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Sodium in PDB 3l28: Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant

Protein crystallography data

The structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant, PDB code: 3l28 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) 33.77 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.381, 91.880, 102.595, 90.00, 99.60, 90.00
R / Rfree (%) 20 / 26.9

Other elements in 3l28:

The structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant (pdb code 3l28). 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant, PDB code: 3l28:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3l28

Go back to Sodium Binding Sites List in 3l28
Sodium binding site 1 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:19.6
occ:1.00
O3 B:SO45 2.4 50.5 1.0
N B:LYS222 3.5 11.6 1.0
CL B:CL341 3.6 36.1 1.0
S B:SO45 3.6 52.3 1.0
N B:ALA221 3.7 8.6 1.0
O1 B:SO45 3.9 51.7 1.0
CB B:LYS222 3.9 12.4 1.0
CB B:ALA221 4.0 8.0 1.0
CB B:SER220 4.0 9.6 1.0
O2 B:SO45 4.0 53.2 1.0
CA B:ALA221 4.2 7.9 1.0
C B:ALA221 4.3 7.9 1.0
CA B:LYS222 4.3 10.7 1.0
C B:SER220 4.5 10.1 1.0
O B:HOH459 4.6 20.3 1.0
OG B:SER220 4.6 12.0 1.0
O4 B:SO45 4.7 51.3 1.0
CA B:SER220 4.7 9.8 1.0
CE B:LYS251 4.8 11.9 1.0
NZ B:LYS251 5.0 12.6 1.0

Sodium binding site 2 out of 5 in 3l28

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Sodium binding site 2 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4

b:18.9
occ:1.00
O3 B:SO41 2.4 22.8 1.0
O B:HOH365 2.9 3.8 1.0
O A:HOH17 2.9 6.7 1.0
NE2 B:GLN274 3.1 2.3 1.0
S B:SO41 3.5 25.9 1.0
O4 B:SO41 3.6 25.0 1.0
OG1 B:THR237 3.6 2.0 1.0
CG B:GLN274 3.9 2.0 1.0
CD B:PRO233 3.9 2.0 1.0
CD B:GLN274 4.0 2.6 1.0
CG B:PRO233 4.2 2.0 1.0
CG2 B:THR237 4.2 2.0 1.0
O2 B:SO41 4.2 23.1 1.0
CD2 B:PHE239 4.2 2.0 1.0
O A:HOH181 4.3 8.0 1.0
CD2 B:LEU232 4.4 2.0 1.0
CB B:THR237 4.4 2.0 1.0
CB B:PHE239 4.6 2.0 1.0
OG A:SER310 4.6 5.5 1.0
O1 B:SO41 4.6 21.4 1.0
CG B:PHE239 4.7 2.0 1.0
O A:HOH66 4.8 2.6 1.0
O A:ILE340 4.9 5.2 1.0
O A:LYS309 4.9 2.0 1.0
CE2 B:PHE239 5.0 2.0 1.0

Sodium binding site 3 out of 5 in 3l28

Go back to Sodium Binding Sites List in 3l28
Sodium binding site 3 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2

b:10.3
occ:1.00
O C:HOH59 2.7 2.0 1.0
O D:GLY270 3.1 2.2 1.0
N C:LYS319 3.2 2.0 1.0
CA C:PRO318 3.6 3.0 1.0
NE1 C:TRP324 3.6 2.0 1.0
C D:GLY270 3.7 4.0 1.0
CD1 C:TRP324 3.7 2.0 1.0
O C:SER317 3.7 7.5 1.0
CB C:ARG322 3.8 2.0 1.0
C C:PRO318 3.8 3.6 1.0
CD C:ARG322 4.0 2.0 1.0
CA D:GLY270 4.0 2.7 1.0
CG C:PRO315 4.1 2.0 1.0
CB C:LYS319 4.1 2.0 1.0
CA C:LYS319 4.2 2.0 1.0
O C:HOH77 4.3 6.1 1.0
O C:LYS319 4.3 2.0 1.0
CG C:ARG322 4.4 2.0 1.0
CG C:LYS319 4.4 2.0 1.0
O D:GLU269 4.4 6.6 1.0
N C:PRO318 4.5 2.9 1.0
C C:SER317 4.5 5.8 1.0
CB C:PRO318 4.6 2.0 1.0
N D:ASP271 4.6 4.4 1.0
O C:PRO316 4.7 2.0 1.0
CB C:PRO315 4.7 2.0 1.0
C C:LYS319 4.8 2.0 1.0
CE2 C:TRP324 4.8 2.0 1.0
O C:PRO318 4.9 2.0 1.0
CG C:TRP324 4.9 2.0 1.0

Sodium binding site 4 out of 5 in 3l28

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Sodium binding site 4 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1

b:14.5
occ:1.00
O D:HOH18 2.5 2.0 1.0
ND1 D:HIS240 2.8 2.1 1.0
O2 D:SO44 2.8 8.8 1.0
OD2 A:ASP332 3.5 2.0 1.0
CB D:LEU232 3.6 2.0 1.0
CA D:GLY234 3.7 2.0 1.0
CG D:HIS240 3.7 2.0 1.0
CB D:HIS240 3.8 2.0 1.0
CE1 D:HIS240 3.8 2.0 1.0
CD1 D:TYR229 3.9 2.7 1.0
O3 D:SO44 3.9 10.1 1.0
N D:GLY234 3.9 4.2 1.0
S D:SO44 4.0 8.7 1.0
CD1 D:LEU232 4.0 2.0 1.0
O D:TYR229 4.2 2.0 1.0
CA D:HIS240 4.2 2.0 1.0
CA D:TYR229 4.4 2.0 1.0
CG D:LEU232 4.4 2.0 1.0
C D:LEU232 4.5 2.0 1.0
O D:LEU232 4.6 3.0 1.0
CE1 D:TYR229 4.6 2.0 1.0
C D:GLY234 4.6 2.0 1.0
CA D:LEU232 4.7 2.0 1.0
O D:HOH199 4.7 31.6 1.0
CG A:ASP332 4.7 2.0 1.0
CG D:TYR229 4.7 2.0 1.0
CB D:TYR229 4.8 2.0 1.0
C D:TYR229 4.8 2.0 1.0
O1 D:SO44 4.9 8.5 1.0
CD2 D:HIS240 4.9 2.0 1.0
NE2 D:HIS240 4.9 2.0 1.0
C D:PRO233 4.9 2.3 1.0
O4 D:SO44 4.9 6.9 1.0

Sodium binding site 5 out of 5 in 3l28

Go back to Sodium Binding Sites List in 3l28
Sodium binding site 5 out of 5 in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain K339A 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 Zaire Ebola VP35 Interferon Inhibitory Domain K339A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na5

b:14.9
occ:1.00
O F:HOH25 2.5 5.7 1.0
O1 F:SO47 2.6 12.2 1.0
O F:HOH20 2.9 5.3 1.0
O F:SER317 3.1 2.0 1.0
O E:GLU269 3.2 3.8 1.0
O E:HOH8 3.5 2.8 1.0
S F:SO47 3.8 12.8 1.0
CD F:ARG322 3.8 2.0 1.0
O E:HOH167 3.9 14.9 1.0
O3 F:SO47 3.9 15.6 1.0
NE F:ARG322 4.0 2.0 1.0
C F:SER317 4.0 2.0 1.0
NZ F:LYS319 4.1 2.0 1.0
CA E:GLY270 4.1 2.0 1.0
C E:GLU269 4.2 2.0 1.0
CG F:LYS319 4.3 2.0 1.0
O4 F:SO47 4.4 14.4 1.0
O E:GLY270 4.6 2.0 1.0
C E:GLY270 4.6 2.0 1.0
N E:GLY270 4.6 2.0 1.0
N F:SER317 4.8 2.0 1.0
CA F:SER317 4.8 2.0 1.0
N F:PRO318 4.8 2.0 1.0
CA F:PRO318 4.8 2.0 1.0
O2 F:SO47 4.9 11.5 1.0
CB F:SER317 4.9 2.0 1.0
N F:LYS319 4.9 2.0 1.0
CB F:PRO315 4.9 2.0 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: Tue Dec 15 06:16:32 2020

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