Sodium in PDB 7zg7: Structure of Human Apoferritin Obtained From Ssdna Coated Grid
Enzymatic activity of Structure of Human Apoferritin Obtained From Ssdna Coated Grid
All present enzymatic activity of Structure of Human Apoferritin Obtained From Ssdna Coated Grid:
1.16.3.1;
Other elements in 7zg7:
The structure of Structure of Human Apoferritin Obtained From Ssdna Coated Grid also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
40;
Page 5, Binding sites: 41 -
50;
Page 6, Binding sites: 51 -
60;
Page 7, Binding sites: 61 -
70;
Page 8, Binding sites: 71 -
80;
Page 9, Binding sites: 81 -
90;
Page 10, Binding sites: 91 -
100;
Page 11, Binding sites: 101 -
110;
Page 12, Binding sites: 111 -
112;
Binding sites:
The binding sites of Sodium atom in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
(pdb code 7zg7). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 112 binding sites of Sodium where determined in the
Structure of Human Apoferritin Obtained From Ssdna Coated Grid, PDB code: 7zg7:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 1 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na208
b:25.5
occ:1.00
|
O
|
F:HOH325
|
2.8
|
13.3
|
1.0
|
O
|
S:HOH353
|
2.8
|
8.4
|
1.0
|
CD
|
A:GLN7
|
4.0
|
5.4
|
1.0
|
NE2
|
A:GLN7
|
4.0
|
1.7
|
1.0
|
NH1
|
F:ARG156
|
4.2
|
11.4
|
0.5
|
ZN
|
S:ZN202
|
4.2
|
73.4
|
1.0
|
CB
|
S:ASP45
|
4.2
|
6.9
|
1.0
|
OE1
|
A:GLN7
|
4.3
|
7.8
|
1.0
|
CB
|
A:GLN7
|
4.3
|
0.3
|
1.0
|
CG
|
A:GLN7
|
4.4
|
1.2
|
1.0
|
O
|
S:HOH359
|
4.4
|
14.8
|
1.0
|
OG1
|
F:THR153
|
4.6
|
5.4
|
1.0
|
OD2
|
S:ASP44
|
4.6
|
8.4
|
1.0
|
N
|
A:GLN7
|
4.7
|
0.1
|
1.0
|
CA
|
S:ASP45
|
4.8
|
6.4
|
1.0
|
|
Sodium binding site 2 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 2 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na209
b:23.7
occ:1.00
|
OD1
|
A:ASN109
|
2.4
|
2.1
|
0.5
|
O
|
A:HIS105
|
2.7
|
3.9
|
1.0
|
CD2
|
A:HIS105
|
3.0
|
8.1
|
1.0
|
NE2
|
A:HIS105
|
3.2
|
10.6
|
1.0
|
CG
|
A:ASN109
|
3.2
|
0.0
|
0.5
|
CG
|
A:HIS105
|
3.3
|
4.8
|
1.0
|
C
|
A:HIS105
|
3.5
|
0.0
|
1.0
|
CE1
|
A:HIS105
|
3.5
|
8.5
|
1.0
|
ND1
|
A:HIS105
|
3.6
|
11.8
|
1.0
|
CA
|
A:HIS105
|
3.6
|
0.0
|
1.0
|
N
|
A:ASN109
|
3.7
|
0.0
|
1.0
|
CB
|
A:LYS108
|
3.8
|
0.0
|
1.0
|
ND2
|
A:ASN109
|
3.8
|
3.3
|
0.5
|
CB
|
A:HIS105
|
4.0
|
1.9
|
1.0
|
CB
|
A:ASN109
|
4.2
|
0.3
|
0.5
|
C
|
A:LYS108
|
4.2
|
0.6
|
1.0
|
CB
|
A:ASN109
|
4.2
|
0.4
|
0.5
|
CA
|
A:ASN109
|
4.2
|
0.0
|
1.0
|
CA
|
A:LYS108
|
4.5
|
1.5
|
1.0
|
N
|
A:LEU106
|
4.7
|
0.0
|
1.0
|
N
|
A:LYS108
|
4.9
|
0.0
|
1.0
|
CG
|
A:LYS108
|
4.9
|
0.0
|
1.0
|
O
|
A:LYS108
|
4.9
|
0.0
|
1.0
|
N
|
A:HIS105
|
5.0
|
0.0
|
1.0
|
O
|
A:LEU104
|
5.0
|
0.0
|
1.0
|
|
Sodium binding site 3 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 3 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na212
b:24.4
occ:1.00
|
O
|
T:HOH325
|
2.6
|
21.9
|
1.0
|
O
|
A:HOH365
|
2.8
|
14.9
|
1.0
|
CG
|
A:LEU104
|
3.9
|
0.0
|
1.0
|
CD
|
A:LYS108
|
4.0
|
2.5
|
1.0
|
CA
|
A:HIS105
|
4.0
|
0.0
|
1.0
|
CD2
|
A:LEU104
|
4.0
|
0.0
|
1.0
|
N
|
A:HIS105
|
4.1
|
0.0
|
1.0
|
CB
|
A:HIS105
|
4.3
|
1.9
|
1.0
|
O
|
A:HOH400
|
4.4
|
15.0
|
1.0
|
C
|
A:LEU104
|
4.4
|
0.0
|
1.0
|
CD2
|
A:HIS105
|
4.5
|
8.1
|
1.0
|
O
|
A:LEU104
|
4.6
|
0.0
|
1.0
|
CB
|
A:LEU104
|
4.6
|
0.0
|
1.0
|
O
|
T:GLN7
|
4.8
|
7.5
|
1.0
|
CG
|
A:HIS105
|
4.8
|
4.8
|
1.0
|
CG
|
A:LYS108
|
4.9
|
0.0
|
1.0
|
O
|
A:GLU101
|
4.9
|
0.0
|
1.0
|
NZ
|
A:LYS108
|
5.0
|
8.8
|
1.0
|
|
Sodium binding site 4 out
of 112 in 7zg7
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Sodium Binding Sites List in 7zg7
Sodium binding site 4 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na215
b:28.0
occ:1.00
|
O
|
A:HOH335
|
2.5
|
11.1
|
1.0
|
O
|
A:HOH410
|
2.6
|
16.6
|
1.0
|
CD1
|
A:LEU26
|
3.4
|
0.0
|
1.0
|
CD2
|
A:TYR29
|
3.8
|
0.0
|
1.0
|
CG
|
A:TYR29
|
4.0
|
0.0
|
1.0
|
CB
|
A:TYR29
|
4.2
|
0.0
|
1.0
|
CE2
|
A:TYR29
|
4.3
|
0.0
|
1.0
|
O
|
A:HOH376
|
4.3
|
10.6
|
1.0
|
CA
|
A:LEU26
|
4.5
|
0.0
|
1.0
|
CD1
|
A:TYR29
|
4.6
|
0.0
|
1.0
|
CG
|
A:LEU26
|
4.6
|
0.0
|
1.0
|
O
|
A:HOH336
|
4.7
|
12.8
|
1.0
|
OD1
|
A:ASN25
|
4.7
|
0.0
|
1.0
|
O
|
A:HOH409
|
4.7
|
18.6
|
1.0
|
CB
|
A:LEU26
|
4.8
|
0.0
|
1.0
|
CZ
|
A:TYR29
|
4.9
|
0.0
|
1.0
|
|
Sodium binding site 5 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 5 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na216
b:26.1
occ:1.00
|
OE1
|
A:GLN112
|
2.2
|
15.5
|
1.0
|
NE2
|
T:GLN10
|
2.8
|
5.3
|
1.0
|
CD
|
A:GLN112
|
3.2
|
7.2
|
1.0
|
CG
|
A:GLN112
|
3.6
|
3.7
|
1.0
|
CD
|
T:GLN10
|
3.8
|
7.8
|
1.0
|
CG
|
T:GLN10
|
3.8
|
4.9
|
1.0
|
CB
|
A:GLN112
|
3.8
|
3.1
|
1.0
|
NE2
|
A:GLN112
|
4.3
|
13.8
|
1.0
|
CA
|
A:GLN112
|
4.8
|
0.0
|
1.0
|
O
|
T:HOH308
|
4.9
|
17.2
|
1.0
|
OE1
|
T:GLN10
|
4.9
|
5.9
|
1.0
|
O
|
A:LYS108
|
4.9
|
0.0
|
1.0
|
|
Sodium binding site 6 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 6 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na208
b:28.1
occ:1.00
|
O
|
S:HOH326
|
2.8
|
12.6
|
1.0
|
O
|
P:HOH354
|
2.8
|
12.5
|
1.0
|
CD
|
B:GLN7
|
4.0
|
10.0
|
1.0
|
NE2
|
B:GLN7
|
4.0
|
1.6
|
1.0
|
NH1
|
S:ARG156
|
4.2
|
11.6
|
0.5
|
ZN
|
P:ZN202
|
4.2
|
66.9
|
1.0
|
CB
|
P:ASP45
|
4.2
|
4.4
|
1.0
|
OE1
|
B:GLN7
|
4.3
|
12.1
|
1.0
|
CB
|
B:GLN7
|
4.3
|
1.0
|
1.0
|
CG
|
B:GLN7
|
4.4
|
2.3
|
1.0
|
O
|
P:HOH359
|
4.4
|
11.5
|
1.0
|
OG1
|
S:THR153
|
4.6
|
5.6
|
1.0
|
OD2
|
P:ASP44
|
4.6
|
7.7
|
1.0
|
N
|
B:GLN7
|
4.7
|
1.5
|
1.0
|
CA
|
P:ASP45
|
4.8
|
4.5
|
1.0
|
|
Sodium binding site 7 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 7 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na209
b:26.2
occ:1.00
|
OD1
|
B:ASN109
|
2.4
|
5.0
|
0.5
|
O
|
B:HIS105
|
2.7
|
9.0
|
1.0
|
CD2
|
B:HIS105
|
3.0
|
12.4
|
1.0
|
NE2
|
B:HIS105
|
3.2
|
15.2
|
1.0
|
CG
|
B:ASN109
|
3.2
|
1.2
|
0.5
|
CG
|
B:HIS105
|
3.3
|
8.4
|
1.0
|
C
|
B:HIS105
|
3.5
|
1.1
|
1.0
|
CE1
|
B:HIS105
|
3.5
|
13.7
|
1.0
|
ND1
|
B:HIS105
|
3.6
|
17.6
|
1.0
|
CA
|
B:HIS105
|
3.6
|
0.0
|
1.0
|
N
|
B:ASN109
|
3.7
|
1.6
|
1.0
|
CB
|
B:LYS108
|
3.8
|
1.9
|
1.0
|
ND2
|
B:ASN109
|
3.8
|
6.8
|
0.5
|
CB
|
B:HIS105
|
4.0
|
2.3
|
1.0
|
CB
|
B:ASN109
|
4.2
|
1.7
|
0.5
|
C
|
B:LYS108
|
4.2
|
0.7
|
1.0
|
CB
|
B:ASN109
|
4.2
|
6.8
|
0.5
|
CA
|
B:ASN109
|
4.2
|
0.8
|
1.0
|
CA
|
B:LYS108
|
4.5
|
0.6
|
1.0
|
N
|
B:LEU106
|
4.7
|
0.0
|
1.0
|
N
|
B:LYS108
|
4.9
|
0.0
|
1.0
|
CG
|
B:LYS108
|
4.9
|
1.4
|
1.0
|
O
|
B:LYS108
|
4.9
|
7.6
|
1.0
|
N
|
B:HIS105
|
5.0
|
0.2
|
1.0
|
O
|
B:LEU104
|
5.0
|
5.5
|
1.0
|
|
Sodium binding site 8 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 8 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na212
b:28.5
occ:1.00
|
O
|
M:HOH325
|
2.6
|
12.2
|
1.0
|
O
|
B:HOH364
|
2.8
|
18.0
|
1.0
|
CG
|
B:LEU104
|
3.9
|
0.0
|
1.0
|
CD
|
B:LYS108
|
4.0
|
6.0
|
1.0
|
CA
|
B:HIS105
|
4.0
|
0.0
|
1.0
|
CD2
|
B:LEU104
|
4.0
|
0.9
|
1.0
|
N
|
B:HIS105
|
4.1
|
0.2
|
1.0
|
CB
|
B:HIS105
|
4.3
|
2.3
|
1.0
|
O
|
B:HOH400
|
4.4
|
19.4
|
1.0
|
C
|
B:LEU104
|
4.4
|
0.0
|
1.0
|
CD2
|
B:HIS105
|
4.5
|
12.4
|
1.0
|
O
|
B:LEU104
|
4.6
|
5.5
|
1.0
|
CB
|
B:LEU104
|
4.6
|
0.0
|
1.0
|
O
|
M:GLN7
|
4.8
|
6.1
|
1.0
|
CG
|
B:HIS105
|
4.8
|
8.4
|
1.0
|
CG
|
B:LYS108
|
4.9
|
1.4
|
1.0
|
O
|
B:GLU101
|
4.9
|
1.7
|
1.0
|
NZ
|
B:LYS108
|
5.0
|
12.3
|
1.0
|
|
Sodium binding site 9 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 9 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na215
b:31.7
occ:1.00
|
O
|
B:HOH335
|
2.5
|
15.9
|
1.0
|
O
|
B:HOH410
|
2.6
|
20.1
|
1.0
|
CD1
|
B:LEU26
|
3.4
|
2.2
|
1.0
|
CD2
|
B:TYR29
|
3.8
|
0.0
|
1.0
|
CG
|
B:TYR29
|
4.0
|
0.0
|
1.0
|
CB
|
B:TYR29
|
4.2
|
0.0
|
1.0
|
CE2
|
B:TYR29
|
4.3
|
1.6
|
1.0
|
O
|
B:HOH376
|
4.3
|
7.6
|
1.0
|
CA
|
B:LEU26
|
4.5
|
0.2
|
1.0
|
CD1
|
B:TYR29
|
4.6
|
0.0
|
1.0
|
CG
|
B:LEU26
|
4.6
|
0.0
|
1.0
|
O
|
B:HOH336
|
4.7
|
13.8
|
1.0
|
OD1
|
B:ASN25
|
4.7
|
7.0
|
1.0
|
O
|
B:HOH409
|
4.7
|
24.3
|
1.0
|
CB
|
B:LEU26
|
4.8
|
0.0
|
1.0
|
CZ
|
B:TYR29
|
4.9
|
0.4
|
1.0
|
|
Sodium binding site 10 out
of 112 in 7zg7
Go back to
Sodium Binding Sites List in 7zg7
Sodium binding site 10 out
of 112 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na216
b:31.0
occ:1.00
|
OE1
|
B:GLN112
|
2.2
|
23.0
|
1.0
|
NE2
|
M:GLN10
|
2.8
|
2.2
|
1.0
|
CD
|
B:GLN112
|
3.2
|
13.8
|
1.0
|
CG
|
B:GLN112
|
3.6
|
6.5
|
1.0
|
CD
|
M:GLN10
|
3.8
|
2.8
|
1.0
|
CG
|
M:GLN10
|
3.8
|
0.0
|
1.0
|
CB
|
B:GLN112
|
3.8
|
3.2
|
1.0
|
NE2
|
B:GLN112
|
4.3
|
19.7
|
1.0
|
CA
|
B:GLN112
|
4.8
|
0.0
|
1.0
|
O
|
M:HOH308
|
4.9
|
23.3
|
1.0
|
OE1
|
M:GLN10
|
4.9
|
3.8
|
1.0
|
O
|
B:LYS108
|
4.9
|
7.6
|
1.0
|
|
Reference:
D.Hrebik,
M.Gondova,
L.Valentova,
T.Fuzik,
A.Pridal,
J.Novacek,
P.Plevka.
Polyelectrolyte Coating of Cryo-Em Grids Improves Lateral Distribution and Prevents Aggregation of Macromolecules. Acta Crystallogr D Struct V. 78 1337 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36322417
DOI: 10.1107/S2059798322009299
Page generated: Wed Oct 9 10:02:30 2024
|