Sodium in PDB 4xhs: Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
Protein crystallography data
The structure of Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction, PDB code: 4xhs
was solved by
T.Jin,
M.Huang,
J.Jiang,
T.Xiao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.99 /
1.70
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.720,
103.620,
186.740,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
19
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
(pdb code 4xhs). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction, PDB code: 4xhs:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 1 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:37.1
occ:1.00
|
O
|
A:ASP237
|
2.3
|
20.8
|
1.0
|
O
|
A:SER239
|
2.4
|
22.4
|
1.0
|
O
|
A:HOH1059
|
2.4
|
44.4
|
1.0
|
O
|
A:HOH618
|
2.4
|
20.4
|
1.0
|
O
|
A:HOH974
|
2.4
|
42.3
|
1.0
|
C
|
A:ASP237
|
3.4
|
18.4
|
1.0
|
C
|
A:SER239
|
3.6
|
19.0
|
1.0
|
O
|
A:HOH701
|
3.9
|
29.9
|
1.0
|
O
|
A:ILE236
|
4.0
|
17.6
|
1.0
|
C
|
A:THR238
|
4.2
|
17.7
|
1.0
|
CA
|
A:ASP237
|
4.2
|
18.9
|
1.0
|
O
|
A:THR238
|
4.2
|
20.5
|
1.0
|
N
|
A:SER239
|
4.3
|
15.8
|
1.0
|
CA
|
A:ALA240
|
4.4
|
25.8
|
1.0
|
N
|
A:THR238
|
4.4
|
16.0
|
1.0
|
N
|
A:ALA240
|
4.5
|
18.2
|
1.0
|
O
|
A:VAL241
|
4.5
|
22.5
|
1.0
|
C
|
A:ALA240
|
4.6
|
28.0
|
1.0
|
CA
|
A:SER239
|
4.6
|
18.3
|
1.0
|
CA
|
A:THR238
|
4.7
|
17.5
|
1.0
|
N
|
A:VAL241
|
4.8
|
20.6
|
1.0
|
O
|
A:ALA240
|
5.0
|
25.3
|
1.0
|
C
|
A:ILE236
|
5.0
|
16.9
|
1.0
|
|
Sodium binding site 2 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 2 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:43.0
occ:1.00
|
CZ
|
A:TYR342
|
2.6
|
23.7
|
0.4
|
CE2
|
A:TYR342
|
2.7
|
24.0
|
0.4
|
CE1
|
A:TYR342
|
2.7
|
24.8
|
0.4
|
CD2
|
A:TYR342
|
2.8
|
21.6
|
0.4
|
CD1
|
A:TYR342
|
2.8
|
21.7
|
0.4
|
CG
|
A:TYR342
|
2.9
|
19.6
|
0.4
|
NH2
|
A:ARG67
|
2.9
|
19.6
|
0.5
|
O
|
A:SER338
|
3.0
|
19.2
|
1.0
|
NH1
|
A:ARG67
|
3.4
|
26.8
|
0.5
|
OH
|
A:TYR342
|
3.5
|
28.1
|
0.4
|
CZ
|
A:ARG67
|
3.6
|
22.5
|
0.5
|
N
|
A:TYR342
|
3.7
|
17.9
|
1.0
|
OG
|
A:SER338
|
3.7
|
38.7
|
1.0
|
O
|
A:HOH628
|
3.8
|
36.3
|
1.0
|
C
|
A:SER338
|
3.9
|
22.5
|
1.0
|
CB
|
A:TRP341
|
3.9
|
17.6
|
1.0
|
CB
|
A:TYR342
|
3.9
|
22.0
|
0.6
|
CB
|
A:TYR342
|
4.0
|
22.0
|
0.4
|
CA
|
A:TYR342
|
4.1
|
19.6
|
0.6
|
CA
|
A:TYR342
|
4.1
|
19.6
|
0.4
|
CA
|
A:SER338
|
4.1
|
20.2
|
1.0
|
O
|
A:HOH982
|
4.1
|
37.1
|
1.0
|
NH1
|
A:ARG67
|
4.2
|
26.2
|
0.5
|
C
|
A:TRP341
|
4.3
|
18.2
|
1.0
|
O
|
A:HOH872
|
4.3
|
39.5
|
1.0
|
CB
|
A:SER338
|
4.5
|
21.9
|
1.0
|
O4
|
A:MAL501
|
4.6
|
15.1
|
1.0
|
CA
|
A:TRP341
|
4.6
|
13.8
|
1.0
|
CD2
|
A:TYR342
|
4.8
|
28.8
|
0.6
|
NE
|
A:ARG67
|
4.9
|
16.8
|
0.5
|
CG
|
A:TYR342
|
4.9
|
23.0
|
0.6
|
|
Sodium binding site 3 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 3 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na504
b:20.5
occ:1.00
|
O
|
B:HOH943
|
2.3
|
25.1
|
1.0
|
OG
|
B:SER234
|
2.4
|
22.7
|
1.0
|
O
|
B:ASP297
|
2.4
|
15.6
|
1.0
|
O
|
B:HOH779
|
2.5
|
23.4
|
1.0
|
O
|
B:LYS296
|
2.5
|
18.9
|
1.0
|
O
|
B:HOH992
|
2.6
|
32.0
|
1.0
|
C
|
B:ASP297
|
3.2
|
17.2
|
1.0
|
CB
|
B:SER234
|
3.3
|
15.5
|
1.0
|
O
|
B:HOH624
|
3.4
|
32.8
|
1.0
|
C
|
B:LYS296
|
3.4
|
19.6
|
1.0
|
CA
|
B:ASP297
|
3.8
|
14.8
|
1.0
|
O
|
B:HOH741
|
3.9
|
29.5
|
1.0
|
O
|
B:HOH881
|
3.9
|
28.0
|
1.0
|
N
|
B:ASP297
|
4.0
|
14.8
|
1.0
|
O
|
B:HOH1056
|
4.1
|
26.1
|
1.0
|
O
|
B:HOH829
|
4.2
|
26.0
|
1.0
|
N
|
B:LYS298
|
4.2
|
13.6
|
1.0
|
O
|
B:HOH664
|
4.3
|
30.2
|
1.0
|
CA
|
B:SER234
|
4.4
|
15.2
|
1.0
|
CA
|
B:LYS296
|
4.5
|
17.9
|
1.0
|
CA
|
B:LYS298
|
4.6
|
14.4
|
0.5
|
CA
|
B:LYS298
|
4.6
|
14.3
|
0.5
|
O
|
B:ASN295
|
4.7
|
17.4
|
1.0
|
O
|
B:HOH1035
|
4.8
|
40.9
|
1.0
|
|
Sodium binding site 4 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 4 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na505
b:38.0
occ:1.00
|
O
|
B:HOH978
|
2.4
|
40.1
|
1.0
|
O
|
B:GLY328
|
2.4
|
22.6
|
1.0
|
O
|
B:GLN326
|
2.5
|
20.7
|
1.0
|
O
|
B:HOH871
|
2.5
|
43.0
|
1.0
|
O
|
B:HOH806
|
2.6
|
32.8
|
1.0
|
O
|
B:HOH614
|
2.7
|
41.4
|
1.0
|
C
|
B:GLN326
|
3.5
|
21.4
|
1.0
|
C
|
B:GLY328
|
3.6
|
21.4
|
1.0
|
O
|
B:HOH970
|
4.0
|
39.3
|
1.0
|
O
|
B:ALA325
|
4.1
|
17.1
|
1.0
|
CA
|
B:GLN326
|
4.2
|
17.9
|
1.0
|
C
|
B:LYS327
|
4.2
|
21.5
|
1.0
|
N
|
B:GLY328
|
4.2
|
16.2
|
1.0
|
OE1
|
B:GLU329
|
4.3
|
39.7
|
1.0
|
CD
|
B:GLU329
|
4.4
|
43.2
|
1.0
|
O
|
B:LYS327
|
4.4
|
20.7
|
1.0
|
N
|
B:LYS327
|
4.4
|
17.6
|
1.0
|
N
|
B:GLU329
|
4.5
|
17.6
|
1.0
|
CA
|
B:GLU329
|
4.5
|
22.2
|
1.0
|
CA
|
B:GLY328
|
4.6
|
17.0
|
1.0
|
OE2
|
B:GLU329
|
4.6
|
49.0
|
1.0
|
CA
|
B:LYS327
|
4.6
|
18.9
|
1.0
|
O
|
B:HOH997
|
4.7
|
50.8
|
1.0
|
O
|
B:HOH1007
|
4.9
|
49.8
|
1.0
|
|
Sodium binding site 5 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 5 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:18.4
occ:1.00
|
O
|
B:SER239
|
2.3
|
19.5
|
1.0
|
O
|
B:ASP237
|
2.4
|
15.3
|
1.0
|
O
|
B:HOH986
|
2.5
|
26.5
|
1.0
|
O
|
B:HOH646
|
2.5
|
17.2
|
1.0
|
NA
|
B:NA507
|
3.2
|
27.3
|
1.0
|
C
|
B:ASP237
|
3.4
|
16.1
|
1.0
|
C
|
B:SER239
|
3.5
|
15.0
|
1.0
|
N
|
B:SER239
|
4.1
|
15.1
|
1.0
|
C
|
B:THR238
|
4.1
|
17.4
|
1.0
|
O
|
B:ILE236
|
4.1
|
15.4
|
1.0
|
O
|
B:HOH1059
|
4.2
|
34.6
|
1.0
|
CA
|
B:ASP237
|
4.3
|
14.4
|
1.0
|
N
|
B:THR238
|
4.3
|
15.8
|
1.0
|
CA
|
B:ALA240
|
4.3
|
17.7
|
1.0
|
O
|
B:HOH1036
|
4.3
|
37.8
|
1.0
|
N
|
B:ALA240
|
4.4
|
15.3
|
1.0
|
CA
|
B:THR238
|
4.4
|
16.2
|
1.0
|
CA
|
B:SER239
|
4.4
|
13.6
|
1.0
|
O
|
B:THR238
|
4.5
|
17.1
|
1.0
|
C
|
B:ALA240
|
4.7
|
21.9
|
1.0
|
O
|
B:HOH710
|
4.7
|
16.9
|
1.0
|
O
|
B:VAL241
|
4.7
|
18.6
|
1.0
|
N
|
B:VAL241
|
4.8
|
16.6
|
1.0
|
O
|
B:HOH1033
|
4.9
|
30.8
|
1.0
|
O
|
B:HOH1003
|
4.9
|
22.9
|
1.0
|
|
Sodium binding site 6 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 6 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na507
b:27.3
occ:1.00
|
O
|
B:HOH1003
|
2.4
|
22.9
|
1.0
|
O
|
B:HOH986
|
2.4
|
26.5
|
1.0
|
O
|
B:HOH1033
|
2.4
|
30.8
|
1.0
|
O
|
B:ASP237
|
2.5
|
15.3
|
1.0
|
NA
|
B:NA506
|
3.2
|
18.4
|
1.0
|
C
|
B:ASP237
|
3.5
|
16.1
|
1.0
|
CA
|
B:THR238
|
4.3
|
16.2
|
1.0
|
N
|
B:THR238
|
4.3
|
15.8
|
1.0
|
CA
|
B:ASP237
|
4.4
|
14.4
|
1.0
|
O
|
B:HOH710
|
4.5
|
16.9
|
1.0
|
CB
|
B:ASP237
|
4.5
|
13.3
|
1.0
|
C
|
B:THR238
|
5.0
|
17.4
|
1.0
|
O
|
B:HOH646
|
5.0
|
17.2
|
1.0
|
|
Sodium binding site 7 out
of 7 in 4xhs
Go back to
Sodium Binding Sites List in 4xhs
Sodium binding site 7 out
of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction
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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na508
b:45.5
occ:1.00
|
O
|
B:SER338
|
2.7
|
21.2
|
1.0
|
CE2
|
B:TYR342
|
2.7
|
26.0
|
0.4
|
CZ
|
B:TYR342
|
2.7
|
30.3
|
0.4
|
CD2
|
B:TYR342
|
2.7
|
26.6
|
0.4
|
CE1
|
B:TYR342
|
2.7
|
29.4
|
0.4
|
CD1
|
B:TYR342
|
2.8
|
26.7
|
0.4
|
CG
|
B:TYR342
|
2.8
|
27.0
|
0.4
|
NH2
|
B:ARG67
|
3.0
|
17.7
|
0.5
|
C
|
B:SER338
|
3.5
|
23.0
|
1.0
|
N
|
B:TYR342
|
3.6
|
19.6
|
1.0
|
OH
|
B:TYR342
|
3.6
|
34.3
|
0.4
|
NH1
|
B:ARG67
|
3.6
|
21.1
|
0.5
|
C
|
B:FMT503
|
3.7
|
43.0
|
1.0
|
CZ
|
B:ARG67
|
3.7
|
23.2
|
0.5
|
CA
|
B:SER338
|
3.8
|
19.9
|
1.0
|
CB
|
B:TYR342
|
3.8
|
24.1
|
0.6
|
CB
|
B:TYR342
|
3.8
|
24.1
|
0.4
|
O2
|
B:FMT503
|
3.9
|
42.8
|
1.0
|
CB
|
B:SER338
|
3.9
|
25.9
|
1.0
|
CB
|
B:TRP341
|
3.9
|
17.0
|
1.0
|
CA
|
B:TYR342
|
4.0
|
22.5
|
0.6
|
CA
|
B:TYR342
|
4.0
|
22.5
|
0.4
|
NH1
|
B:ARG345
|
4.1
|
46.9
|
1.0
|
C
|
B:TRP341
|
4.3
|
20.2
|
1.0
|
NH2
|
B:ARG67
|
4.3
|
22.7
|
0.5
|
NH2
|
B:ARG345
|
4.4
|
38.0
|
1.0
|
CD1
|
B:TYR342
|
4.5
|
34.0
|
0.6
|
CA
|
B:TRP341
|
4.6
|
17.4
|
1.0
|
CZ
|
B:ARG345
|
4.7
|
41.1
|
1.0
|
CG
|
B:TYR342
|
4.7
|
28.8
|
0.6
|
O4
|
B:MAL501
|
4.7
|
18.6
|
1.0
|
N
|
B:ALA339
|
4.8
|
21.9
|
1.0
|
O1
|
B:FMT503
|
4.8
|
39.5
|
1.0
|
OG
|
B:SER338
|
4.8
|
30.6
|
1.0
|
N
|
B:TRP341
|
5.0
|
17.5
|
1.0
|
NE
|
B:ARG67
|
5.0
|
17.7
|
0.5
|
|
Reference:
T.Jin,
M.Huang,
J.Jiang,
P.Smith,
T.Xiao.
Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction To Be Published.
Page generated: Mon Oct 7 19:06:26 2024
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