Magnesium in PDB 6jim: Viral Helicase Protein

The structure of Viral Helicase Protein, PDB code: 6jim was solved by Y.S.Law, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.32 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.888, 53.905, 100.718, 96.93, 94.07, 97.04
R / Rfree (%)	17.7 / 21.5

The structure of Viral Helicase Protein also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Magnesium atom in the Viral Helicase Protein (pdb code 6jim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Viral Helicase Protein, PDB code: 6jim:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:29.2 occ:1.00 F A:F2006 1.8 26.8 1.0 O A:HOH2107 1.8 27.5 1.0 O A:HOH2106 1.8 28.9 1.0 OG A:SER193 1.9 26.5 1.0 O3B A:ADP2001 1.9 28.1 1.0 O A:HOH2123 2.0 26.5 1.0 CB A:SER193 2.9 27.1 1.0 PB A:ADP2001 3.1 27.8 1.0 O1B A:ADP2001 3.4 27.4 1.0 AL A:AL2003 3.5 25.5 1.0 F A:F2004 3.6 28.4 1.0 OE2 A:GLU253 3.7 28.3 1.0 OD2 A:ASP252 3.7 32.3 1.0 O1A A:ADP2001 3.8 30.5 1.0 N A:SER193 3.8 26.3 1.0 CA A:SER193 3.9 25.2 1.0 OD1 A:ASP252 4.0 32.7 1.0 O3A A:ADP2001 4.0 28.2 1.0 F A:F2005 4.1 29.0 1.0 O A:HOH2142 4.2 36.0 1.0 O A:GLY384 4.2 34.3 1.0 CA A:GLY384 4.2 25.1 1.0 O2B A:ADP2001 4.2 29.2 1.0 OD1 A:ASN213 4.2 33.0 1.0 CG A:ASP252 4.3 37.1 1.0 PA A:ADP2001 4.3 30.0 1.0 O A:HOH2126 4.3 25.3 1.0 O A:HOH2139 4.3 32.2 1.0 CD A:GLU253 4.6 34.4 1.0 C A:GLY384 4.7 33.7 1.0 O2A A:ADP2001 4.7 28.2 1.0 C A:LYS192 4.9 29.6 1.0 CG A:ASN213 5.0 29.8 1.0

Magnesium binding site 2 out of 2 in the Viral Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Viral Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:26.5 occ:1.00 O1B B:ADP2001 1.8 25.0 1.0 O B:HOH2136 1.8 30.9 1.0 OG B:SER193 1.9 29.6 1.0 F B:F2006 1.9 30.4 1.0 O B:HOH2114 1.9 24.9 1.0 O B:HOH2117 2.0 28.2 1.0 CB B:SER193 3.0 28.0 1.0 PB B:ADP2001 3.0 29.2 1.0 O3B B:ADP2001 3.5 27.5 1.0 AL B:AL2003 3.5 28.6 1.0 N B:SER193 3.6 27.7 1.0 F B:F2004 3.8 29.8 1.0 OD2 B:ASP252 3.8 33.7 1.0 OE2 B:GLU253 3.8 35.1 1.0 OD1 B:ASP252 3.9 35.5 1.0 CA B:SER193 3.9 25.8 1.0 O2A B:ADP2001 3.9 39.0 1.0 O2B B:ADP2001 4.0 33.8 1.0 O3A B:ADP2001 4.1 30.6 1.0 F B:F2005 4.1 30.3 1.0 O B:HOH2128 4.2 33.5 1.0 CG B:ASP252 4.2 33.7 1.0 O B:GLY384 4.4 32.4 1.0 O B:HOH2113 4.4 26.3 1.0 PA B:ADP2001 4.4 30.3 1.0 CA B:GLY384 4.4 25.1 1.0 OD1 B:ASN213 4.4 34.9 1.0 O B:HOH2124 4.4 39.4 1.0 CD B:GLU253 4.6 30.5 1.0 C B:LYS192 4.7 32.4 1.0 O1A B:ADP2001 4.8 31.1 1.0 CB B:LYS192 4.8 27.3 1.0 C B:GLY384 4.9 32.2 1.0

Y.S.Law, A.Utt, Y.B.Tan, J.Zheng, S.Wang, M.W.Chen, P.R.Griffin, A.Merits, D.Luo. Structural Insights Into Rna Recognition By the Chikungunya Virus NSP2 Helicase. Proc.Natl.Acad.Sci.Usa V. 116 9558 2019.
ISSN: ESSN 1091-6490
PubMed: 31000599
DOI: 10.1073/PNAS.1900656116