Sodium in PDB 7p4l: Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
Protein crystallography data
The structure of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1), PDB code: 7p4l
was solved by
S.Nishio,
K.Tunyasuvunakool,
J.Jumper,
D.De Sanctis,
L.Jovine,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
67.32 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
262.51,
111.33,
68.51,
90,
100.71,
90
|
R / Rfree (%)
|
19.9 /
24.3
|
Other elements in 7p4l:
The structure of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
(pdb code 7p4l). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the
Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1), PDB code: 7p4l:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 1 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na612
b:34.5
occ:1.00
|
OE2
|
A:GLU250
|
2.2
|
51.4
|
1.0
|
OE2
|
B:GLU250
|
2.3
|
56.7
|
1.0
|
O
|
A:HOH827
|
2.3
|
50.6
|
1.0
|
O
|
B:HOH843
|
2.3
|
41.3
|
1.0
|
O
|
C:HOH795
|
2.4
|
47.9
|
1.0
|
OE2
|
C:GLU250
|
2.4
|
66.9
|
1.0
|
CD
|
A:GLU250
|
3.0
|
59.2
|
1.0
|
OE1
|
A:GLU250
|
3.2
|
57.4
|
1.0
|
CD
|
C:GLU250
|
3.2
|
57.0
|
1.0
|
CD
|
B:GLU250
|
3.2
|
47.6
|
1.0
|
OE1
|
C:GLU250
|
3.2
|
56.9
|
1.0
|
OE1
|
B:GLU250
|
3.5
|
64.8
|
1.0
|
O
|
B:HOH830
|
4.0
|
40.3
|
1.0
|
O
|
C:HOH782
|
4.1
|
38.6
|
1.0
|
O
|
A:HOH771
|
4.2
|
33.5
|
1.0
|
OE1
|
A:GLN247
|
4.3
|
69.8
|
1.0
|
OE1
|
C:GLN247
|
4.4
|
63.0
|
1.0
|
CG
|
A:GLU250
|
4.5
|
41.9
|
1.0
|
OE1
|
B:GLN247
|
4.5
|
64.5
|
1.0
|
CG
|
B:GLU250
|
4.6
|
48.4
|
1.0
|
CG
|
C:GLU250
|
4.6
|
46.1
|
1.0
|
|
Sodium binding site 2 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 2 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na613
b:55.8
occ:1.00
|
O
|
A:SER387
|
2.6
|
47.6
|
1.0
|
O
|
B:ASP197
|
2.7
|
49.2
|
1.0
|
C
|
A:SER387
|
3.7
|
38.5
|
1.0
|
C
|
B:ASP197
|
3.8
|
38.2
|
1.0
|
CB
|
A:SER387
|
4.2
|
35.9
|
1.0
|
CA
|
A:SER387
|
4.3
|
36.8
|
1.0
|
CA
|
B:ALA198
|
4.4
|
40.1
|
1.0
|
N
|
B:ALA198
|
4.5
|
34.7
|
1.0
|
OD2
|
B:ASP197
|
4.6
|
60.3
|
1.0
|
CB
|
B:ASP197
|
4.6
|
41.6
|
1.0
|
O
|
A:HOH763
|
4.7
|
65.4
|
1.0
|
N
|
A:SER388
|
4.7
|
31.1
|
1.0
|
CA
|
B:ASP197
|
4.7
|
34.8
|
1.0
|
CB
|
A:SER388
|
4.7
|
42.3
|
1.0
|
C
|
B:ALA198
|
4.7
|
42.3
|
1.0
|
O
|
B:HOH824
|
4.7
|
47.4
|
1.0
|
O
|
B:GLY199
|
4.8
|
45.2
|
1.0
|
O
|
A:HOH828
|
4.8
|
60.8
|
1.0
|
N
|
B:GLY199
|
4.9
|
46.6
|
1.0
|
CA
|
A:SER388
|
5.0
|
45.9
|
1.0
|
OG
|
A:SER387
|
5.0
|
55.1
|
1.0
|
CG
|
B:ASP197
|
5.0
|
55.9
|
1.0
|
|
Sodium binding site 3 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 3 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na614
b:60.8
occ:1.00
|
OE1
|
C:GLN499
|
2.6
|
68.5
|
1.0
|
OE1
|
A:GLU108
|
2.6
|
70.6
|
1.0
|
OE2
|
C:GLU507
|
3.2
|
75.2
|
1.0
|
CD
|
A:GLU108
|
3.4
|
71.8
|
1.0
|
OE2
|
A:GLU108
|
3.5
|
68.4
|
1.0
|
CD
|
C:GLN499
|
3.6
|
47.0
|
1.0
|
NE2
|
C:GLN499
|
3.9
|
55.3
|
1.0
|
CD
|
C:GLU507
|
4.3
|
68.0
|
1.0
|
OE1
|
C:GLU507
|
4.5
|
79.2
|
1.0
|
O
|
A:HOH811
|
4.6
|
45.1
|
1.0
|
CG
|
A:GLU108
|
4.9
|
50.7
|
1.0
|
O
|
A:TYR107
|
4.9
|
55.0
|
1.0
|
|
Sodium binding site 4 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 4 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na615
b:54.5
occ:1.00
|
OD2
|
A:ASP263
|
2.1
|
63.4
|
1.0
|
O
|
C:HOH733
|
2.3
|
49.5
|
1.0
|
O
|
A:HOH797
|
2.4
|
66.9
|
1.0
|
O
|
C:HOH753
|
2.5
|
53.8
|
1.0
|
O
|
A:HOH772
|
2.6
|
58.2
|
1.0
|
CG
|
A:ASP263
|
3.1
|
70.0
|
1.0
|
OD1
|
A:ASP263
|
3.4
|
84.4
|
1.0
|
O
|
B:HOH822
|
4.3
|
46.4
|
1.0
|
OD1
|
C:ASP260
|
4.3
|
54.5
|
1.0
|
CB
|
A:ASP263
|
4.4
|
46.8
|
1.0
|
O
|
A:GLY259
|
4.4
|
37.5
|
1.0
|
CB
|
C:ASP263
|
4.5
|
57.2
|
1.0
|
O
|
C:ASP260
|
4.5
|
41.8
|
1.0
|
CG
|
C:ASP260
|
4.5
|
54.6
|
1.0
|
CB
|
C:ASP260
|
4.6
|
38.6
|
1.0
|
OD1
|
A:ASP260
|
4.7
|
51.3
|
1.0
|
C
|
A:GLY259
|
4.7
|
40.2
|
1.0
|
CA
|
C:ASP260
|
4.9
|
50.5
|
1.0
|
OD2
|
C:ASP263
|
4.9
|
66.4
|
1.0
|
OD2
|
C:ASP267
|
4.9
|
67.3
|
1.0
|
|
Sodium binding site 5 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 5 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na616
b:41.7
occ:1.00
|
OD1
|
A:ASP319
|
2.2
|
37.4
|
1.0
|
O
|
A:SER85
|
2.2
|
36.7
|
1.0
|
O
|
A:THR320
|
2.3
|
40.2
|
1.0
|
OD1
|
A:ASP84
|
2.4
|
43.6
|
1.0
|
O
|
A:HOH807
|
2.5
|
38.4
|
1.0
|
O
|
A:HOH825
|
2.7
|
40.1
|
1.0
|
N
|
A:THR320
|
3.2
|
34.2
|
1.0
|
OG1
|
A:THR320
|
3.2
|
65.2
|
1.0
|
C
|
A:THR320
|
3.3
|
40.8
|
1.0
|
C
|
A:SER85
|
3.4
|
37.6
|
1.0
|
CG
|
A:ASP84
|
3.4
|
38.2
|
1.0
|
CG
|
A:ASP319
|
3.4
|
39.9
|
1.0
|
CA
|
A:CA608
|
3.4
|
50.0
|
1.0
|
C
|
A:ASP319
|
3.6
|
29.1
|
1.0
|
N
|
A:SER85
|
3.6
|
39.9
|
1.0
|
CA
|
A:THR320
|
3.7
|
43.6
|
1.0
|
OD2
|
A:ASP84
|
3.8
|
38.3
|
1.0
|
CA
|
A:SER85
|
4.0
|
37.0
|
1.0
|
CA
|
A:ASP319
|
4.0
|
31.8
|
1.0
|
CB
|
A:THR320
|
4.1
|
53.0
|
1.0
|
O
|
A:ASP319
|
4.1
|
46.3
|
1.0
|
O
|
A:HOH901
|
4.2
|
42.7
|
1.0
|
OD2
|
A:ASP319
|
4.3
|
42.7
|
1.0
|
CB
|
A:ASP319
|
4.3
|
35.2
|
1.0
|
N
|
A:LYS86
|
4.4
|
35.1
|
1.0
|
N
|
A:PRO321
|
4.5
|
59.0
|
1.0
|
CB
|
A:SER85
|
4.5
|
27.2
|
1.0
|
O
|
A:GLU322
|
4.5
|
37.9
|
1.0
|
C
|
A:ASP84
|
4.5
|
37.4
|
1.0
|
CB
|
A:ASP84
|
4.6
|
27.1
|
1.0
|
CG
|
A:LYS86
|
4.6
|
50.6
|
1.0
|
CA
|
A:ASP84
|
4.7
|
32.3
|
1.0
|
O
|
A:HOH881
|
4.7
|
50.7
|
1.0
|
CA
|
A:LYS86
|
4.8
|
35.9
|
1.0
|
O
|
A:HOH879
|
4.9
|
51.4
|
1.0
|
CA
|
A:PRO321
|
4.9
|
43.9
|
1.0
|
|
Sodium binding site 6 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 6 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na612
b:70.3
occ:1.00
|
O
|
C:ASP197
|
2.8
|
43.2
|
1.0
|
O
|
B:SER387
|
3.0
|
53.4
|
1.0
|
C
|
C:ASP197
|
3.7
|
34.5
|
1.0
|
CA
|
C:ALA198
|
4.0
|
40.0
|
1.0
|
OD2
|
C:ASP197
|
4.2
|
74.5
|
1.0
|
C
|
B:SER387
|
4.2
|
45.5
|
1.0
|
N
|
C:ALA198
|
4.2
|
44.0
|
1.0
|
CB
|
C:ASP197
|
4.5
|
41.9
|
1.0
|
C
|
C:ALA198
|
4.6
|
44.1
|
1.0
|
CG
|
C:ASP197
|
4.7
|
52.3
|
1.0
|
CA
|
C:ASP197
|
4.7
|
44.7
|
1.0
|
N
|
C:GLY199
|
4.8
|
35.5
|
1.0
|
CA
|
B:SER387
|
4.9
|
42.6
|
1.0
|
|
Sodium binding site 7 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 7 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na613
b:58.7
occ:1.00
|
O
|
B:HOH777
|
2.5
|
67.9
|
1.0
|
OE1
|
B:GLU108
|
2.7
|
81.8
|
1.0
|
OE1
|
A:GLN499
|
2.7
|
94.8
|
1.0
|
OE2
|
A:GLU507
|
3.3
|
82.1
|
1.0
|
OE2
|
B:GLU108
|
3.4
|
74.0
|
1.0
|
CD
|
B:GLU108
|
3.4
|
77.5
|
1.0
|
O
|
B:HOH708
|
3.5
|
66.5
|
1.0
|
CD
|
A:GLN499
|
3.6
|
69.5
|
1.0
|
NE2
|
A:GLN499
|
3.7
|
57.5
|
1.0
|
CD
|
A:GLU507
|
4.3
|
93.6
|
1.0
|
O
|
B:HOH721
|
4.4
|
51.6
|
1.0
|
O
|
B:TYR107
|
4.5
|
49.5
|
1.0
|
OE1
|
A:GLU507
|
4.5
|
98.6
|
1.0
|
O
|
A:ALA498
|
4.6
|
55.0
|
1.0
|
CG
|
B:GLU108
|
4.8
|
50.4
|
1.0
|
|
Sodium binding site 8 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 8 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
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 Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na614
b:68.8
occ:1.00
|
OE2
|
B:GLU507
|
2.5
|
95.4
|
1.0
|
OE1
|
C:GLU108
|
2.7
|
72.0
|
1.0
|
OE1
|
B:GLN499
|
2.8
|
74.2
|
1.0
|
CD
|
B:GLU507
|
3.4
|
95.6
|
1.0
|
CD
|
C:GLU108
|
3.5
|
90.0
|
1.0
|
NE2
|
B:GLN499
|
3.5
|
55.2
|
1.0
|
CD
|
B:GLN499
|
3.5
|
68.8
|
1.0
|
OE2
|
C:GLU108
|
3.6
|
93.2
|
1.0
|
OE1
|
B:GLU507
|
3.6
|
85.0
|
1.0
|
O
|
C:TYR107
|
4.5
|
62.4
|
1.0
|
CG
|
B:GLU507
|
4.8
|
69.1
|
1.0
|
O
|
B:ALA498
|
4.8
|
68.2
|
1.0
|
CG
|
C:GLU108
|
4.9
|
69.2
|
1.0
|
|
Sodium binding site 9 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 9 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na615
b:47.9
occ:1.00
|
O
|
A:HOH739
|
2.3
|
52.5
|
1.0
|
O
|
B:HOH822
|
2.4
|
46.4
|
1.0
|
O
|
B:HOH750
|
2.4
|
48.1
|
1.0
|
OD2
|
B:ASP263
|
2.5
|
63.3
|
1.0
|
O
|
A:HOH799
|
2.6
|
57.6
|
1.0
|
CG
|
B:ASP263
|
3.3
|
52.5
|
1.0
|
O
|
B:HOH782
|
3.4
|
54.7
|
1.0
|
OD1
|
B:ASP263
|
3.6
|
65.2
|
1.0
|
O
|
B:HOH831
|
4.3
|
62.0
|
1.0
|
CB
|
A:ASP263
|
4.3
|
46.8
|
1.0
|
O
|
A:ASP260
|
4.3
|
45.6
|
1.0
|
O
|
B:HOH759
|
4.4
|
50.8
|
1.0
|
OD1
|
A:ASP260
|
4.4
|
51.3
|
1.0
|
CB
|
A:ASP260
|
4.6
|
43.8
|
1.0
|
CG
|
A:ASP260
|
4.6
|
57.8
|
1.0
|
OD2
|
A:ASP267
|
4.7
|
78.9
|
1.0
|
CB
|
B:ASP263
|
4.7
|
43.8
|
1.0
|
O
|
B:GLY259
|
4.7
|
52.4
|
1.0
|
CA
|
A:ASP260
|
4.7
|
41.0
|
1.0
|
OD1
|
B:ASP260
|
4.8
|
66.0
|
1.0
|
OD2
|
A:ASP263
|
4.9
|
63.4
|
1.0
|
C
|
B:GLY259
|
5.0
|
43.2
|
1.0
|
C
|
A:ASP260
|
5.0
|
43.8
|
1.0
|
|
Sodium binding site 10 out
of 14 in 7p4l
Go back to
Sodium Binding Sites List in 7p4l
Sodium binding site 10 out
of 14 in the Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of the Trimeric Ectodomain of Archaeal FUSEXIN1 (FSX1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na616
b:41.2
occ:1.00
|
OD1
|
B:ASP319
|
2.2
|
38.9
|
1.0
|
O
|
B:HOH771
|
2.2
|
37.3
|
1.0
|
O
|
B:SER85
|
2.2
|
30.0
|
1.0
|
O
|
B:THR320
|
2.3
|
50.5
|
1.0
|
OD1
|
B:ASP84
|
2.5
|
49.4
|
1.0
|
N
|
B:THR320
|
3.3
|
38.4
|
1.0
|
C
|
B:THR320
|
3.3
|
39.4
|
1.0
|
C
|
B:SER85
|
3.4
|
39.5
|
1.0
|
CG
|
B:ASP319
|
3.4
|
47.0
|
1.0
|
CG
|
B:ASP84
|
3.5
|
46.1
|
1.0
|
N
|
B:SER85
|
3.5
|
38.7
|
1.0
|
CA
|
B:CA606
|
3.6
|
53.7
|
1.0
|
C
|
B:ASP319
|
3.7
|
41.7
|
1.0
|
CG2
|
B:THR320
|
3.7
|
43.9
|
1.0
|
CA
|
B:THR320
|
3.8
|
48.1
|
1.0
|
O
|
B:HOH894
|
3.9
|
45.3
|
1.0
|
CA
|
B:SER85
|
3.9
|
37.9
|
1.0
|
OD2
|
B:ASP84
|
4.1
|
57.8
|
1.0
|
CA
|
B:ASP319
|
4.1
|
36.5
|
1.0
|
O
|
B:ASP319
|
4.2
|
44.4
|
1.0
|
OD2
|
B:ASP319
|
4.3
|
43.9
|
1.0
|
CB
|
B:SER85
|
4.3
|
34.2
|
1.0
|
O
|
B:HOH753
|
4.3
|
54.4
|
1.0
|
O
|
B:GLU322
|
4.4
|
45.2
|
1.0
|
CB
|
B:THR320
|
4.4
|
45.6
|
1.0
|
CB
|
B:ASP319
|
4.4
|
40.6
|
1.0
|
N
|
B:PRO321
|
4.5
|
54.3
|
1.0
|
N
|
B:LYS86
|
4.5
|
31.9
|
1.0
|
C
|
B:ASP84
|
4.5
|
45.3
|
1.0
|
CB
|
B:ASP84
|
4.7
|
38.2
|
1.0
|
CA
|
B:ASP84
|
4.7
|
40.3
|
1.0
|
CG
|
B:LYS86
|
4.8
|
39.3
|
1.0
|
CA
|
B:PRO321
|
4.8
|
44.3
|
1.0
|
C
|
B:PRO321
|
4.9
|
48.3
|
1.0
|
CA
|
B:LYS86
|
4.9
|
36.5
|
1.0
|
N
|
B:GLU322
|
4.9
|
49.6
|
1.0
|
O
|
B:HOH885
|
4.9
|
46.3
|
1.0
|
|
Reference:
D.Moi,
S.Nishio,
X.Li,
C.Valansi,
M.Langleib,
N.G.Brukman,
K.Flyak,
C.Dessimoz,
D.De Sanctis,
K.Tunyasuvunakool,
J.Jumper,
M.Grana,
H.Romero,
P.S.Aguilar,
L.Jovine,
B.Podbilewicz.
Discovery of Archaeal Fusexins Homologous to Eukaryotic HAP2/GCS1 Gamete Fusion Proteins Nat Commun V. 13 3880 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-31564-1
Page generated: Tue Oct 8 18:27:13 2024
|