Bromine in PDB 4ibd: Ebola Virus VP35 Bound to Small Molecule

The structure of Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibd was solved by C.S.Brown, D.W.Leung, W.Xu, D.M.Borek, Z.Otwinowski, P.Ramanan, A.J.Stubbs, D.S.Peterson, J.M.Binning, G.K.Amarasinghe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.38 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.562, 65.485, 72.596, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 23.3

The structure of Ebola Virus VP35 Bound to Small Molecule also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Bromine atom in the Ebola Virus VP35 Bound to Small Molecule (pdb code 4ibd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibd:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:17.9 occ:0.84 BRA A:1DL401 0.0 17.9 0.8 CAY A:1DL401 1.9 15.2 1.0 CAO A:1DL401 2.9 21.5 1.0 CAP A:1DL401 2.9 11.7 1.0 CG A:PRO293 3.5 12.2 1.0 CB A:PRO293 3.5 15.4 1.0 CG A:LYS248 3.6 14.5 1.0 CB A:LYS248 3.8 9.4 1.0 CD1 A:LEU249 3.9 21.7 1.0 O B:HOH579 4.0 44.0 1.0 CG2 A:VAL245 4.0 7.6 1.0 CA A:VAL245 4.1 11.2 1.0 CBA A:1DL401 4.1 17.4 1.0 CD1 A:ILE295 4.2 14.5 1.0 SAR A:1DL401 4.3 19.2 1.0 CG1 A:ILE295 4.4 15.8 1.0 O B:HOH585 4.4 54.6 1.0 CB A:VAL245 4.5 8.6 1.0 CG1 A:VAL245 4.6 7.2 1.0 O A:VAL245 4.7 7.2 1.0 CD A:PRO293 4.9 14.5 1.0 CD A:LYS248 4.9 21.9 1.0 O A:GLN244 4.9 8.1 1.0 N A:VAL245 5.0 7.4 1.0 C A:VAL245 5.0 9.1 1.0

Bromine binding site 2 out of 2 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:24.0 occ:1.00 BRA B:1DL401 0.0 24.0 1.0 CAY B:1DL401 1.9 22.2 1.0 CAO B:1DL401 2.9 18.7 1.0 CAP B:1DL401 2.9 14.6 1.0 CG B:PRO293 3.5 10.9 1.0 CB B:PRO293 3.6 10.3 1.0 CG B:LYS248 3.6 20.1 1.0 CB B:LYS248 3.8 20.1 1.0 CG2 B:VAL245 4.1 8.0 1.0 CA B:VAL245 4.1 8.8 1.0 CD1 B:ILE295 4.2 8.9 1.0 CBA B:1DL401 4.2 18.0 1.0 CG1 B:ILE295 4.3 9.4 1.0 SAR B:1DL401 4.3 22.3 1.0 O A:HOH588 4.5 44.5 1.0 CB B:VAL245 4.5 7.2 1.0 CD2 B:LEU249 4.6 22.2 1.0 CG1 B:VAL245 4.7 7.2 1.0 O B:VAL245 4.7 8.0 1.0 CD B:LYS248 4.8 24.9 1.0 CD B:PRO293 4.9 10.9 1.0 O B:GLN244 4.9 10.0 1.0 C B:VAL245 5.0 7.3 1.0 N B:VAL245 5.0 7.8 1.0

C.S.Brown, M.S.Lee, D.W.Leung, T.Wang, W.Xu, P.Luthra, M.Anantpadma, R.S.Shabman, L.M.Melito, K.S.Macmillan, D.M.Borek, Z.Otwinowski, P.Ramanan, A.J.Stubbs, D.S.Peterson, J.M.Binning, M.Tonelli, M.A.Olson, R.A.Davey, J.M.Ready, C.F.Basler, G.K.Amarasinghe. In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. J.Mol.Biol. V. 426 2045 2014.
ISSN: ISSN 0022-2836
PubMed: 24495995
DOI: 10.1016/J.JMB.2014.01.010