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Chlorine in PDB 4ibk: Ebola Virus VP35 Bound to Small Molecule

Protein crystallography data

The structure of Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibk 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) 41.90 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.222, 65.689, 72.831, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ebola Virus VP35 Bound to Small Molecule (pdb code 4ibk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibk:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4ibk

Go back to Chlorine Binding Sites List in 4ibk
Chlorine binding site 1 out of 4 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:14.2
occ:1.00
CL2 A:1DE401 0.0 14.2 1.0
CAZ A:1DE401 1.7 11.4 1.0
CBF A:1DE401 2.6 13.5 1.0
CAM A:1DE401 2.7 11.4 1.0
OAR A:1DE401 3.1 12.4 1.0
CG A:PRO293 3.3 10.4 1.0
CB A:PRO293 3.6 10.9 1.0
CG A:LYS248 3.8 16.7 1.0
CG2 A:VAL245 3.9 13.1 1.0
CB A:LYS248 3.9 9.8 1.0
CA A:VAL245 3.9 6.5 1.0
CBD A:1DE401 3.9 15.9 1.0
CD1 A:ILE295 4.0 15.8 1.0
CBB A:1DE401 4.0 13.0 1.0
CG1 A:ILE295 4.3 11.1 1.0
CB A:VAL245 4.3 11.1 1.0
CG1 A:VAL245 4.4 10.5 1.0
CAP A:1DE401 4.4 19.7 1.0
CAO A:1DE401 4.5 15.9 1.0
O A:HOH557 4.5 42.0 1.0
O A:VAL245 4.6 8.6 1.0
CD2 A:LEU249 4.6 28.7 1.0
O A:GLN244 4.7 10.3 1.0
CD A:PRO293 4.7 8.4 1.0
N A:VAL245 4.7 7.7 1.0
C A:VAL245 4.8 6.6 1.0
OAQ A:1DE401 4.8 20.1 1.0

Chlorine binding site 2 out of 4 in 4ibk

Go back to Chlorine Binding Sites List in 4ibk
Chlorine binding site 2 out of 4 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:23.0
occ:1.00
CL1 A:1DE401 0.0 23.0 1.0
CAY A:1DE401 1.7 21.9 1.0
CAK A:1DE401 2.8 22.7 1.0
SAS A:1DE401 3.0 17.2 1.0
O A:ASP302 3.3 18.2 1.0
O A:HOH559 3.8 40.6 1.0
CG2 A:ILE297 3.8 19.7 1.0
O A:HOH584 3.8 35.4 1.0
C A:ASP302 3.9 21.0 1.0
CE2 A:PHE328 3.9 11.8 1.0
CAL A:1DE401 4.0 26.3 1.0
CA A:ILE303 4.1 11.2 1.0
N A:ILE303 4.2 17.3 1.0
CBE A:1DE401 4.2 23.7 1.0
CG1 A:ILE303 4.3 15.0 1.0
O A:HOH560 4.4 32.6 1.0
CZ A:PHE328 4.5 11.4 1.0
CB A:ASP302 4.5 15.4 1.0
CD A:PRO304 4.6 24.5 1.0
CD2 A:PHE328 4.6 11.3 1.0
CB A:ILE303 4.8 12.8 1.0
CA A:ASP302 4.8 14.8 1.0
CB A:ILE297 4.9 14.1 1.0
CD1 A:ILE297 4.9 17.5 1.0

Chlorine binding site 3 out of 4 in 4ibk

Go back to Chlorine Binding Sites List in 4ibk
Chlorine binding site 3 out of 4 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:16.1
occ:1.00
CL2 B:1DE401 0.0 16.1 1.0
CAZ B:1DE401 1.7 15.9 1.0
CBF B:1DE401 2.7 13.8 1.0
CAM B:1DE401 2.7 16.2 1.0
OAR B:1DE401 3.1 18.9 1.0
CG B:PRO293 3.4 8.8 1.0
CB B:PRO293 3.7 9.6 1.0
CG B:LYS248 3.7 18.2 1.0
CB B:LYS248 3.9 12.4 1.0
CA B:VAL245 4.0 7.5 1.0
CBD B:1DE401 4.0 22.4 1.0
CG2 B:VAL245 4.0 10.7 1.0
CBB B:1DE401 4.0 17.0 1.0
CD1 B:ILE295 4.2 15.5 1.0
CB B:VAL245 4.3 6.4 1.0
CG1 B:VAL245 4.4 9.0 1.0
CG1 B:ILE295 4.4 13.8 1.0
CAO B:1DE401 4.5 20.8 1.0
CAP B:1DE401 4.5 20.0 1.0
O B:VAL245 4.5 9.6 1.0
O B:GLN244 4.7 12.3 1.0
C B:VAL245 4.8 6.0 1.0
N B:VAL245 4.8 6.6 1.0
CD2 B:LEU249 4.8 21.1 1.0
CD B:PRO293 4.8 6.7 1.0
OAQ B:1DE401 4.9 21.9 1.0
CG B:LEU249 4.9 19.9 1.0

Chlorine binding site 4 out of 4 in 4ibk

Go back to Chlorine Binding Sites List in 4ibk
Chlorine binding site 4 out of 4 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:24.6
occ:1.00
CL1 B:1DE401 0.0 24.6 1.0
CAY B:1DE401 1.7 27.8 1.0
CAK B:1DE401 2.8 19.9 1.0
SAS B:1DE401 3.0 17.2 1.0
O B:ASP302 3.2 17.1 1.0
C B:ASP302 3.8 20.8 1.0
CG2 B:ILE297 3.8 18.1 1.0
CE2 B:PHE328 3.8 13.6 1.0
O B:HOH586 4.0 33.5 1.0
CAL B:1DE401 4.0 22.9 1.0
CA B:ILE303 4.1 13.2 1.0
N B:ILE303 4.2 14.1 1.0
CBE B:1DE401 4.2 21.7 1.0
CB B:ASP302 4.2 18.2 1.0
CG1 B:ILE303 4.2 16.1 1.0
O B:HOH589 4.3 33.7 1.0
CZ B:PHE328 4.4 16.0 1.0
CD2 B:PHE328 4.5 12.0 1.0
CD B:PRO304 4.6 20.1 1.0
CA B:ASP302 4.7 16.0 1.0
CB B:ILE297 4.8 18.0 1.0
CB B:ILE303 4.8 16.7 1.0
CD1 B:ILE297 4.9 17.1 1.0

Reference:

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
Page generated: Fri Jul 11 16:46:50 2025

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