9 10.5 1.0 CA A:GLU102 4.9 6.8 1.0 HA A:CYS103 5.0 7.9 1.0

Magnesium binding site 2 out of 2 in the High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:12.7 occ:1.00 OD1 A:ASP89 1.9 9.2 1.0 O A:HOH405 2.1 11.8 1.0 O A:HOH438 2.1 18.7 1.0 O A:HOH404 2.1 18.9 1.0 O A:HOH437 2.2 14.6 1.0 O A:HOH406 2.3 25.7 1.0 CG A:ASP89 3.1 9.0 1.0 O A:HOH454 3.1 46.5 1.0 HA A:ASP89 3.6 7.2 1.0 OD2 A:ASP89 3.7 10.9 1.0 O A:HOH450 3.7 32.5 1.0 MG A:MG201 3.8 15.4 1.0 OE2 A:GLU51 4.0 14.5 1.0 O A:HOH408 4.1 23.0 1.0 CA A:ASP89 4.2 6.0 1.0 CB A:ASP89 4.2 8.8 1.0 O A:VAL87 4.2 12.2 1.0 N A:ASP89 4.3 6.0 1.0 OE1 A:GLU102 4.3 16.2 1.0 O A:HOH439 4.3 23.0 1.0 O A:PRO88 4.4 8.3 1.0 C A:PRO88 4.4 7.9 1.0 H A:ASP89 4.6 7.2 1.0 HB3 A:ASP89 4.7 10.5 1.0 HG12 A:VAL87 4.7 12.6 1.0 CD A:GLU51 4.7 18.7 1.0 HB2 A:ASP89 4.9 10.5 1.0 O A:HOH399 4.9 42.2 1.0 O A:HOH325 4.9 22.2 1.0 HA A:PRO88 4.9 9.4 1.0 OE1 A:GLU51 5.0 14.1 1.0

G.D.Wallat, Q.Huang, W.Wang, H.Dong, H.Ly, Y.Liang, C.Dong. High-Resolution Structure of the N-Terminal Endonuclease Domain of the Lassa Virus L Polymerase in Complex with Magnesium Ions. Plos One V. 9 87577 2014.
ISSN: ESSN 1932-6203
PubMed: 24516554
DOI: 10.1371/JOURNAL.PONE.0087577