Magnesium in PDB 2xi3: Hcv-H77 NS5B Polymerase Complexed with Gtp

All present enzymatic activity of Hcv-H77 NS5B Polymerase Complexed with Gtp:
2.7.7.48;

The structure of Hcv-H77 NS5B Polymerase Complexed with Gtp, PDB code: 2xi3 was solved by D.Harrus, N.Ahmed-El-Sayed, P.C.Simister, S.Miller, M.Triconnet, C.H.Hagedorn, K.Mahias, F.A.Rey, T.Astier-Gin, S.Bressanelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.654 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.010, 91.898, 61.054, 89.62, 99.74, 92.95
R / Rfree (%)	16.98 / 19.76

The binding sites of Magnesium atom in the Hcv-H77 NS5B Polymerase Complexed with Gtp (pdb code 2xi3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Hcv-H77 NS5B Polymerase Complexed with Gtp, PDB code: 2xi3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Hcv-H77 NS5B Polymerase Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hcv-H77 NS5B Polymerase Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:39.7 occ:0.84 O A:HOH2281 2.1 40.6 1.0 O A:HOH2396 2.1 46.0 1.0 O A:HOH2394 2.1 27.2 1.0 O1B A:GTP1001 2.1 23.4 0.8 O1G A:GTP1001 2.3 39.5 0.8 PG A:GTP1001 3.1 32.4 0.8 PB A:GTP1001 3.3 23.6 0.8 O2G A:GTP1001 3.3 33.7 0.8 O3B A:GTP1001 3.5 21.4 0.8 NH2 A:ARG158 3.9 28.0 1.0 O3A A:GTP1001 3.9 26.0 0.8 OG A:SER367 4.1 29.8 1.0 O5' A:GTP1002 4.5 52.5 0.9 O3G A:GTP1001 4.5 35.5 0.8 O2B A:GTP1001 4.5 17.1 0.8 O4' A:GTP1002 4.6 32.2 0.9 C4' A:GTP1002 4.6 39.4 0.9 O1A A:GTP1002 4.7 0.6 0.9 NZ A:LYS155 4.9 60.3 1.0

Magnesium binding site 2 out of 5 in the Hcv-H77 NS5B Polymerase Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hcv-H77 NS5B Polymerase Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:28.9 occ:0.50 O A:THR221 2.1 18.1 1.0 O A:HOH2187 2.1 28.7 1.0 OD1 A:ASP220 2.3 31.8 1.0 O2A A:GTP1002 2.5 0.2 0.9 O A:HOH2242 3.0 34.2 1.0 C A:THR221 3.3 14.9 1.0 O3A A:GTP1002 3.5 0.8 0.9 CG A:ASP220 3.5 31.1 1.0 PA A:GTP1002 3.5 0.8 0.9 N A:THR221 3.8 14.3 1.0 O A:HOH2186 4.0 41.8 1.0 C5' A:GTP1002 4.0 46.7 0.9 OD2 A:ASP220 4.1 39.1 1.0 CA A:THR221 4.1 9.9 1.0 C A:ASP220 4.2 18.1 1.0 N A:CYS223 4.2 17.7 1.0 O5' A:GTP1002 4.2 52.5 0.9 N A:ARG222 4.3 15.7 1.0 CA A:ARG222 4.5 15.2 1.0 CA A:ASP220 4.6 14.4 1.0 CB A:ASP220 4.6 18.5 1.0 CB A:THR221 4.6 14.6 1.0 OD2 A:ASP318 4.6 42.3 1.0 N A:PHE224 4.7 13.0 1.0 C A:ARG222 4.7 14.4 1.0 O1A A:GTP1002 4.8 0.6 0.9 O A:ASP220 4.8 23.1 1.0 PB A:GTP1002 4.9 92.0 0.9 CG A:ASP318 5.0 29.9 1.0

Magnesium binding site 3 out of 5 in the Hcv-H77 NS5B Polymerase Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hcv-H77 NS5B Polymerase Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:25.5 occ:0.90 OD1 A:ASP359 2.2 28.1 1.0 O A:TYR358 2.4 12.8 1.0 C A:TYR358 3.3 12.0 1.0 CG A:ASP359 3.4 28.0 1.0 CA A:ASP359 3.9 16.2 1.0 N A:ASP359 3.9 13.3 1.0 O A:HOH2182 4.1 17.4 1.0 CB A:ASP359 4.2 18.1 1.0 CB A:TYR358 4.3 11.1 1.0 OD2 A:ASP359 4.3 35.8 1.0 CA A:TYR358 4.4 12.5 1.0

Magnesium binding site 4 out of 5 in the Hcv-H77 NS5B Polymerase Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hcv-H77 NS5B Polymerase Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1005 b:37.4 occ:0.78 O B:HOH2394 2.1 41.2 1.0 O B:HOH2393 2.1 49.7 1.0 O1B B:GTP1001 2.1 22.5 0.7 O2G B:GTP1001 2.4 34.8 0.7 PG B:GTP1001 3.3 35.8 0.7 PB B:GTP1001 3.4 23.1 0.7 O1G B:GTP1001 3.5 26.8 0.7 NH2 B:ARG158 3.6 29.1 1.0 O3B B:GTP1001 3.7 23.3 0.7 O3A B:GTP1001 4.1 40.5 0.7 NZ B:LYS155 4.1 54.1 1.0 OG B:SER367 4.5 35.4 1.0 O1A B:GTP1002 4.6 0.0 0.7 O2B B:GTP1001 4.6 17.0 0.7 O5' B:GTP1002 4.6 57.5 0.7 O3G B:GTP1001 4.7 37.5 0.7 O4' B:GTP1002 4.7 42.6 0.7 C4' B:GTP1002 4.9 47.6 0.7 CZ B:ARG158 4.9 30.7 1.0

Magnesium binding site 5 out of 5 in the Hcv-H77 NS5B Polymerase Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hcv-H77 NS5B Polymerase Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1006 b:34.7 occ:0.51 OD1 B:ASP220 2.1 33.6 1.0 O B:THR221 2.2 20.9 1.0 O2A B:GTP1002 2.2 0.7 0.7 O B:HOH2247 2.9 29.0 1.0 CG B:ASP220 3.2 34.3 1.0 C B:THR221 3.3 17.4 1.0 PA B:GTP1002 3.4 0.2 0.7 O3A B:GTP1002 3.5 0.5 0.7 O B:HOH2192 3.5 37.1 1.0 OD2 B:ASP220 3.6 42.3 1.0 N B:THR221 3.9 16.1 1.0 N B:CYS223 4.0 17.3 1.0 CA B:ARG222 4.1 18.2 1.0 N B:ARG222 4.1 15.0 1.0 C B:ASP220 4.2 18.5 1.0 CA B:THR221 4.2 12.0 1.0 C5' B:GTP1002 4.3 54.1 0.7 O B:HOH2395 4.4 75.6 1.0 O5' B:GTP1002 4.4 57.5 0.7 CB B:ASP220 4.4 26.6 1.0 C B:ARG222 4.4 16.0 1.0 O1A B:GTP1002 4.5 0.0 0.7 O B:HOH2190 4.5 42.1 1.0 CA B:ASP220 4.6 18.0 1.0 O B:ASP220 4.7 22.3 1.0 OD2 B:ASP318 5.0 40.6 1.0 CA B:CYS223 5.0 15.0 1.0 CB B:THR221 5.0 13.4 1.0

D.Harrus, N.Ahmed-El-Sayed, P.C.Simister, S.Miller, M.Triconnet, C.H.Hagedorn, K.Mahias, F.A.Rey, T.Astier-Gin, S.Bressanelli. Further Insights Into the Roles of Gtp and the C- Terminus of the Hepatitis C Virus Polymerase in the Initiation of Rna Synthesis J.Biol.Chem. V. 285 32906 2010.
ISSN: ISSN 0021-9258
PubMed: 20729191
DOI: 10.1074/JBC.M110.151316