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

Protein crystallography data

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

Other elements in 3l26:

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

Magnesium Binding Sites:

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 3l26

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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 3l26

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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 3l26

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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 3l26

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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 3l26

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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

Reference:

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
Page generated: Mon Dec 14 08:23:39 2020

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