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Sodium in PDB 3ezq: Crystal Structure of the Fas/Fadd Death Domain Complex

Protein crystallography data

The structure of Crystal Structure of the Fas/Fadd Death Domain Complex, PDB code: 3ezq was solved by R.Schwarzenbacher, H.Robinson, B.Stec, S.J.Riedl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.73
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 126.218, 126.218, 299.274, 90.00, 90.00, 120.00
R / Rfree (%) 23.4 / 27.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Fas/Fadd Death Domain Complex (pdb code 3ezq). 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 the Fas/Fadd Death Domain Complex, PDB code: 3ezq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3ezq

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Sodium binding site 1 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na15

b:62.7
occ:1.00
 NE2 G:GLN311 4.1 83.6 1.0
NE2 E:GLN311 4.3 81.8 1.0
O C:ALA307 4.4 78.0 1.0
O A:ALA307 4.4 78.5 1.0
CB C:GLN311 4.4 76.0 1.0
N C:GLN311 4.6 75.4 1.0
CA C:GLN311 4.6 75.5 1.0
CB A:GLN311 4.6 75.9 1.0
N A:GLN311 4.6 75.6 1.0
CA A:GLN311 4.7 75.5 1.0
CG2 A:ILE310 5.0 70.8 1.0

Sodium binding site 2 out of 8 in 3ezq

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Sodium binding site 2 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na21

b:84.2
occ:1.00
 OE1 B:GLU179 3.5 89.3 1.0
OE2 B:GLU179 4.1 86.7 1.0
CD B:GLU179 4.2 86.3 1.0
CG B:GLN182 4.2 75.7 1.0
CB A:ASN302 4.5 82.5 1.0
ND2 A:ASN302 4.7 80.8 1.0
CD2 A:LEU303 4.7 77.9 1.0
CB B:GLN182 4.7 77.4 1.0
CG A:LEU303 4.8 80.6 1.0
CD2 C:PHE327 4.8 94.4 1.0
OE1 B:GLN182 4.8 79.6 1.0
CB C:PHE327 4.8 91.6 1.0
CG A:LYS299 4.8 84.5 1.0
CG C:PHE327 4.8 92.4 1.0
O A:LYS299 4.9 83.8 1.0
CD B:GLN182 5.0 75.6 1.0

Sodium binding site 3 out of 8 in 3ezq

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Sodium binding site 3 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na14

b:63.3
occ:1.00
 NE2 A:GLN311 3.9 82.1 1.0
O E:ALA307 4.1 77.9 1.0
CB E:GLN311 4.4 75.1 1.0
NE2 C:GLN311 4.5 81.2 1.0
N E:GLN311 4.5 75.3 1.0
CA E:GLN311 4.5 75.2 1.0
O G:ALA307 4.6 78.4 1.0
CB G:GLN311 4.7 74.8 1.0
O E:HOH56 4.7 50.7 1.0
CA G:GLN311 4.8 75.4 1.0
N G:GLN311 4.8 75.8 1.0
NE2 E:GLN311 4.8 81.8 1.0
CA E:ALA307 4.9 78.5 1.0
C E:ALA307 4.9 79.1 1.0
CG2 E:ILE310 4.9 73.6 1.0

Sodium binding site 4 out of 8 in 3ezq

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Sodium binding site 4 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na20

b:77.6
occ:1.00
 OE1 H:GLU179 3.6 88.3 1.0
OE1 H:GLN182 3.6 78.7 1.0
OE2 H:GLU179 3.9 86.9 1.0
CD H:GLU179 4.2 85.8 1.0
CG H:GLN182 4.3 75.5 1.0
CD H:GLN182 4.4 75.2 1.0
CB E:PHE327 4.4 91.6 1.0
CD2 E:PHE327 4.5 94.8 1.0
CG E:PHE327 4.5 93.1 1.0
CD2 G:LEU303 4.7 77.6 1.0
CB H:GLN182 4.8 77.5 1.0
CB G:ASN302 4.8 82.2 1.0
CG G:LYS299 4.9 83.8 1.0
ND2 G:ASN302 5.0 79.2 1.0

Sodium binding site 5 out of 8 in 3ezq

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Sodium binding site 5 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na19

b:76.0
occ:1.00
 OE1 J:GLN182 3.5 77.2 1.0
OE1 J:GLU179 3.6 88.8 1.0
OE2 J:GLU179 3.9 87.0 1.0
CD J:GLU179 4.2 85.8 1.0
CG J:GLN182 4.2 76.2 1.0
CD J:GLN182 4.2 74.8 1.0
CB K:PHE327 4.4 91.9 1.0
CD2 K:PHE327 4.5 95.1 1.0
CG K:PHE327 4.6 93.1 1.0
CB J:GLN182 4.8 77.7 1.0
CB I:ASN302 4.8 82.3 1.0
CD2 I:LEU303 4.8 76.4 1.0
CG I:LYS299 4.9 84.3 1.0
ND2 I:ASN302 4.9 78.7 1.0
CG I:LEU303 5.0 80.4 1.0

Sodium binding site 6 out of 8 in 3ezq

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Sodium binding site 6 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 the Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na16

b:62.2
occ:1.00
 NE2 O:GLN311 4.0 83.2 1.0
O K:ALA307 4.2 77.9 1.0
OE1 M:GLN311 4.4 89.8 1.0
CB K:GLN311 4.4 75.2 1.0
O I:ALA307 4.5 78.2 1.0
N K:GLN311 4.5 75.2 1.0
CA K:GLN311 4.6 75.3 1.0
CB I:GLN311 4.6 75.6 1.0
N I:GLN311 4.7 75.7 1.0
CA I:GLN311 4.7 75.4 1.0
CG2 K:ILE310 4.8 73.0 1.0
O I:HOH164 4.8 50.4 1.0
CA K:ALA307 5.0 78.4 1.0

Sodium binding site 7 out of 8 in 3ezq

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Sodium binding site 7 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 the Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na17

b:64.2
occ:1.00
 NE2 I:GLN311 4.1 83.7 1.0
NE2 K:GLN311 4.3 81.3 1.0
O O:ALA307 4.3 78.6 1.0
CB O:GLN311 4.4 75.5 1.0
N O:GLN311 4.5 75.7 1.0
O M:ALA307 4.5 78.2 1.0
CA O:GLN311 4.5 75.5 1.0
CB M:GLN311 4.6 76.1 1.0
N M:GLN311 4.7 75.5 1.0
CA M:GLN311 4.7 75.4 1.0
OE1 M:GLN311 4.9 89.8 1.0
CG2 O:ILE310 5.0 72.2 1.0

Sodium binding site 8 out of 8 in 3ezq

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Sodium binding site 8 out of 8 in the Crystal Structure of the Fas/Fadd Death Domain Complex


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 the Fas/Fadd Death Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na18

b:88.3
occ:1.00
 OE1 P:GLU179 3.3 88.9 1.0
OE2 P:GLU179 3.7 86.4 1.0
CD P:GLU179 3.9 86.3 1.0
O I:HOH162 4.1 69.3 1.0
CB O:ASN302 4.5 82.3 1.0
CG O:LYS299 4.5 83.8 1.0
CG P:GLN182 4.6 75.1 1.0
CD2 O:LEU303 4.6 78.6 1.0
CG O:LEU303 4.6 80.5 1.0
ND2 O:ASN302 4.7 80.4 1.0
O O:LYS299 4.7 83.8 1.0
CA O:LYS299 4.8 83.0 1.0
CB M:PHE327 4.9 91.3 1.0
CD2 M:PHE327 4.9 94.8 1.0
CG M:PHE327 5.0 92.4 1.0

Reference:

F.L.Scott, B.Stec, C.Pop, M.K.Dobaczewska, J.J.Lee, E.Monosov, H.Robinson, G.S.Salvesen, R.Schwarzenbacher, S.J.Riedl. The Fas-Fadd Death Domain Complex Structure Unravels Signalling By Receptor Clustering Nature V. 457 1019 2009.
ISSN: ISSN 0028-0836
PubMed: 19118384
DOI: 10.1038/NATURE07606
Page generated: Mon Oct 7 08:55:40 2024

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