Magnesium in PDB 3l26: Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna

The structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna, PDB code: 3l26 was solved by D.W.Leung, K.C.Prins, D.M.Borek, M.Farahbakhsh, J.M.Tufariello, P.Ramanan, J.C.Nix, L.A.Helgeson, Z.Otwinowski, R.B.Honzatko, C.F.Basler, G.K.Amarasinghe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.025, 81.025, 90.249, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 25.4

The structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna (pdb code 3l26). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna, PDB code: 3l26:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna


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 Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:5.5 occ:1.00 O A:HOH123 2.3 16.5 1.0 O A:LEU232 2.3 5.3 1.0 O A:HOH122 2.4 2.0 1.0 O A:GLY234 2.5 5.7 1.0 O A:HOH63 2.6 4.6 1.0 N A:GLY234 3.4 6.2 1.0 C A:GLY234 3.5 6.0 1.0 C A:LEU232 3.5 4.9 1.0 CE1 A:PHE235 3.6 8.8 1.0 C A:PRO233 3.7 5.2 1.0 CZ A:PHE235 3.8 10.1 1.0 CA A:GLY234 3.9 6.3 1.0 CD1 A:PHE235 4.0 8.1 1.0 CA A:PRO233 4.0 5.6 1.0 O A:TYR229 4.1 5.5 1.0 NE2 A:HIS240 4.2 7.5 1.0 N A:PRO233 4.2 5.0 1.0 O A:PRO233 4.3 4.3 1.0 CE2 A:PHE235 4.3 10.6 1.0 O A:HOH166 4.4 3.7 1.0 CG A:PHE235 4.5 8.5 1.0 CE1 A:HIS240 4.6 7.2 1.0 CD2 A:PHE235 4.6 9.7 1.0 N A:PHE235 4.6 6.2 1.0 CA A:LEU232 4.6 4.5 1.0 CB A:LEU232 4.9 3.8 1.0 O A:HOH162 5.0 12.0 1.0 N A:LEU232 5.0 5.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna


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 Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4 b:2.0 occ:0.50 NH2 A:ARG305 3.3 4.0 1.0 NH1 A:ARG305 3.9 4.0 1.0 CZ A:ARG305 4.1 3.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna


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 Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:4.9 occ:0.50 O B:HOH104 2.3 10.0 0.5 O B:PRO315 2.6 4.0 1.0 O B:PRO316 2.7 6.7 1.0 C B:PRO316 3.2 6.5 1.0 CA B:PRO316 3.5 6.6 1.0 C B:PRO315 3.6 4.5 1.0 CD B:PRO318 4.0 3.6 1.0 N B:PRO316 4.0 5.7 1.0 CG2 B:VAL314 4.1 2.9 1.0 N B:SER317 4.2 6.4 1.0 O B:HOH35 4.5 3.5 1.0 CB B:VAL314 4.7 2.1 1.0 CA B:SER317 4.8 6.6 1.0 CG B:PRO318 4.9 2.5 1.0 CA B:PRO315 4.9 4.0 1.0 CB B:PRO316 5.0 8.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg5 b:8.7 occ:1.00 O B:LEU232 2.6 5.0 1.0 O B:HOH71 2.8 2.0 1.0 O B:GLY234 2.9 5.2 1.0 O B:HOH164 3.0 22.1 1.0 N B:GLY234 3.4 6.5 1.0 C B:PRO233 3.7 5.4 1.0 C B:LEU232 3.7 4.3 1.0 C B:GLY234 3.8 5.7 1.0 CA B:PRO233 3.9 6.1 1.0 CA B:GLY234 4.1 6.5 1.0 O B:TYR229 4.1 5.8 1.0 O B:PRO233 4.3 4.2 1.0 N B:PRO233 4.3 4.9 1.0 NE2 B:HIS240 4.4 5.7 1.0 CE1 B:HIS240 4.8 5.3 1.0 CA B:LEU232 4.9 3.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg9 b:2.0 occ:0.50 O2 C:U5 2.3 3.8 1.0 O C:HOH98 2.5 2.0 1.0 O C:HOH25 2.8 2.0 1.0 C2 C:U5 3.4 3.8 1.0 C2 C:A4 4.1 3.9 1.0 C1' C:U5 4.1 4.6 1.0 N1 C:U5 4.2 4.1 1.0 N3 C:U5 4.3 3.5 1.0 O2' C:U5 4.5 5.3 1.0 C2' C:U5 4.6 4.8 1.0 N1 C:A4 4.6 3.5 1.0 O C:HOH88 4.8 3.8 1.0 N3 C:A4 4.9 4.2 1.0 O4' C:G6 4.9 4.5 1.0 O C:HOH49 5.0 2.2 1.0

D.W.Leung, K.C.Prins, D.M.Borek, M.Farahbakhsh, J.M.Tufariello, P.Ramanan, J.C.Nix, L.A.Helgeson, Z.Otwinowski, R.B.Honzatko, C.F.Basler, G.K.Amarasinghe. Structural Basis For Dsrna Recognition and Interferon Antagonism By Ebola VP35. Nat.Struct.Mol.Biol. V. 17 165 2010.
ISSN: ISSN 1545-9993
PubMed: 20081868
DOI: 10.1038/NSMB.1765