Atomistry » Sodium » PDB 3k9g-3la1 » 3l25
Atomistry »
  Sodium »
    PDB 3k9g-3la1 »
      3l25 »

Sodium in PDB 3l25: 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: 3l25 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) 44.68 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.947, 84.571, 89.316, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.7

Other elements in 3l25:

The structure of Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna (pdb code 3l25). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Zaire Ebola VP35 Interferon Inhibitory Domain Bound to 8 Bp Dsrna, PDB code: 3l25:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 1 out of 8 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 Sodium with other atoms in the Na 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:Na10

b:14.0
occ:1.00
 O A:HOH185 2.2 22.7 1.0
O A:HOH353 2.3 25.5 1.0
O A:HOH32 2.4 10.7 1.0
O A:LEU232 2.4 13.5 1.0
O A:GLY234 2.4 11.2 1.0
C A:GLY234 3.5 11.9 1.0
N A:GLY234 3.5 12.5 1.0
C A:LEU232 3.6 13.0 1.0
CE1 A:PHE235 3.7 21.6 1.0
C A:PRO233 3.7 12.3 1.0
CZ A:PHE235 3.8 22.0 1.0
CD1 A:PHE235 4.0 18.9 1.0
CA A:GLY234 4.0 12.0 1.0
CA A:PRO233 4.1 13.6 1.0
NE2 A:HIS240 4.1 10.2 1.0
O A:TYR229 4.1 16.1 1.0
O A:PRO233 4.3 11.7 1.0
CE2 A:PHE235 4.3 22.2 1.0
N A:PRO233 4.3 12.9 1.0
CG A:PHE235 4.4 17.2 1.0
CD2 A:PHE235 4.5 19.6 1.0
CE1 A:HIS240 4.6 9.0 1.0
N A:PHE235 4.6 11.2 1.0
CA A:LEU232 4.6 12.3 1.0
CB A:LEU232 4.9 10.9 1.0
N A:LEU232 4.9 13.8 1.0

Sodium binding site 2 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 2 out of 8 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 Sodium with other atoms in the Na 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
B:Na6

b:26.4
occ:1.00
 O B:GLY234 2.4 19.3 1.0
O B:HOH71 2.5 15.4 1.0
O B:LEU232 2.5 20.6 1.0
N B:GLY234 3.5 19.9 1.0
C B:GLY234 3.5 19.4 1.0
CE1 B:PHE235 3.6 25.9 1.0
C B:LEU232 3.6 18.5 1.0
C B:PRO233 3.7 18.7 1.0
CZ B:PHE235 3.7 28.8 1.0
CD1 B:PHE235 4.0 25.1 1.0
CA B:PRO233 4.0 19.5 1.0
CA B:GLY234 4.0 19.7 1.0
O B:TYR229 4.1 21.5 1.0
CE2 B:PHE235 4.1 28.3 1.0
NE2 B:HIS240 4.2 13.0 1.0
O B:PRO233 4.2 16.3 1.0
N B:PRO233 4.3 18.2 1.0
CG B:PHE235 4.4 25.1 1.0
O B:HOH346 4.4 36.0 1.0
CD2 B:PHE235 4.5 27.3 1.0
CE1 B:HIS240 4.6 14.1 1.0
N B:PHE235 4.6 19.8 1.0
CA B:LEU232 4.7 17.0 1.0
CB B:LEU232 4.9 15.2 1.0

Sodium binding site 3 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 3 out of 8 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 Sodium with other atoms in the Na 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:Na13

b:17.8
occ:1.00
 O B:HOH29 2.4 25.1 1.0
O B:PRO315 2.5 12.2 1.0
O B:PRO316 2.5 12.5 1.0
C B:PRO316 3.1 12.8 1.0
CA B:PRO316 3.5 13.5 1.0
C B:PRO315 3.5 12.6 1.0
CD B:PRO318 3.9 9.3 1.0
N B:PRO316 3.9 13.4 1.0
CG2 B:VAL314 4.1 13.5 1.0
N B:SER317 4.2 11.7 1.0
O B:HOH76 4.6 19.7 1.0
CB B:VAL314 4.7 11.4 1.0
CA B:SER317 4.8 12.6 1.0
CG B:PRO318 4.8 9.2 1.0
CA B:PRO315 4.8 12.5 1.0
N B:PRO315 4.9 11.8 1.0
CB B:PRO316 4.9 15.2 1.0

Sodium binding site 4 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 4 out of 8 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 Sodium with other atoms in the Na 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
C:Na9

b:9.6
occ:1.00
 O2 F:U5 2.3 7.3 1.0
O2 C:U5 2.3 8.6 1.0
O D:HOH34 2.4 10.6 1.0
O C:HOH89 2.4 12.5 1.0
O A:HOH33 2.5 11.5 1.0
O F:HOH54 2.5 10.9 1.0
C2 F:U5 3.5 8.2 1.0
C2 C:U5 3.5 8.4 1.0
O2 A:FMT19 3.8 45.7 1.0
O1 D:FMT20 3.9 35.9 1.0
O D:HOH357 4.1 22.9 1.0
C1' C:U5 4.1 6.5 1.0
C1' F:U5 4.1 7.0 1.0
O A:HOH363 4.2 23.8 1.0
C2 C:A4 4.3 5.6 1.0
C2 F:A4 4.3 5.5 1.0
N1 C:U5 4.3 6.8 1.0
N1 F:U5 4.3 6.1 1.0
N3 F:U5 4.4 8.1 1.0
N3 C:U5 4.5 8.0 1.0
O2' F:U5 4.5 6.9 1.0
O2' C:U5 4.5 8.1 1.0
C2' F:U5 4.6 6.2 1.0
C2' C:U5 4.6 7.2 1.0
N1 C:A4 4.8 3.5 1.0
C A:FMT19 4.8 46.2 1.0
N1 F:A4 4.8 5.1 1.0
O C:HOH96 4.9 13.0 1.0
O F:HOH21 4.9 10.2 1.0
C D:FMT20 4.9 36.8 1.0
O4' F:G6 4.9 9.1 1.0
O4' C:G6 4.9 9.5 1.0

Sodium binding site 5 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 5 out of 8 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 Sodium with other atoms in the Na 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:Na10

b:14.2
occ:1.00
 O F:HOH121 2.4 19.3 1.0
O C:HOH40 2.4 15.0 1.0
O C:HOH285 2.5 26.1 1.0
O4 C:U5 2.5 6.1 1.0
O6 C:G6 2.5 8.4 1.0
O C:HOH37 2.6 10.2 1.0
C4 C:U5 3.3 6.9 1.0
C6 C:G6 3.6 8.2 1.0
C5 C:U5 3.8 9.0 1.0
N4 F:C3 3.9 7.2 1.0
O B:HOH347 3.9 41.1 1.0
N7 C:G6 4.0 6.5 1.0
O C:HOH291 4.1 27.8 1.0
C5 C:G6 4.2 6.6 1.0
O6 F:G2 4.2 10.4 1.0
N6 F:A4 4.3 6.3 1.0
O C:HOH68 4.3 16.2 1.0
N4 C:C7 4.3 7.3 1.0
N3 C:U5 4.3 8.0 1.0
O B:HOH105 4.6 13.9 1.0
O B:HOH195 4.6 17.1 1.0
O C:HOH99 4.7 11.5 1.0
O C:HOH63 4.7 13.8 1.0
N1 C:G6 4.8 6.9 1.0
O F:HOH266 4.9 30.5 1.0
O F:HOH136 4.9 31.1 1.0

Sodium binding site 6 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 6 out of 8 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 Sodium with other atoms in the Na binding site number 6 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:Na12

b:29.8
occ:1.00
 O D:HOH362 2.2 33.0 1.0
O C:HOH307 2.4 30.0 1.0
O D:HOH151 2.5 21.2 1.0
O D:HOH344 2.7 28.3 1.0
OG D:SER310 2.7 14.7 1.0
O4' C:C3 3.4 10.2 1.0
O2' C:C3 3.4 11.4 1.0
CB D:SER310 3.6 12.8 1.0
C1' C:C3 3.7 10.1 1.0
CA D:SER310 3.9 12.7 1.0
C4' C:C3 3.9 10.5 1.0
O D:HOH363 3.9 23.3 1.0
O D:LYS339 4.1 15.6 1.0
O C:HOH108 4.1 18.0 1.0
O D:LYS309 4.2 13.2 1.0
C2' C:C3 4.2 10.7 1.0
O D:HOH80 4.5 30.0 1.0
N D:SER310 4.6 12.4 1.0
C D:LYS309 4.7 13.0 1.0
O D:HOH342 4.7 12.4 1.0
O2' C:G2 4.8 17.2 1.0
C3' C:C3 4.8 10.7 1.0
C5' C:C3 4.9 12.8 1.0

Sodium binding site 7 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 7 out of 8 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 Sodium with other atoms in the Na binding site number 7 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
D:Na8

b:15.6
occ:1.00
 O D:HOH59 2.3 20.5 1.0
O D:HOH10 2.4 6.8 1.0
O D:GLY234 2.4 11.5 1.0
O D:HOH343 2.4 26.5 1.0
O D:LEU232 2.4 13.5 1.0
C D:GLY234 3.5 12.0 1.0
N D:GLY234 3.5 12.7 1.0
C D:LEU232 3.6 12.5 1.0
CE1 D:PHE235 3.7 23.3 1.0
C D:PRO233 3.7 11.7 1.0
CZ D:PHE235 3.8 26.0 1.0
CD1 D:PHE235 4.0 21.1 1.0
NE2 D:HIS240 4.0 8.9 1.0
CA D:GLY234 4.0 12.6 1.0
O D:TYR229 4.1 15.3 1.0
CA D:PRO233 4.1 13.4 1.0
CE2 D:PHE235 4.3 25.2 1.0
N D:PRO233 4.3 13.1 1.0
O D:PRO233 4.3 9.7 1.0
CG D:PHE235 4.4 18.7 1.0
CE1 D:HIS240 4.5 8.9 1.0
CD2 D:PHE235 4.6 20.7 1.0
N D:PHE235 4.6 11.3 1.0
CA D:LEU232 4.6 11.6 1.0
CB D:LEU232 4.8 9.9 1.0
N D:LEU232 4.9 13.0 1.0
CA D:PHE235 5.0 12.3 1.0

Sodium binding site 8 out of 8 in 3l25

Go back to Sodium Binding Sites List in 3l25
Sodium binding site 8 out of 8 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 Sodium with other atoms in the Na binding site number 8 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
F:Na11

b:15.8
occ:1.00
 O C:HOH217 2.2 20.3 1.0
O F:HOH297 2.4 21.5 1.0
O6 F:G6 2.5 7.0 1.0
O F:HOH16 2.5 9.0 1.0
O4 F:U5 2.6 6.7 1.0
O F:HOH58 2.6 13.3 1.0
C4 F:U5 3.4 6.8 1.0
C6 F:G6 3.5 5.9 1.0
N4 C:C3 3.8 8.2 1.0
C5 F:U5 3.9 5.6 1.0
N7 F:G6 4.0 6.9 1.0
C5 F:G6 4.1 6.2 1.0
O6 C:G2 4.2 12.5 1.0
N6 C:A4 4.2 6.5 1.0
O F:HOH24 4.4 12.6 1.0
N4 F:C7 4.4 8.1 1.0
N3 F:U5 4.4 8.1 1.0
O E:HOH134 4.6 18.9 1.0
O E:HOH82 4.6 17.9 1.0
N1 F:G6 4.7 5.9 1.0
O F:HOH10 4.8 10.8 1.0
O C:HOH241 4.8 27.1 1.0
O F:HOH60 4.9 12.7 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 06:16:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy