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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 11:16:25 2024

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