Magnesium in PDB 7jy8: Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
(pdb code 7jy8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas, PDB code: 7jy8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 1 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:23.5
occ:1.00
|
OG1
|
A:THR73
|
2.2
|
23.7
|
1.0
|
|
O2G
|
A:AGS402
|
2.2
|
24.9
|
1.0
|
|
O1B
|
A:AGS402
|
2.2
|
23.9
|
1.0
|
|
HG1
|
A:THR73
|
2.5
|
23.8
|
1.0
|
|
PG
|
A:AGS402
|
3.0
|
25.4
|
1.0
|
|
HOG2
|
A:AGS402
|
3.0
|
25.3
|
1.0
|
|
S1G
|
A:AGS402
|
3.1
|
25.0
|
1.0
|
|
H
|
A:THR73
|
3.1
|
23.2
|
1.0
|
|
HB2
|
A:LYS72
|
3.2
|
22.5
|
1.0
|
|
HE2
|
A:LYS72
|
3.3
|
22.7
|
1.0
|
|
PB
|
A:AGS402
|
3.3
|
24.5
|
1.0
|
|
OD1
|
A:ASP144
|
3.4
|
23.2
|
1.0
|
|
HG22
|
A:ILE192
|
3.4
|
21.7
|
1.0
|
|
CB
|
A:THR73
|
3.5
|
23.8
|
1.0
|
|
O3B
|
A:AGS402
|
3.6
|
25.4
|
1.0
|
|
N
|
A:THR73
|
3.7
|
22.8
|
1.0
|
|
HD13
|
A:ILE192
|
3.7
|
21.7
|
1.0
|
|
OE1
|
A:GLU96
|
3.7
|
25.1
|
1.0
|
|
HB
|
A:THR73
|
3.7
|
24.2
|
1.0
|
|
OD2
|
A:ASP144
|
3.8
|
23.5
|
1.0
|
|
CG
|
A:ASP144
|
4.0
|
23.3
|
1.0
|
|
O2B
|
A:AGS402
|
4.0
|
24.4
|
1.0
|
|
CA
|
A:THR73
|
4.0
|
23.1
|
1.0
|
|
CB
|
A:LYS72
|
4.1
|
22.1
|
1.0
|
|
HA
|
A:THR73
|
4.2
|
22.8
|
1.0
|
|
CE
|
A:LYS72
|
4.2
|
22.7
|
1.0
|
|
HB3
|
A:LYS72
|
4.3
|
21.7
|
1.0
|
|
O3G
|
A:AGS402
|
4.3
|
26.5
|
1.0
|
|
OE2
|
A:GLU96
|
4.3
|
24.9
|
1.0
|
|
CG2
|
A:ILE192
|
4.4
|
21.3
|
1.0
|
|
CD
|
A:GLU96
|
4.4
|
25.1
|
1.0
|
|
HZ2
|
A:LYS72
|
4.5
|
24.0
|
1.0
|
|
C
|
A:LYS72
|
4.6
|
22.3
|
1.0
|
|
CG2
|
A:THR73
|
4.6
|
24.3
|
1.0
|
|
CD1
|
A:ILE192
|
4.6
|
21.4
|
1.0
|
|
HD11
|
A:ILE192
|
4.6
|
21.7
|
1.0
|
|
HG21
|
A:ILE192
|
4.6
|
21.4
|
1.0
|
|
HZ3
|
A:LYS72
|
4.6
|
23.8
|
1.0
|
|
HG22
|
A:THR73
|
4.6
|
24.9
|
1.0
|
|
HE3
|
A:LYS72
|
4.6
|
22.6
|
1.0
|
|
O3A
|
A:AGS402
|
4.7
|
25.1
|
1.0
|
|
HG23
|
A:THR73
|
4.7
|
24.0
|
1.0
|
|
NZ
|
A:LYS72
|
4.7
|
23.6
|
1.0
|
|
HG23
|
A:ILE192
|
4.7
|
21.1
|
1.0
|
|
H
|
A:LYS72
|
4.8
|
23.5
|
1.0
|
|
O2A
|
A:AGS402
|
4.8
|
25.8
|
1.0
|
|
CA
|
A:LYS72
|
4.8
|
22.3
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 7jy8
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Magnesium Binding Sites List in 7jy8
Magnesium binding site 2 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:21.6
occ:1.00
|
O2G
|
B:AGS402
|
2.2
|
21.9
|
1.0
|
|
OG1
|
B:THR73
|
2.2
|
21.4
|
1.0
|
|
O1B
|
B:AGS402
|
2.2
|
21.7
|
1.0
|
|
HOG2
|
B:AGS402
|
2.6
|
22.0
|
1.0
|
|
HG1
|
B:THR73
|
2.8
|
21.2
|
1.0
|
|
HB
|
B:THR73
|
3.2
|
21.7
|
1.0
|
|
CB
|
B:THR73
|
3.2
|
21.5
|
1.0
|
|
H
|
B:THR73
|
3.4
|
21.4
|
1.0
|
|
PG
|
B:AGS402
|
3.4
|
22.4
|
1.0
|
|
PB
|
B:AGS402
|
3.5
|
22.1
|
1.0
|
|
OE1
|
B:GLU96
|
3.6
|
21.7
|
1.0
|
|
HZ2
|
A:LYS250
|
3.7
|
18.0
|
1.0
|
|
OD2
|
B:ASP144
|
3.7
|
21.2
|
1.0
|
|
O3B
|
B:AGS402
|
3.8
|
22.4
|
1.0
|
|
HE3
|
A:LYS250
|
3.8
|
18.6
|
1.0
|
|
OD1
|
B:ASP144
|
4.0
|
21.0
|
1.0
|
|
O2A
|
B:AGS402
|
4.0
|
22.4
|
1.0
|
|
HG22
|
B:THR73
|
4.0
|
21.9
|
1.0
|
|
N
|
B:THR73
|
4.1
|
21.3
|
1.0
|
|
HB2
|
B:LYS72
|
4.2
|
21.2
|
1.0
|
|
CA
|
B:THR73
|
4.2
|
21.4
|
1.0
|
|
CG2
|
B:THR73
|
4.2
|
21.7
|
1.0
|
|
HE2
|
B:LYS72
|
4.3
|
21.3
|
1.0
|
|
O3G
|
B:AGS402
|
4.3
|
22.7
|
1.0
|
|
CG
|
B:ASP144
|
4.3
|
21.1
|
1.0
|
|
HE2
|
A:LYS250
|
4.4
|
18.5
|
1.0
|
|
CE
|
A:LYS250
|
4.4
|
18.4
|
1.0
|
|
NZ
|
A:LYS250
|
4.4
|
18.0
|
1.0
|
|
O2B
|
B:AGS402
|
4.4
|
22.1
|
1.0
|
|
HA
|
B:THR73
|
4.5
|
21.2
|
1.0
|
|
CD
|
B:GLU96
|
4.6
|
21.8
|
1.0
|
|
HG23
|
B:THR73
|
4.6
|
21.6
|
1.0
|
|
O3A
|
B:AGS402
|
4.6
|
22.4
|
1.0
|
|
HG22
|
B:ILE192
|
4.7
|
20.6
|
1.0
|
|
HZ1
|
A:LYS250
|
4.7
|
17.9
|
1.0
|
|
OE2
|
B:GLU96
|
4.8
|
21.8
|
1.0
|
|
HD13
|
B:ILE192
|
4.8
|
20.6
|
1.0
|
|
PA
|
B:AGS402
|
4.8
|
22.5
|
1.0
|
|
S1G
|
B:AGS402
|
4.9
|
22.6
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 3 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:16.7
occ:1.00
|
O2G
|
C:AGS402
|
2.2
|
17.1
|
1.0
|
|
OG1
|
C:THR73
|
2.2
|
16.3
|
1.0
|
|
O1B
|
C:AGS402
|
2.2
|
16.6
|
1.0
|
|
HOG2
|
C:AGS402
|
2.7
|
17.1
|
1.0
|
|
HG1
|
C:THR73
|
2.8
|
16.0
|
1.0
|
|
HB
|
C:THR73
|
3.0
|
17.0
|
1.0
|
|
CB
|
C:THR73
|
3.1
|
16.7
|
1.0
|
|
PG
|
C:AGS402
|
3.4
|
17.7
|
1.0
|
|
PB
|
C:AGS402
|
3.4
|
17.0
|
1.0
|
|
HZ2
|
B:LYS250
|
3.5
|
20.2
|
1.0
|
|
H
|
C:THR73
|
3.5
|
16.1
|
1.0
|
|
O3B
|
C:AGS402
|
3.6
|
17.6
|
1.0
|
|
HE3
|
B:LYS250
|
3.7
|
20.5
|
1.0
|
|
HG22
|
C:THR73
|
3.8
|
17.7
|
1.0
|
|
OE1
|
C:GLU96
|
3.8
|
16.8
|
1.0
|
|
O2A
|
C:AGS402
|
3.9
|
18.5
|
1.0
|
|
O3G
|
C:AGS402
|
4.0
|
18.6
|
1.0
|
|
OD2
|
C:ASP144
|
4.0
|
16.0
|
1.0
|
|
CG2
|
C:THR73
|
4.0
|
17.3
|
1.0
|
|
N
|
C:THR73
|
4.1
|
15.9
|
1.0
|
|
NZ
|
B:LYS250
|
4.2
|
20.1
|
1.0
|
|
CA
|
C:THR73
|
4.2
|
16.2
|
1.0
|
|
CE
|
B:LYS250
|
4.2
|
20.3
|
1.0
|
|
HE2
|
B:LYS250
|
4.2
|
20.4
|
1.0
|
|
OD1
|
C:ASP144
|
4.3
|
15.4
|
1.0
|
|
HB2
|
C:LYS72
|
4.3
|
15.2
|
1.0
|
|
O3A
|
C:AGS402
|
4.4
|
17.7
|
1.0
|
|
HZ1
|
B:LYS250
|
4.5
|
20.1
|
1.0
|
|
HE2
|
C:LYS72
|
4.5
|
15.2
|
1.0
|
|
HG23
|
C:THR73
|
4.5
|
17.1
|
1.0
|
|
HA
|
C:THR73
|
4.5
|
15.9
|
1.0
|
|
O2B
|
C:AGS402
|
4.5
|
16.7
|
1.0
|
|
CG
|
C:ASP144
|
4.5
|
15.7
|
1.0
|
|
PA
|
C:AGS402
|
4.6
|
18.2
|
1.0
|
|
HG21
|
C:THR73
|
4.8
|
17.7
|
1.0
|
|
HD13
|
C:ILE192
|
4.8
|
14.7
|
1.0
|
|
CD
|
C:GLU96
|
4.9
|
16.7
|
1.0
|
|
HZ3
|
B:LYS250
|
4.9
|
20.0
|
1.0
|
|
HG22
|
C:ILE192
|
4.9
|
14.4
|
1.0
|
|
S1G
|
C:AGS402
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 4 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:18.8
occ:1.00
|
O2G
|
D:AGS402
|
2.2
|
18.9
|
1.0
|
|
OG1
|
D:THR73
|
2.2
|
18.7
|
1.0
|
|
O1B
|
D:AGS402
|
2.2
|
18.6
|
1.0
|
|
HOG2
|
D:AGS402
|
2.6
|
18.9
|
1.0
|
|
HG1
|
D:THR73
|
2.8
|
18.6
|
1.0
|
|
HB
|
D:THR73
|
3.0
|
19.0
|
1.0
|
|
CB
|
D:THR73
|
3.1
|
18.9
|
1.0
|
|
HZ2
|
C:LYS250
|
3.2
|
16.0
|
1.0
|
|
PG
|
D:AGS402
|
3.4
|
19.2
|
1.0
|
|
PB
|
D:AGS402
|
3.5
|
18.8
|
1.0
|
|
H
|
D:THR73
|
3.6
|
18.5
|
1.0
|
|
OE1
|
D:GLU96
|
3.7
|
19.0
|
1.0
|
|
O3B
|
D:AGS402
|
3.7
|
19.1
|
1.0
|
|
HG22
|
D:THR73
|
3.8
|
19.6
|
1.0
|
|
OD2
|
D:ASP144
|
3.8
|
18.8
|
1.0
|
|
O2A
|
D:AGS402
|
3.9
|
19.5
|
1.0
|
|
HE3
|
C:LYS250
|
4.0
|
16.5
|
1.0
|
|
NZ
|
C:LYS250
|
4.0
|
15.7
|
1.0
|
|
O3G
|
D:AGS402
|
4.0
|
19.6
|
1.0
|
|
CG2
|
D:THR73
|
4.0
|
19.4
|
1.0
|
|
OD1
|
D:ASP144
|
4.2
|
18.4
|
1.0
|
|
N
|
D:THR73
|
4.2
|
18.4
|
1.0
|
|
CA
|
D:THR73
|
4.2
|
18.7
|
1.0
|
|
HZ1
|
C:LYS250
|
4.2
|
15.4
|
1.0
|
|
HB2
|
D:LYS72
|
4.4
|
18.0
|
1.0
|
|
CE
|
C:LYS250
|
4.4
|
16.1
|
1.0
|
|
CG
|
D:ASP144
|
4.4
|
18.7
|
1.0
|
|
HE2
|
C:LYS250
|
4.4
|
16.5
|
1.0
|
|
HG23
|
D:THR73
|
4.4
|
19.4
|
1.0
|
|
O3A
|
D:AGS402
|
4.5
|
19.2
|
1.0
|
|
HE2
|
D:LYS72
|
4.5
|
18.0
|
1.0
|
|
HA
|
D:THR73
|
4.6
|
18.6
|
1.0
|
|
O2B
|
D:AGS402
|
4.6
|
18.7
|
1.0
|
|
HZ3
|
C:LYS250
|
4.6
|
15.4
|
1.0
|
|
PA
|
D:AGS402
|
4.7
|
19.5
|
1.0
|
|
CD
|
D:GLU96
|
4.7
|
19.0
|
1.0
|
|
HG21
|
D:THR73
|
4.8
|
19.7
|
1.0
|
|
HD13
|
D:ILE192
|
4.8
|
17.9
|
1.0
|
|
HG22
|
D:ILE192
|
4.9
|
17.7
|
1.0
|
|
OE2
|
D:GLU96
|
5.0
|
18.8
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 5 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg401
b:16.8
occ:1.00
|
O2G
|
E:AGS402
|
2.2
|
16.8
|
1.0
|
|
OG1
|
E:THR73
|
2.2
|
16.8
|
1.0
|
|
O1B
|
E:AGS402
|
2.2
|
16.8
|
1.0
|
|
HOG2
|
E:AGS402
|
2.6
|
16.8
|
1.0
|
|
HG1
|
E:THR73
|
2.8
|
16.7
|
1.0
|
|
HB
|
E:THR73
|
3.1
|
17.2
|
1.0
|
|
CB
|
E:THR73
|
3.2
|
17.1
|
1.0
|
|
PG
|
E:AGS402
|
3.4
|
17.1
|
1.0
|
|
HZ2
|
D:LYS250
|
3.4
|
18.6
|
1.0
|
|
PB
|
E:AGS402
|
3.5
|
17.0
|
1.0
|
|
H
|
E:THR73
|
3.6
|
16.8
|
1.0
|
|
O3B
|
E:AGS402
|
3.7
|
17.1
|
1.0
|
|
OE1
|
E:GLU96
|
3.7
|
16.9
|
1.0
|
|
HE3
|
D:LYS250
|
3.8
|
19.0
|
1.0
|
|
OD2
|
E:ASP144
|
3.8
|
16.9
|
1.0
|
|
HG22
|
E:THR73
|
3.8
|
17.7
|
1.0
|
|
O3G
|
E:AGS402
|
4.0
|
17.4
|
1.0
|
|
CG2
|
E:THR73
|
4.1
|
17.6
|
1.0
|
|
O2A
|
E:AGS402
|
4.1
|
17.7
|
1.0
|
|
OD1
|
E:ASP144
|
4.1
|
16.5
|
1.0
|
|
NZ
|
D:LYS250
|
4.2
|
18.5
|
1.0
|
|
N
|
E:THR73
|
4.2
|
16.8
|
1.0
|
|
CA
|
E:THR73
|
4.2
|
17.0
|
1.0
|
|
HB2
|
E:LYS72
|
4.3
|
16.3
|
1.0
|
|
CE
|
D:LYS250
|
4.3
|
18.9
|
1.0
|
|
HE2
|
D:LYS250
|
4.3
|
19.1
|
1.0
|
|
CG
|
E:ASP144
|
4.4
|
16.7
|
1.0
|
|
HZ1
|
D:LYS250
|
4.4
|
18.3
|
1.0
|
|
HE2
|
E:LYS72
|
4.4
|
16.2
|
1.0
|
|
HG23
|
E:THR73
|
4.5
|
17.6
|
1.0
|
|
O3A
|
E:AGS402
|
4.5
|
17.4
|
1.0
|
|
HA
|
E:THR73
|
4.5
|
16.9
|
1.0
|
|
O2B
|
E:AGS402
|
4.5
|
16.9
|
1.0
|
|
PA
|
E:AGS402
|
4.7
|
17.7
|
1.0
|
|
CD
|
E:GLU96
|
4.7
|
16.9
|
1.0
|
|
HD13
|
E:ILE192
|
4.8
|
16.2
|
1.0
|
|
HG21
|
E:THR73
|
4.8
|
17.9
|
1.0
|
|
HG22
|
E:ILE192
|
4.9
|
15.9
|
1.0
|
|
HZ3
|
D:LYS250
|
4.9
|
18.4
|
1.0
|
|
S1G
|
E:AGS402
|
5.0
|
17.1
|
1.0
|
|
OE2
|
E:GLU96
|
5.0
|
16.7
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 6 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg401
b:16.1
occ:1.00
|
O2G
|
F:AGS402
|
2.2
|
17.0
|
1.0
|
|
OG1
|
F:THR73
|
2.2
|
15.5
|
1.0
|
|
O1B
|
F:AGS402
|
2.2
|
16.1
|
1.0
|
|
HOG2
|
F:AGS402
|
2.6
|
17.0
|
1.0
|
|
HG1
|
F:THR73
|
2.8
|
15.1
|
1.0
|
|
HB
|
F:THR73
|
3.0
|
16.4
|
1.0
|
|
CB
|
F:THR73
|
3.2
|
15.9
|
1.0
|
|
PG
|
F:AGS402
|
3.4
|
17.7
|
1.0
|
|
PB
|
F:AGS402
|
3.5
|
16.7
|
1.0
|
|
HZ2
|
E:LYS250
|
3.5
|
20.0
|
1.0
|
|
H
|
F:THR73
|
3.6
|
15.4
|
1.0
|
|
O3B
|
F:AGS402
|
3.7
|
17.6
|
1.0
|
|
HE3
|
E:LYS250
|
3.8
|
20.6
|
1.0
|
|
HG22
|
F:THR73
|
3.9
|
17.0
|
1.0
|
|
OE1
|
F:GLU96
|
3.9
|
16.9
|
1.0
|
|
OD2
|
F:ASP144
|
3.9
|
15.1
|
1.0
|
|
O2A
|
F:AGS402
|
4.0
|
18.4
|
1.0
|
|
O3G
|
F:AGS402
|
4.1
|
18.8
|
1.0
|
|
CG2
|
F:THR73
|
4.1
|
16.6
|
1.0
|
|
OD1
|
F:ASP144
|
4.1
|
14.4
|
1.0
|
|
N
|
F:THR73
|
4.2
|
15.1
|
1.0
|
|
CA
|
F:THR73
|
4.2
|
15.4
|
1.0
|
|
NZ
|
E:LYS250
|
4.2
|
19.7
|
1.0
|
|
HB2
|
F:LYS72
|
4.3
|
14.5
|
1.0
|
|
HE2
|
E:LYS250
|
4.3
|
20.6
|
1.0
|
|
CE
|
E:LYS250
|
4.3
|
20.2
|
1.0
|
|
CG
|
F:ASP144
|
4.5
|
14.7
|
1.0
|
|
HE2
|
F:LYS72
|
4.5
|
14.5
|
1.0
|
|
HA
|
F:THR73
|
4.5
|
14.9
|
1.0
|
|
O3A
|
F:AGS402
|
4.5
|
17.6
|
1.0
|
|
HG23
|
F:THR73
|
4.5
|
16.2
|
1.0
|
|
O2B
|
F:AGS402
|
4.5
|
16.4
|
1.0
|
|
HZ1
|
E:LYS250
|
4.5
|
19.5
|
1.0
|
|
PA
|
F:AGS402
|
4.8
|
18.1
|
1.0
|
|
CD
|
F:GLU96
|
4.8
|
16.5
|
1.0
|
|
HD13
|
F:ILE192
|
4.8
|
13.4
|
1.0
|
|
HG22
|
F:ILE192
|
4.8
|
13.2
|
1.0
|
|
HG21
|
F:THR73
|
4.9
|
17.0
|
1.0
|
|
S1G
|
F:AGS402
|
4.9
|
17.8
|
1.0
|
|
HZ3
|
E:LYS250
|
4.9
|
19.5
|
1.0
|
|
OE2
|
F:GLU96
|
5.0
|
15.9
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 7 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg401
b:11.8
occ:1.00
|
O2G
|
G:AGS402
|
2.2
|
11.8
|
1.0
|
|
O1B
|
G:AGS402
|
2.2
|
11.7
|
1.0
|
|
OG1
|
G:THR73
|
2.2
|
11.8
|
1.0
|
|
HOG2
|
G:AGS402
|
2.7
|
11.8
|
1.0
|
|
HG1
|
G:THR73
|
2.9
|
11.7
|
1.0
|
|
HB
|
G:THR73
|
2.9
|
12.5
|
1.0
|
|
CB
|
G:THR73
|
3.1
|
12.3
|
1.0
|
|
HZ2
|
F:LYS250
|
3.3
|
12.9
|
1.0
|
|
PG
|
G:AGS402
|
3.4
|
12.2
|
1.0
|
|
PB
|
G:AGS402
|
3.4
|
12.0
|
1.0
|
|
H
|
G:THR73
|
3.5
|
11.6
|
1.0
|
|
O3B
|
G:AGS402
|
3.6
|
12.3
|
1.0
|
|
HE3
|
F:LYS250
|
3.6
|
13.7
|
1.0
|
|
HG22
|
G:THR73
|
3.7
|
13.2
|
1.0
|
|
OE1
|
G:GLU96
|
3.8
|
12.0
|
1.0
|
|
O2A
|
G:AGS402
|
3.8
|
13.3
|
1.0
|
|
O3G
|
G:AGS402
|
3.8
|
12.8
|
1.0
|
|
CG2
|
G:THR73
|
4.0
|
13.0
|
1.0
|
|
NZ
|
F:LYS250
|
4.1
|
12.7
|
1.0
|
|
OD2
|
G:ASP144
|
4.1
|
11.8
|
1.0
|
|
N
|
G:THR73
|
4.1
|
11.6
|
1.0
|
|
CE
|
F:LYS250
|
4.2
|
13.3
|
1.0
|
|
CA
|
G:THR73
|
4.2
|
12.0
|
1.0
|
|
HE2
|
F:LYS250
|
4.2
|
13.7
|
1.0
|
|
HZ1
|
F:LYS250
|
4.3
|
12.5
|
1.0
|
|
O3A
|
G:AGS402
|
4.3
|
12.6
|
1.0
|
|
HB2
|
G:LYS72
|
4.4
|
10.8
|
1.0
|
|
HG23
|
G:THR73
|
4.4
|
12.9
|
1.0
|
|
O2B
|
G:AGS402
|
4.5
|
11.8
|
1.0
|
|
PA
|
G:AGS402
|
4.5
|
13.2
|
1.0
|
|
OD1
|
G:ASP144
|
4.5
|
11.2
|
1.0
|
|
HA
|
G:THR73
|
4.5
|
11.9
|
1.0
|
|
HE2
|
G:LYS72
|
4.6
|
10.7
|
1.0
|
|
CG
|
G:ASP144
|
4.7
|
11.6
|
1.0
|
|
HG21
|
G:THR73
|
4.7
|
13.4
|
1.0
|
|
HZ3
|
F:LYS250
|
4.8
|
12.4
|
1.0
|
|
CD
|
G:GLU96
|
4.8
|
11.9
|
1.0
|
|
O1A
|
G:AGS402
|
4.9
|
13.3
|
1.0
|
|
S1G
|
G:AGS402
|
4.9
|
12.1
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 8 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg401
b:16.8
occ:1.00
|
O1B
|
H:AGS402
|
2.2
|
16.9
|
1.0
|
|
O2G
|
H:AGS402
|
2.2
|
16.6
|
1.0
|
|
OG1
|
H:THR73
|
2.2
|
17.1
|
1.0
|
|
HOG2
|
H:AGS402
|
2.7
|
16.6
|
1.0
|
|
HG1
|
H:THR73
|
2.9
|
17.1
|
1.0
|
|
HB
|
H:THR73
|
2.9
|
17.3
|
1.0
|
|
CB
|
H:THR73
|
3.1
|
17.3
|
1.0
|
|
PG
|
H:AGS402
|
3.3
|
16.8
|
1.0
|
|
HZ2
|
G:LYS250
|
3.4
|
18.7
|
1.0
|
|
PB
|
H:AGS402
|
3.4
|
17.1
|
1.0
|
|
H
|
H:THR73
|
3.5
|
17.2
|
1.0
|
|
O3B
|
H:AGS402
|
3.5
|
17.0
|
1.0
|
|
HE3
|
G:LYS250
|
3.7
|
19.2
|
1.0
|
|
HG22
|
H:THR73
|
3.8
|
17.6
|
1.0
|
|
O2A
|
H:AGS402
|
3.9
|
17.4
|
1.0
|
|
O3G
|
H:AGS402
|
3.9
|
16.8
|
1.0
|
|
OD2
|
H:ASP144
|
4.0
|
17.2
|
1.0
|
|
CG2
|
H:THR73
|
4.0
|
17.6
|
1.0
|
|
N
|
H:THR73
|
4.1
|
17.4
|
1.0
|
|
NZ
|
G:LYS250
|
4.1
|
18.1
|
1.0
|
|
CA
|
H:THR73
|
4.2
|
17.5
|
1.0
|
|
HE2
|
G:LYS250
|
4.2
|
19.3
|
1.0
|
|
CE
|
G:LYS250
|
4.2
|
18.7
|
1.0
|
|
O3A
|
H:AGS402
|
4.3
|
17.4
|
1.0
|
|
HB2
|
H:LYS72
|
4.3
|
17.1
|
1.0
|
|
HZ1
|
G:LYS250
|
4.4
|
17.6
|
1.0
|
|
OE1
|
H:GLU96
|
4.4
|
16.8
|
1.0
|
|
HA
|
H:THR73
|
4.5
|
17.5
|
1.0
|
|
HG23
|
H:THR73
|
4.5
|
17.7
|
1.0
|
|
OD1
|
H:ASP144
|
4.5
|
16.9
|
1.0
|
|
HE2
|
H:LYS72
|
4.5
|
16.9
|
1.0
|
|
O2B
|
H:AGS402
|
4.5
|
17.2
|
1.0
|
|
PA
|
H:AGS402
|
4.5
|
17.6
|
1.0
|
|
CG
|
H:ASP144
|
4.6
|
17.1
|
1.0
|
|
HG21
|
H:THR73
|
4.8
|
17.9
|
1.0
|
|
HZ3
|
G:LYS250
|
4.8
|
17.7
|
1.0
|
|
OE2
|
H:GLU96
|
4.8
|
16.6
|
1.0
|
|
O1A
|
H:AGS402
|
4.9
|
17.8
|
1.0
|
|
S1G
|
H:AGS402
|
4.9
|
16.8
|
1.0
|
|
HG22
|
H:ILE192
|
5.0
|
17.0
|
1.0
|
|
HD13
|
H:ILE192
|
5.0
|
17.2
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 7jy8
Go back to
Magnesium Binding Sites List in 7jy8
Magnesium binding site 9 out
of 9 in the Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Analysis of A Strand Exchange Reaction with A Mini Filament of 9-Reca, 27-Mer Ssdna, Partially-Homologous 67 Bp Dsdna and Atpgammas within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg401
b:17.9
occ:1.00
|
O2G
|
I:AGS402
|
2.2
|
17.8
|
1.0
|
|
OG1
|
I:THR73
|
2.2
|
18.2
|
1.0
|
|
O1B
|
I:AGS402
|
2.2
|
18.6
|
1.0
|
|
HOG2
|
I:AGS402
|
2.7
|
17.5
|
1.0
|
|
HG1
|
I:THR73
|
2.8
|
18.2
|
1.0
|
|
HB
|
I:THR73
|
3.1
|
18.9
|
1.0
|
|
CB
|
I:THR73
|
3.2
|
18.7
|
1.0
|
|
PG
|
I:AGS402
|
3.4
|
18.1
|
1.0
|
|
HE3
|
H:LYS250
|
3.5
|
28.4
|
1.0
|
|
PB
|
I:AGS402
|
3.5
|
19.0
|
1.0
|
|
HZ2
|
H:LYS250
|
3.6
|
28.0
|
1.0
|
|
OE1
|
I:GLU96
|
3.6
|
17.1
|
1.0
|
|
H
|
I:THR73
|
3.6
|
19.1
|
1.0
|
|
O3B
|
I:AGS402
|
3.8
|
18.8
|
1.0
|
|
HG22
|
I:THR73
|
3.8
|
18.8
|
1.0
|
|
O2A
|
I:AGS402
|
3.9
|
19.3
|
1.0
|
|
OD2
|
I:ASP144
|
4.0
|
17.9
|
1.0
|
|
CG2
|
I:THR73
|
4.0
|
18.9
|
1.0
|
|
O3G
|
I:AGS402
|
4.1
|
18.1
|
1.0
|
|
CE
|
H:LYS250
|
4.1
|
27.8
|
1.0
|
|
OD1
|
I:ASP144
|
4.1
|
17.5
|
1.0
|
|
HE2
|
H:LYS250
|
4.2
|
28.2
|
1.0
|
|
NZ
|
H:LYS250
|
4.2
|
27.4
|
1.0
|
|
N
|
I:THR73
|
4.2
|
19.2
|
1.0
|
|
CA
|
I:THR73
|
4.3
|
19.1
|
1.0
|
|
HB2
|
I:LYS72
|
4.4
|
19.0
|
1.0
|
|
HZ1
|
H:LYS250
|
4.4
|
27.0
|
1.0
|
|
HG23
|
I:THR73
|
4.5
|
18.8
|
1.0
|
|
CG
|
I:ASP144
|
4.5
|
17.7
|
1.0
|
|
O3A
|
I:AGS402
|
4.5
|
19.7
|
1.0
|
|
O2B
|
I:AGS402
|
4.5
|
19.4
|
1.0
|
|
HE2
|
I:LYS72
|
4.6
|
18.5
|
1.0
|
|
HA
|
I:THR73
|
4.6
|
18.9
|
1.0
|
|
PA
|
I:AGS402
|
4.6
|
19.8
|
1.0
|
|
CD
|
I:GLU96
|
4.6
|
17.0
|
1.0
|
|
HD13
|
I:ILE192
|
4.8
|
18.4
|
1.0
|
|
HG21
|
I:THR73
|
4.8
|
19.3
|
1.0
|
|
OE2
|
I:GLU96
|
4.8
|
17.0
|
1.0
|
|
O1A
|
I:AGS402
|
4.9
|
20.0
|
1.0
|
|
HZ3
|
H:LYS250
|
5.0
|
26.9
|
1.0
|
|
HG22
|
I:ILE192
|
5.0
|
18.2
|
1.0
|
|
Reference:
H.Yang,
C.Zhou,
A.Dhar,
N.P.Pavletich.
Mechanism of Strand Exchange From Reca-Dna Synaptic and D-Loop Structures. Nature V. 586 801 2020.
ISSN: ESSN 1476-4687
PubMed: 33057191
DOI: 10.1038/S41586-020-2820-9
Page generated: Wed Oct 2 22:02:21 2024
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