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Sodium in PDB 4ije: Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant

Protein crystallography data

The structure of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant, PDB code: 4ije was solved by J.B.Binning, T.Wang, D.W.Leung, W.Xu, D.Borek, G.K.Amarasinghe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.10 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.012, 81.012, 344.410, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 22.8

Other elements in 4ije:

The structure of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant (pdb code 4ije). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant, PDB code: 4ije:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4ije

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Sodium binding site 1 out of 5 in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:26.3
occ:1.00
 O A:HOH509 2.5 18.1 1.0
OG1 A:THR237 2.6 16.5 1.0
O A:PRO233 2.7 15.3 1.0
CG2 A:THR237 3.4 15.2 1.0
CB A:THR237 3.4 19.6 1.0
CD A:PRO233 3.7 22.1 1.0
CG A:PRO233 3.7 23.9 1.0
CE1 A:HIS240 3.7 18.2 1.0
C A:PRO233 3.8 16.1 1.0
ND1 A:HIS240 3.9 19.5 1.0
N A:PRO233 3.9 15.5 1.0
CB A:LEU232 4.0 14.2 1.0
CB A:PHE239 4.1 10.3 1.0
CD2 A:LEU232 4.1 12.2 1.0
NE2 A:GLN274 4.3 19.4 1.0
CA A:PRO233 4.4 16.2 1.0
C A:LEU232 4.4 13.6 1.0
CG A:LEU232 4.5 18.0 1.0
CD2 A:PHE239 4.5 22.6 1.0
CA A:LEU232 4.6 13.8 1.0
CB A:PRO233 4.6 16.2 1.0
CD1 A:LEU232 4.6 16.0 1.0
CG A:PHE239 4.7 13.3 1.0
O A:HOH557 4.7 41.0 1.0
CA A:THR237 4.8 16.6 1.0
NE2 A:HIS240 4.9 13.7 1.0
N A:GLY234 5.0 19.9 1.0
CA A:PHE239 5.0 14.5 1.0
N A:PHE239 5.0 14.2 1.0

Sodium binding site 2 out of 5 in 4ije

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Sodium binding site 2 out of 5 in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:24.5
occ:1.00
 O B:HOH507 2.5 21.1 1.0
OG1 B:THR237 2.6 20.2 1.0
O B:PRO233 2.8 19.1 1.0
CB B:THR237 3.4 22.2 1.0
CG2 B:THR237 3.5 17.2 1.0
CD B:PRO233 3.6 21.4 1.0
CG B:PRO233 3.7 28.5 1.0
CE1 B:HIS240 3.8 14.6 1.0
N B:PRO233 3.9 19.8 1.0
ND1 B:HIS240 3.9 15.7 1.0
C B:PRO233 3.9 20.8 1.0
CB B:LEU232 4.0 13.1 1.0
CB B:PHE239 4.1 16.3 1.0
CD2 B:LEU232 4.1 17.8 1.0
C B:LEU232 4.4 19.3 1.0
CA B:PRO233 4.4 22.3 1.0
NE2 B:GLN274 4.4 19.2 1.0
CD2 B:PHE239 4.4 22.4 1.0
CG B:LEU232 4.5 15.5 1.0
CA B:LEU232 4.5 15.4 1.0
CB B:PRO233 4.6 25.3 1.0
CD1 B:LEU232 4.6 13.3 1.0
CG B:PHE239 4.7 17.0 1.0
CA B:THR237 4.9 16.6 1.0
NE2 B:HIS240 4.9 15.4 1.0
CA B:PHE239 4.9 15.9 1.0
N B:PHE239 5.0 16.0 1.0

Sodium binding site 3 out of 5 in 4ije

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Sodium binding site 3 out of 5 in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:17.7
occ:1.00
 O C:HOH537 2.4 44.7 1.0
O B:HOH547 2.5 20.9 0.6
O C:PRO316 2.7 26.1 1.0
O C:PRO315 2.8 20.8 1.0
O B:PRO315 2.8 21.9 1.0
O B:PRO316 2.8 32.0 1.0
C B:PRO316 3.4 29.6 1.0
C C:PRO316 3.4 26.9 1.0
CA C:PRO316 3.6 27.8 1.0
CA B:PRO316 3.7 24.2 1.0
C C:PRO315 3.8 26.1 1.0
C B:PRO315 3.8 23.3 1.0
CG1 B:VAL314 3.8 33.2 1.0
CG1 C:VAL314 3.9 27.6 1.0
O B:HOH543 4.1 49.7 1.0
CD B:PRO318 4.1 19.9 1.0
CD C:PRO318 4.1 17.8 1.0
N C:PRO316 4.2 27.5 1.0
N B:PRO316 4.3 24.7 1.0
O C:HOH551 4.3 41.5 1.0
N B:SER317 4.4 26.6 1.0
N C:SER317 4.5 20.6 1.0
O C:VAL314 4.8 25.1 1.0
O B:VAL314 4.8 26.3 1.0
CB B:VAL314 4.8 31.6 1.0
CB C:VAL314 4.8 29.0 1.0
CG C:PRO318 4.9 19.2 1.0
CG B:PRO318 4.9 19.0 1.0
C B:VAL314 4.9 21.4 1.0
C C:VAL314 5.0 21.8 1.0

Sodium binding site 4 out of 5 in 4ije

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Sodium binding site 4 out of 5 in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:24.1
occ:1.00
 O D:HOH586 2.5 29.5 1.0
O D:TYR229 2.5 16.8 1.0
O D:HOH590 2.8 0.0 1.0
O D:LEU232 3.1 18.8 1.0
NE2 D:HIS240 3.1 16.7 1.0
C D:TYR229 3.5 18.1 1.0
O D:GLY234 3.7 20.7 1.0
CA D:TYR229 3.8 15.6 1.0
CB D:TYR229 3.9 16.2 1.0
CD2 D:HIS240 4.0 16.2 1.0
C D:LEU232 4.1 19.7 1.0
CE1 D:HIS240 4.1 14.0 1.0
CB D:LEU232 4.3 14.9 1.0
CG D:TYR229 4.5 16.0 1.0
CA D:LEU232 4.5 19.2 1.0
N D:LEU232 4.6 21.5 1.0
N D:ASP230 4.6 17.5 1.0
C D:GLY234 4.9 21.9 1.0
CD1 D:TYR229 5.0 20.5 1.0

Sodium binding site 5 out of 5 in 4ije

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Sodium binding site 5 out of 5 in the Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Zaire Ebolavirus VP35 Interferon Inhibitory Domain R312A/K319A/R322A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:22.9
occ:1.00
 O D:HOH507 2.5 19.1 1.0
OG1 D:THR237 2.6 13.7 1.0
O D:PRO233 2.8 20.4 1.0
CB D:THR237 3.4 21.0 1.0
CG2 D:THR237 3.4 17.0 1.0
CD D:PRO233 3.6 20.4 1.0
CG D:PRO233 3.7 22.5 1.0
CE1 D:HIS240 3.7 14.0 1.0
ND1 D:HIS240 3.8 13.2 1.0
C D:PRO233 3.9 21.6 1.0
N D:PRO233 3.9 14.5 1.0
CB D:LEU232 4.0 14.9 1.0
CB D:PHE239 4.1 15.6 1.0
CD2 D:LEU232 4.1 11.1 1.0
O D:HOH517 4.2 40.9 1.0
NE2 D:GLN274 4.3 16.9 1.0
CD2 D:PHE239 4.4 19.5 1.0
CA D:PRO233 4.4 18.9 1.0
C D:LEU232 4.4 19.7 1.0
CG D:LEU232 4.5 13.8 1.0
CA D:LEU232 4.6 19.2 1.0
CB D:PRO233 4.6 19.1 1.0
CG D:PHE239 4.7 18.5 1.0
CD1 D:LEU232 4.7 13.0 1.0
CA D:THR237 4.8 12.6 1.0
O D:HOH511 4.8 30.2 1.0
NE2 D:HIS240 4.9 16.7 1.0
O D:HOH575 5.0 38.4 1.0
CA D:PHE239 5.0 16.9 1.0
N D:PHE239 5.0 15.5 1.0

Reference:

J.M.Binning, T.Wang, P.Luthra, R.S.Shabman, D.M.Borek, G.Liu, W.Xu, D.W.Leung, C.F.Basler, G.K.Amarasinghe. Development of Rna Aptamers Targeting Ebola Virus VP35. Biochemistry V. 52 8406 2013.
ISSN: ISSN 0006-2960
PubMed: 24067086
DOI: 10.1021/BI400704D
Page generated: Tue Dec 15 06:44:50 2020

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