Magnesium in PDB 5k8t: Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion

The structure of Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion, PDB code: 5k8t was solved by X.Cao, Y.Li, T.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.40 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.950, 53.420, 65.390, 90.00, 105.04, 90.00
R / Rfree (%)	18.5 / 24.7

The structure of Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion (pdb code 5k8t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion, PDB code: 5k8t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion


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 Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:12.9 occ:1.00 O A:HOH823 1.9 35.3 1.0 O3G A:GSP701 1.9 32.7 1.0 O2B A:GSP701 2.1 32.8 1.0 OE2 A:GLU286 2.1 27.4 1.0 O A:HOH893 2.2 32.9 1.0 OG1 A:THR201 2.3 27.8 1.0 CD A:GLU286 3.2 34.2 1.0 PG A:GSP701 3.2 40.7 1.0 CB A:THR201 3.4 33.2 1.0 PB A:GSP701 3.4 34.3 1.0 OE1 A:GLU286 3.6 35.2 1.0 O3B A:GSP701 3.6 35.5 1.0 O2A A:GSP701 3.9 44.9 1.0 O A:HOH842 3.9 38.9 1.0 N A:THR201 4.0 29.9 1.0 OD1 A:ASP285 4.0 33.0 1.0 OD2 A:ASP285 4.2 32.7 1.0 O2G A:GSP701 4.2 40.0 1.0 O A:HOH859 4.2 33.4 1.0 CA A:THR201 4.3 29.4 1.0 O A:HOH860 4.3 32.5 1.0 O1B A:GSP701 4.3 40.3 1.0 S1G A:GSP701 4.4 55.8 1.0 CG2 A:THR201 4.4 38.6 1.0 CG A:ASP285 4.5 39.4 1.0 CG A:GLU286 4.5 31.8 1.0 O A:HOH908 4.5 37.3 1.0 O3A A:GSP701 4.6 35.1 1.0 O A:HOH894 4.6 25.8 1.0 PA A:GSP701 4.6 53.6 1.0 CB A:LYS200 4.7 34.0 1.0 CE A:LYS200 4.7 33.8 1.0 O1A A:GSP701 4.9 45.2 1.0 CA A:GLY415 4.9 31.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion


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 Zikv NS3 Helicase in Complex with Gtp-Gammar S and An Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:19.2 occ:1.00 O A:HOH934 2.0 35.4 1.0 O A:HOH838 2.1 43.0 1.0 NE2 A:HIS195 2.2 28.7 1.0 CE1 A:HIS195 3.1 30.1 1.0 CD2 A:HIS195 3.2 29.4 1.0 OD2 A:ASP328 4.0 35.6 1.0 OD1 A:ASN330 4.2 31.7 1.0 ND1 A:HIS195 4.3 24.3 1.0 CG A:HIS195 4.4 28.3 1.0 O A:HOH847 4.5 37.6 1.0 CG A:ASP328 4.8 40.3 1.0 CB A:ALA198 4.8 35.0 1.0 O A:SER329 4.9 26.2 1.0

X.Cao, Y.Li, X.Jin, Y.Li, F.Guo, T.Jin. Molecular Mechanism of Divalent-Metal-Induced Activation of NS3 Helicase and Insights Into Zika Virus Inhibitor Design. Nucleic Acids Res. V. 44 10505 2016.
ISSN: ESSN 1362-4962
PubMed: 27915293
DOI: 10.1093/NAR/GKW941