Sodium in PDB 7ujj: STX2A and Darpin Complex
Enzymatic activity of STX2A and Darpin Complex
All present enzymatic activity of STX2A and Darpin Complex:
3.2.2.22;
Sodium Binding Sites:
The binding sites of Sodium atom in the STX2A and Darpin Complex
(pdb code 7ujj). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
STX2A and Darpin Complex, PDB code: 7ujj:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 7ujj
Go back to
Sodium Binding Sites List in 7ujj
Sodium binding site 1 out
of 5 in the STX2A and Darpin Complex
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of STX2A and Darpin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na4001
b:20.8
occ:1.00
|
O
|
A:HOH4338
|
2.2
|
22.1
|
1.0
|
O
|
A:THR22
|
2.2
|
16.4
|
1.0
|
O
|
A:HOH4298
|
2.3
|
29.0
|
1.0
|
O
|
A:SER25
|
2.4
|
15.2
|
1.0
|
O
|
A:HOH4398
|
2.4
|
27.6
|
1.0
|
O
|
A:HOH4392
|
2.4
|
22.5
|
1.0
|
C
|
A:THR22
|
3.4
|
15.7
|
1.0
|
C
|
A:SER25
|
3.5
|
13.2
|
1.0
|
CA
|
A:THR22
|
4.0
|
16.0
|
1.0
|
CG2
|
A:THR22
|
4.1
|
18.2
|
0.7
|
O
|
A:HOH4300
|
4.1
|
19.1
|
1.0
|
OG1
|
A:THR26
|
4.2
|
16.9
|
1.0
|
CA
|
A:THR26
|
4.3
|
13.9
|
1.0
|
N
|
A:SER25
|
4.3
|
11.4
|
1.0
|
N
|
A:THR26
|
4.4
|
12.9
|
1.0
|
N
|
A:GLU23
|
4.5
|
16.5
|
1.0
|
OD1
|
A:ASN42
|
4.5
|
19.7
|
1.0
|
CA
|
A:SER25
|
4.5
|
11.9
|
1.0
|
O
|
A:ARG21
|
4.6
|
13.1
|
1.0
|
C
|
A:GLU23
|
4.6
|
18.6
|
1.0
|
O
|
A:GLU23
|
4.7
|
18.2
|
1.0
|
CA
|
A:GLU23
|
4.7
|
17.8
|
1.0
|
CB
|
A:THR22
|
4.7
|
17.6
|
1.0
|
CD
|
A:PRO27
|
4.8
|
15.6
|
1.0
|
CB
|
A:THR26
|
4.9
|
15.8
|
1.0
|
|
Sodium binding site 2 out
of 5 in 7ujj
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Sodium Binding Sites List in 7ujj
Sodium binding site 2 out
of 5 in the STX2A and Darpin Complex
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of STX2A and Darpin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na4002
b:30.2
occ:1.00
|
OD1
|
A:ASN279
|
2.2
|
22.2
|
1.0
|
O
|
C:HOH248
|
2.2
|
26.2
|
1.0
|
O1
|
A:FMT4007
|
2.3
|
28.1
|
1.0
|
O
|
A:ARG266
|
2.5
|
17.0
|
1.0
|
O
|
A:HOH4269
|
2.6
|
21.4
|
1.0
|
C
|
A:FMT4007
|
2.8
|
26.8
|
1.0
|
O
|
A:HOH4215
|
3.2
|
20.4
|
1.0
|
OG
|
A:SER278
|
3.2
|
17.3
|
1.0
|
CG
|
A:ASN279
|
3.3
|
18.6
|
1.0
|
C
|
A:ARG266
|
3.4
|
15.5
|
1.0
|
ND2
|
A:ASN279
|
3.7
|
16.8
|
1.0
|
CA
|
A:PRO267
|
3.7
|
14.5
|
1.0
|
O
|
A:PRO267
|
3.8
|
12.7
|
1.0
|
N
|
A:PRO267
|
3.9
|
15.0
|
1.0
|
ND2
|
A:ASN207
|
4.0
|
16.2
|
1.0
|
O2
|
A:FMT4007
|
4.1
|
29.7
|
1.0
|
C
|
A:PRO267
|
4.1
|
14.0
|
1.0
|
N
|
A:ARG266
|
4.1
|
14.6
|
1.0
|
O
|
A:THR263
|
4.2
|
14.8
|
1.0
|
OG1
|
C:THR45
|
4.2
|
19.4
|
0.7
|
N
|
A:ASN279
|
4.3
|
9.3
|
1.0
|
CA
|
A:ARG266
|
4.4
|
15.0
|
1.0
|
CB
|
A:SER278
|
4.4
|
11.0
|
1.0
|
CB
|
A:ASN279
|
4.6
|
11.9
|
1.0
|
N
|
A:SER278
|
4.6
|
10.7
|
1.0
|
CG
|
A:GLU277
|
4.7
|
12.1
|
1.0
|
O
|
A:HOH4202
|
4.7
|
30.2
|
1.0
|
O
|
A:HOH4245
|
4.8
|
20.7
|
1.0
|
CA
|
A:SER278
|
4.9
|
11.7
|
1.0
|
CA
|
A:ASN279
|
5.0
|
10.4
|
1.0
|
|
Sodium binding site 3 out
of 5 in 7ujj
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Sodium Binding Sites List in 7ujj
Sodium binding site 3 out
of 5 in the STX2A and Darpin Complex
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of STX2A and Darpin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na4003
b:40.7
occ:1.00
|
O
|
A:HOH4390
|
2.2
|
22.4
|
1.0
|
OG
|
A:SER19
|
2.2
|
22.5
|
1.0
|
O
|
A:HOH4401
|
2.3
|
41.5
|
1.0
|
O
|
A:HOH4382
|
2.4
|
29.5
|
1.0
|
O
|
A:SER15
|
2.5
|
11.9
|
1.0
|
OG
|
A:SER15
|
2.5
|
15.2
|
1.0
|
C
|
A:SER15
|
3.2
|
11.0
|
1.0
|
CB
|
A:SER19
|
3.3
|
19.4
|
1.0
|
CB
|
A:SER15
|
3.6
|
13.3
|
1.0
|
CA
|
A:SER15
|
3.7
|
11.2
|
1.0
|
O
|
A:HOH4432
|
3.7
|
46.8
|
1.0
|
O
|
A:HOH4241
|
3.8
|
21.1
|
1.0
|
N
|
A:SER19
|
3.9
|
16.3
|
1.0
|
CA
|
A:SER19
|
4.0
|
16.7
|
1.0
|
N
|
A:SER16
|
4.1
|
9.9
|
1.0
|
O
|
A:HOH4399
|
4.3
|
31.4
|
1.0
|
CA
|
A:SER16
|
4.6
|
10.6
|
1.0
|
O
|
A:HOH4244
|
4.8
|
25.4
|
1.0
|
C
|
A:ASN18
|
4.9
|
15.1
|
1.0
|
C1
|
A:EDO4005
|
4.9
|
39.8
|
1.0
|
CB
|
A:ASN18
|
5.0
|
16.8
|
1.0
|
|
Sodium binding site 4 out
of 5 in 7ujj
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Sodium Binding Sites List in 7ujj
Sodium binding site 4 out
of 5 in the STX2A and Darpin Complex
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of STX2A and Darpin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na101
b:52.3
occ:1.00
|
HH21
|
G:ARG34
|
1.3
|
1.0
|
1.0
|
HG21
|
G:VAL42
|
1.6
|
1.0
|
1.0
|
NH2
|
G:ARG34
|
2.0
|
1.0
|
1.0
|
O
|
B:THR55
|
2.3
|
48.9
|
1.0
|
O
|
B:GLY61
|
2.4
|
24.8
|
1.0
|
HH22
|
G:ARG34
|
2.6
|
1.0
|
1.0
|
CG2
|
G:VAL42
|
2.6
|
1.0
|
1.0
|
OG
|
B:SER60
|
2.6
|
38.7
|
1.0
|
OG
|
B:SER53
|
2.6
|
37.2
|
1.0
|
HE
|
G:ARG34
|
2.8
|
1.0
|
1.0
|
CZ
|
G:ARG34
|
2.9
|
1.0
|
1.0
|
HG22
|
G:VAL42
|
2.9
|
1.0
|
1.0
|
HG13
|
G:VAL42
|
3.0
|
1.0
|
1.0
|
HG23
|
G:VAL42
|
3.1
|
1.0
|
1.0
|
NE
|
G:ARG34
|
3.2
|
1.0
|
1.0
|
OG1
|
B:THR55
|
3.3
|
49.8
|
1.0
|
C
|
B:THR55
|
3.3
|
47.7
|
1.0
|
HD12
|
G:LEU72
|
3.3
|
0.9
|
1.0
|
CB
|
B:SER60
|
3.4
|
34.3
|
1.0
|
CB
|
B:SER53
|
3.5
|
33.8
|
1.0
|
C
|
B:GLY61
|
3.6
|
24.8
|
1.0
|
CB
|
G:VAL42
|
3.6
|
1.0
|
1.0
|
CG1
|
G:VAL42
|
3.7
|
1.0
|
1.0
|
HG
|
G:LEU72
|
3.7
|
0.9
|
1.0
|
HB
|
G:VAL42
|
3.7
|
1.0
|
1.0
|
N
|
B:GLY61
|
3.7
|
27.5
|
1.0
|
HD13
|
G:LEU39
|
3.8
|
0.8
|
1.0
|
HD11
|
G:LEU72
|
3.8
|
0.9
|
1.0
|
HG12
|
G:VAL42
|
3.9
|
1.0
|
1.0
|
N
|
B:THR55
|
4.0
|
44.8
|
1.0
|
CD1
|
G:LEU72
|
4.0
|
0.9
|
1.0
|
NH1
|
G:ARG34
|
4.0
|
1.0
|
1.0
|
CA
|
B:THR55
|
4.0
|
47.8
|
1.0
|
C
|
B:SER60
|
4.1
|
30.8
|
1.0
|
O
|
B:HOH228
|
4.2
|
40.3
|
1.0
|
CB
|
B:THR55
|
4.2
|
48.2
|
1.0
|
CA
|
B:GLY61
|
4.2
|
26.0
|
1.0
|
HA
|
G:LEU39
|
4.3
|
0.8
|
1.0
|
N
|
B:CYS56
|
4.3
|
47.2
|
1.0
|
CA
|
B:SER60
|
4.3
|
33.3
|
1.0
|
HH12
|
G:ARG34
|
4.3
|
1.0
|
1.0
|
CG
|
G:LEU72
|
4.4
|
0.9
|
1.0
|
HD12
|
G:LEU39
|
4.4
|
0.8
|
1.0
|
CD
|
G:ARG34
|
4.5
|
1.0
|
1.0
|
HB3
|
G:LEU72
|
4.5
|
0.9
|
1.0
|
CD1
|
G:LEU39
|
4.5
|
0.8
|
1.0
|
CA
|
B:CYS56
|
4.5
|
47.1
|
1.0
|
HG11
|
G:VAL42
|
4.6
|
1.0
|
1.0
|
HD2
|
G:ARG34
|
4.6
|
1.0
|
1.0
|
N
|
B:PHE62
|
4.6
|
18.4
|
1.0
|
HB3
|
G:HIS38
|
4.7
|
0.7
|
1.0
|
O
|
G:HIS38
|
4.7
|
0.7
|
1.0
|
O
|
B:SER60
|
4.7
|
27.4
|
1.0
|
HD3
|
G:ARG34
|
4.8
|
1.0
|
1.0
|
HH11
|
G:ARG34
|
4.8
|
1.0
|
1.0
|
CA
|
B:SER53
|
4.8
|
32.9
|
1.0
|
CA
|
B:PHE62
|
4.8
|
16.1
|
1.0
|
HD11
|
G:LEU39
|
4.9
|
0.8
|
1.0
|
N
|
B:SER54
|
4.9
|
38.7
|
1.0
|
HD13
|
G:LEU72
|
5.0
|
0.9
|
1.0
|
|
Sodium binding site 5 out
of 5 in 7ujj
Go back to
Sodium Binding Sites List in 7ujj
Sodium binding site 5 out
of 5 in the STX2A and Darpin Complex
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/uj/7ujj-NA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of STX2A and Darpin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na101
b:30.9
occ:1.00
|
O
|
F:GLY61
|
2.2
|
20.3
|
1.0
|
O
|
F:THR55
|
2.3
|
32.5
|
1.0
|
OG
|
F:SER53
|
2.4
|
24.8
|
1.0
|
OG
|
F:SER60
|
2.5
|
29.1
|
1.0
|
CB
|
F:SER53
|
3.1
|
21.7
|
1.0
|
CB
|
F:SER60
|
3.3
|
24.6
|
1.0
|
C
|
F:GLY61
|
3.3
|
20.1
|
1.0
|
C
|
F:THR55
|
3.4
|
31.9
|
1.0
|
N
|
F:GLY61
|
3.4
|
21.6
|
1.0
|
CB
|
F:THR55
|
3.6
|
34.6
|
1.0
|
O
|
G:GLY176
|
3.7
|
1.5
|
1.0
|
HA
|
G:ASN177
|
3.8
|
1.6
|
1.0
|
CA
|
F:THR55
|
3.9
|
32.6
|
1.0
|
C
|
F:SER60
|
3.9
|
23.0
|
1.0
|
CA
|
F:GLY61
|
3.9
|
21.5
|
1.0
|
N
|
F:THR55
|
4.0
|
31.6
|
1.0
|
O
|
G:HOH306
|
4.0
|
31.0
|
1.0
|
H
|
G:GLU178
|
4.1
|
1.6
|
1.0
|
HD21
|
G:ASN177
|
4.1
|
1.6
|
1.0
|
CG2
|
F:THR55
|
4.2
|
37.0
|
1.0
|
CA
|
F:SER60
|
4.2
|
24.1
|
1.0
|
HG2
|
G:GLU178
|
4.3
|
1.6
|
1.0
|
N
|
F:PHE62
|
4.4
|
18.1
|
1.0
|
N
|
F:CYS56
|
4.5
|
30.2
|
1.0
|
O
|
F:SER60
|
4.5
|
21.3
|
1.0
|
CA
|
F:SER53
|
4.6
|
22.9
|
1.0
|
CA
|
F:PHE62
|
4.7
|
17.2
|
1.0
|
OG1
|
F:THR55
|
4.8
|
37.8
|
1.0
|
CD1
|
F:TYR28
|
4.8
|
24.3
|
1.0
|
CA
|
G:ASN177
|
4.8
|
1.6
|
1.0
|
CA
|
F:CYS56
|
4.9
|
30.7
|
1.0
|
C
|
G:GLY176
|
4.9
|
1.5
|
1.0
|
ND2
|
G:ASN177
|
4.9
|
1.6
|
1.0
|
N
|
G:GLU178
|
4.9
|
1.6
|
1.0
|
C
|
F:SER53
|
5.0
|
25.2
|
1.0
|
N
|
F:SER54
|
5.0
|
27.1
|
1.0
|
CB
|
F:PHE62
|
5.0
|
16.3
|
1.0
|
|
Reference:
Y.Zeng,
M.Jiang,
S.Robinson,
Z.Peng,
V.Chonira,
R.Simeon,
S.Tzipori,
J.Zhang,
Z.Chen.
A Multi-Specific Darpin Potently Neutralizes Shiga Toxin 2 Via Simultaneous Modulation of Both Toxin Subunits. Bioengineering (Basel) V. 9 2022.
ISSN: ISSN 2306-5354
PubMed: 36290479
DOI: 10.3390/BIOENGINEERING9100511
Page generated: Wed Apr 26 00:00:23 2023
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