Magnesium in PDB 7npf: Vibrio Cholerae PARA2-Atpys-Dna Filament
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Vibrio Cholerae PARA2-Atpys-Dna Filament
(pdb code 7npf). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Vibrio Cholerae PARA2-Atpys-Dna Filament, PDB code: 7npf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 1 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:90.6
occ:1.00
|
O1B
|
A:AGS502
|
2.0
|
85.5
|
1.0
|
|
O2B
|
A:AGS502
|
2.1
|
85.5
|
1.0
|
|
PB
|
A:AGS502
|
2.4
|
85.5
|
1.0
|
|
CG
|
A:PRO260
|
2.8
|
94.1
|
1.0
|
|
CD
|
A:PRO260
|
3.2
|
94.1
|
1.0
|
|
O3B
|
A:AGS502
|
3.3
|
85.5
|
1.0
|
|
O3G
|
A:AGS502
|
3.6
|
85.5
|
1.0
|
|
OD2
|
A:ASP151
|
3.7
|
113.5
|
1.0
|
|
O3A
|
A:AGS502
|
3.7
|
85.5
|
1.0
|
|
OG
|
A:SER125
|
3.8
|
88.5
|
1.0
|
|
PG
|
A:AGS502
|
4.1
|
85.5
|
1.0
|
|
NZ
|
A:LYS124
|
4.1
|
90.0
|
1.0
|
|
CB
|
A:PRO260
|
4.1
|
94.1
|
1.0
|
|
N
|
A:PRO260
|
4.2
|
94.1
|
1.0
|
|
CG
|
A:LYS124
|
4.2
|
90.0
|
1.0
|
|
CD
|
A:LYS124
|
4.3
|
90.0
|
1.0
|
|
N
|
A:GLY121
|
4.7
|
90.3
|
1.0
|
|
CA
|
A:PRO260
|
4.8
|
94.1
|
1.0
|
|
CA
|
A:GLY259
|
4.8
|
97.2
|
1.0
|
|
C
|
A:GLY259
|
4.8
|
97.2
|
1.0
|
|
CE
|
A:LYS124
|
4.8
|
90.0
|
1.0
|
|
O2A
|
A:AGS502
|
4.8
|
85.5
|
1.0
|
|
CG
|
A:ASP151
|
4.9
|
113.5
|
1.0
|
|
PA
|
A:AGS502
|
5.0
|
85.5
|
1.0
|
|
CB
|
A:SER125
|
5.0
|
88.5
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 2 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:88.2
occ:1.00
|
O
|
B:VAL115
|
2.0
|
100.2
|
1.0
|
|
OG1
|
B:THR258
|
2.0
|
113.6
|
1.0
|
|
ND2
|
B:ASN114
|
2.0
|
105.1
|
1.0
|
|
CB
|
B:GLN116
|
2.4
|
102.8
|
1.0
|
|
C
|
B:VAL115
|
2.4
|
100.2
|
1.0
|
|
CA
|
B:GLN116
|
2.5
|
102.8
|
1.0
|
|
N
|
B:GLN116
|
2.7
|
102.8
|
1.0
|
|
CG2
|
B:THR258
|
2.8
|
113.6
|
1.0
|
|
CB
|
B:THR258
|
2.9
|
113.6
|
1.0
|
|
CG
|
B:ASN114
|
3.1
|
105.1
|
1.0
|
|
CG
|
B:GLN116
|
3.4
|
102.8
|
1.0
|
|
N
|
B:THR258
|
3.4
|
113.6
|
1.0
|
|
N
|
B:VAL115
|
3.5
|
100.2
|
1.0
|
|
OD1
|
B:ASN114
|
3.5
|
105.1
|
1.0
|
|
CA
|
B:VAL115
|
3.5
|
100.2
|
1.0
|
|
CA
|
B:THR258
|
3.8
|
113.6
|
1.0
|
|
C
|
B:GLN116
|
4.0
|
102.8
|
1.0
|
|
O
|
B:ILE256
|
4.0
|
118.2
|
1.0
|
|
NE2
|
B:GLN116
|
4.1
|
102.8
|
1.0
|
|
CD
|
B:GLN116
|
4.3
|
102.8
|
1.0
|
|
C
|
B:ASN114
|
4.3
|
105.1
|
1.0
|
|
CB
|
B:ASN114
|
4.4
|
105.1
|
1.0
|
|
CA
|
B:ASN114
|
4.6
|
105.1
|
1.0
|
|
N
|
B:ASN117
|
4.6
|
97.1
|
1.0
|
|
CG2
|
B:VAL115
|
4.6
|
100.2
|
1.0
|
|
CB
|
B:VAL115
|
4.6
|
100.2
|
1.0
|
|
C
|
B:ASP257
|
4.6
|
114.6
|
1.0
|
|
C
|
B:THR258
|
4.7
|
113.6
|
1.0
|
|
N
|
B:GLY259
|
4.7
|
98.3
|
1.0
|
|
NZ
|
B:LYS124
|
4.8
|
97.5
|
1.0
|
|
CD1
|
B:LEU276
|
4.8
|
98.3
|
1.0
|
|
O
|
B:GLN116
|
4.8
|
102.8
|
1.0
|
|
CA
|
B:ASP257
|
5.0
|
114.6
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 3 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:90.6
occ:1.00
|
O1B
|
C:AGS502
|
2.0
|
85.5
|
1.0
|
|
O2B
|
C:AGS502
|
2.1
|
85.5
|
1.0
|
|
PB
|
C:AGS502
|
2.4
|
85.5
|
1.0
|
|
CG
|
C:PRO260
|
2.8
|
94.1
|
1.0
|
|
CD
|
C:PRO260
|
3.2
|
94.1
|
1.0
|
|
O3B
|
C:AGS502
|
3.3
|
85.5
|
1.0
|
|
O3G
|
C:AGS502
|
3.6
|
85.5
|
1.0
|
|
OD2
|
C:ASP151
|
3.7
|
113.5
|
1.0
|
|
O3A
|
C:AGS502
|
3.7
|
85.5
|
1.0
|
|
OG
|
C:SER125
|
3.8
|
88.5
|
1.0
|
|
PG
|
C:AGS502
|
4.1
|
85.5
|
1.0
|
|
NZ
|
C:LYS124
|
4.1
|
90.0
|
1.0
|
|
CB
|
C:PRO260
|
4.1
|
94.1
|
1.0
|
|
N
|
C:PRO260
|
4.2
|
94.1
|
1.0
|
|
CG
|
C:LYS124
|
4.2
|
90.0
|
1.0
|
|
CD
|
C:LYS124
|
4.3
|
90.0
|
1.0
|
|
N
|
C:GLY121
|
4.7
|
90.3
|
1.0
|
|
CA
|
C:PRO260
|
4.8
|
94.1
|
1.0
|
|
CA
|
C:GLY259
|
4.8
|
97.2
|
1.0
|
|
C
|
C:GLY259
|
4.8
|
97.2
|
1.0
|
|
CE
|
C:LYS124
|
4.8
|
90.0
|
1.0
|
|
O2A
|
C:AGS502
|
4.8
|
85.5
|
1.0
|
|
CG
|
C:ASP151
|
4.9
|
113.5
|
1.0
|
|
PA
|
C:AGS502
|
5.0
|
85.5
|
1.0
|
|
CB
|
C:SER125
|
5.0
|
88.5
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 4 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:88.2
occ:1.00
|
O
|
D:VAL115
|
2.0
|
100.2
|
1.0
|
|
OG1
|
D:THR258
|
2.0
|
113.6
|
1.0
|
|
ND2
|
D:ASN114
|
2.0
|
105.1
|
1.0
|
|
CB
|
D:GLN116
|
2.4
|
102.8
|
1.0
|
|
C
|
D:VAL115
|
2.4
|
100.2
|
1.0
|
|
CA
|
D:GLN116
|
2.5
|
102.8
|
1.0
|
|
N
|
D:GLN116
|
2.7
|
102.8
|
1.0
|
|
CG2
|
D:THR258
|
2.8
|
113.6
|
1.0
|
|
CB
|
D:THR258
|
2.9
|
113.6
|
1.0
|
|
CG
|
D:ASN114
|
3.1
|
105.1
|
1.0
|
|
CG
|
D:GLN116
|
3.4
|
102.8
|
1.0
|
|
N
|
D:THR258
|
3.4
|
113.6
|
1.0
|
|
N
|
D:VAL115
|
3.5
|
100.2
|
1.0
|
|
OD1
|
D:ASN114
|
3.5
|
105.1
|
1.0
|
|
CA
|
D:VAL115
|
3.5
|
100.2
|
1.0
|
|
CA
|
D:THR258
|
3.8
|
113.6
|
1.0
|
|
C
|
D:GLN116
|
4.0
|
102.8
|
1.0
|
|
O
|
D:ILE256
|
4.0
|
118.2
|
1.0
|
|
NE2
|
D:GLN116
|
4.1
|
102.8
|
1.0
|
|
CD
|
D:GLN116
|
4.3
|
102.8
|
1.0
|
|
C
|
D:ASN114
|
4.3
|
105.1
|
1.0
|
|
CB
|
D:ASN114
|
4.4
|
105.1
|
1.0
|
|
CA
|
D:ASN114
|
4.6
|
105.1
|
1.0
|
|
N
|
D:ASN117
|
4.6
|
97.1
|
1.0
|
|
CG2
|
D:VAL115
|
4.6
|
100.2
|
1.0
|
|
CB
|
D:VAL115
|
4.6
|
100.2
|
1.0
|
|
C
|
D:ASP257
|
4.6
|
114.6
|
1.0
|
|
C
|
D:THR258
|
4.7
|
113.6
|
1.0
|
|
N
|
D:GLY259
|
4.7
|
98.3
|
1.0
|
|
NZ
|
D:LYS124
|
4.8
|
97.5
|
1.0
|
|
CD1
|
D:LEU276
|
4.8
|
98.3
|
1.0
|
|
O
|
D:GLN116
|
4.8
|
102.8
|
1.0
|
|
CA
|
D:ASP257
|
5.0
|
114.6
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 5 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg501
b:90.6
occ:1.00
|
O1B
|
E:AGS502
|
2.0
|
85.5
|
1.0
|
|
O2B
|
E:AGS502
|
2.1
|
85.5
|
1.0
|
|
PB
|
E:AGS502
|
2.4
|
85.5
|
1.0
|
|
CG
|
E:PRO260
|
2.8
|
94.1
|
1.0
|
|
CD
|
E:PRO260
|
3.2
|
94.1
|
1.0
|
|
O3B
|
E:AGS502
|
3.3
|
85.5
|
1.0
|
|
O3G
|
E:AGS502
|
3.6
|
85.5
|
1.0
|
|
OD2
|
E:ASP151
|
3.7
|
113.5
|
1.0
|
|
O3A
|
E:AGS502
|
3.7
|
85.5
|
1.0
|
|
OG
|
E:SER125
|
3.8
|
88.5
|
1.0
|
|
PG
|
E:AGS502
|
4.1
|
85.5
|
1.0
|
|
NZ
|
E:LYS124
|
4.1
|
90.0
|
1.0
|
|
CB
|
E:PRO260
|
4.1
|
94.1
|
1.0
|
|
N
|
E:PRO260
|
4.2
|
94.1
|
1.0
|
|
CG
|
E:LYS124
|
4.2
|
90.0
|
1.0
|
|
CD
|
E:LYS124
|
4.3
|
90.0
|
1.0
|
|
N
|
E:GLY121
|
4.7
|
90.3
|
1.0
|
|
CA
|
E:PRO260
|
4.8
|
94.1
|
1.0
|
|
CA
|
E:GLY259
|
4.8
|
97.2
|
1.0
|
|
C
|
E:GLY259
|
4.8
|
97.2
|
1.0
|
|
CE
|
E:LYS124
|
4.8
|
90.0
|
1.0
|
|
O2A
|
E:AGS502
|
4.8
|
85.5
|
1.0
|
|
CG
|
E:ASP151
|
4.9
|
113.5
|
1.0
|
|
PA
|
E:AGS502
|
5.0
|
85.5
|
1.0
|
|
CB
|
E:SER125
|
5.0
|
88.5
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 6 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg501
b:88.2
occ:1.00
|
O
|
F:VAL115
|
2.0
|
100.2
|
1.0
|
|
OG1
|
F:THR258
|
2.0
|
113.6
|
1.0
|
|
ND2
|
F:ASN114
|
2.0
|
105.1
|
1.0
|
|
CB
|
F:GLN116
|
2.4
|
102.8
|
1.0
|
|
C
|
F:VAL115
|
2.4
|
100.2
|
1.0
|
|
CA
|
F:GLN116
|
2.5
|
102.8
|
1.0
|
|
N
|
F:GLN116
|
2.7
|
102.8
|
1.0
|
|
CG2
|
F:THR258
|
2.8
|
113.6
|
1.0
|
|
CB
|
F:THR258
|
2.9
|
113.6
|
1.0
|
|
CG
|
F:ASN114
|
3.1
|
105.1
|
1.0
|
|
CG
|
F:GLN116
|
3.4
|
102.8
|
1.0
|
|
N
|
F:THR258
|
3.4
|
113.6
|
1.0
|
|
N
|
F:VAL115
|
3.5
|
100.2
|
1.0
|
|
OD1
|
F:ASN114
|
3.5
|
105.1
|
1.0
|
|
CA
|
F:VAL115
|
3.5
|
100.2
|
1.0
|
|
CA
|
F:THR258
|
3.8
|
113.6
|
1.0
|
|
C
|
F:GLN116
|
4.0
|
102.8
|
1.0
|
|
O
|
F:ILE256
|
4.0
|
118.2
|
1.0
|
|
NE2
|
F:GLN116
|
4.1
|
102.8
|
1.0
|
|
CD
|
F:GLN116
|
4.3
|
102.8
|
1.0
|
|
C
|
F:ASN114
|
4.3
|
105.1
|
1.0
|
|
CB
|
F:ASN114
|
4.4
|
105.1
|
1.0
|
|
CA
|
F:ASN114
|
4.6
|
105.1
|
1.0
|
|
N
|
F:ASN117
|
4.6
|
97.1
|
1.0
|
|
CG2
|
F:VAL115
|
4.6
|
100.2
|
1.0
|
|
C
|
F:ASP257
|
4.6
|
114.6
|
1.0
|
|
CB
|
F:VAL115
|
4.6
|
100.2
|
1.0
|
|
C
|
F:THR258
|
4.7
|
113.6
|
1.0
|
|
N
|
F:GLY259
|
4.7
|
98.3
|
1.0
|
|
NZ
|
F:LYS124
|
4.8
|
97.5
|
1.0
|
|
CD1
|
F:LEU276
|
4.8
|
98.3
|
1.0
|
|
O
|
F:GLN116
|
4.8
|
102.8
|
1.0
|
|
CA
|
F:ASP257
|
5.0
|
114.6
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 7 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg501
b:90.6
occ:1.00
|
O1B
|
G:AGS502
|
2.0
|
85.5
|
1.0
|
|
O2B
|
G:AGS502
|
2.1
|
85.5
|
1.0
|
|
PB
|
G:AGS502
|
2.4
|
85.5
|
1.0
|
|
CG
|
G:PRO260
|
2.8
|
94.1
|
1.0
|
|
CD
|
G:PRO260
|
3.2
|
94.1
|
1.0
|
|
O3B
|
G:AGS502
|
3.3
|
85.5
|
1.0
|
|
O3G
|
G:AGS502
|
3.6
|
85.5
|
1.0
|
|
OD2
|
G:ASP151
|
3.7
|
113.5
|
1.0
|
|
O3A
|
G:AGS502
|
3.7
|
85.5
|
1.0
|
|
OG
|
G:SER125
|
3.8
|
88.5
|
1.0
|
|
PG
|
G:AGS502
|
4.1
|
85.5
|
1.0
|
|
NZ
|
G:LYS124
|
4.1
|
90.0
|
1.0
|
|
CB
|
G:PRO260
|
4.1
|
94.1
|
1.0
|
|
N
|
G:PRO260
|
4.2
|
94.1
|
1.0
|
|
CG
|
G:LYS124
|
4.2
|
90.0
|
1.0
|
|
CD
|
G:LYS124
|
4.3
|
90.0
|
1.0
|
|
N
|
G:GLY121
|
4.7
|
90.3
|
1.0
|
|
CA
|
G:PRO260
|
4.8
|
94.1
|
1.0
|
|
CA
|
G:GLY259
|
4.8
|
97.2
|
1.0
|
|
C
|
G:GLY259
|
4.8
|
97.2
|
1.0
|
|
CE
|
G:LYS124
|
4.8
|
90.0
|
1.0
|
|
O2A
|
G:AGS502
|
4.8
|
85.5
|
1.0
|
|
CG
|
G:ASP151
|
4.9
|
113.5
|
1.0
|
|
PA
|
G:AGS502
|
5.0
|
85.5
|
1.0
|
|
CB
|
G:SER125
|
5.0
|
88.5
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7npf
Go back to
Magnesium Binding Sites List in 7npf
Magnesium binding site 8 out
of 8 in the Vibrio Cholerae PARA2-Atpys-Dna Filament
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Vibrio Cholerae PARA2-Atpys-Dna Filament within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg501
b:88.2
occ:1.00
|
O
|
H:VAL115
|
2.0
|
100.2
|
1.0
|
|
OG1
|
H:THR258
|
2.0
|
113.6
|
1.0
|
|
ND2
|
H:ASN114
|
2.0
|
105.1
|
1.0
|
|
CB
|
H:GLN116
|
2.4
|
102.8
|
1.0
|
|
C
|
H:VAL115
|
2.4
|
100.2
|
1.0
|
|
CA
|
H:GLN116
|
2.5
|
102.8
|
1.0
|
|
N
|
H:GLN116
|
2.7
|
102.8
|
1.0
|
|
CG2
|
H:THR258
|
2.8
|
113.6
|
1.0
|
|
CB
|
H:THR258
|
2.9
|
113.6
|
1.0
|
|
CG
|
H:ASN114
|
3.1
|
105.1
|
1.0
|
|
CG
|
H:GLN116
|
3.4
|
102.8
|
1.0
|
|
N
|
H:THR258
|
3.4
|
113.6
|
1.0
|
|
N
|
H:VAL115
|
3.5
|
100.2
|
1.0
|
|
OD1
|
H:ASN114
|
3.5
|
105.1
|
1.0
|
|
CA
|
H:VAL115
|
3.5
|
100.2
|
1.0
|
|
CA
|
H:THR258
|
3.8
|
113.6
|
1.0
|
|
C
|
H:GLN116
|
4.0
|
102.8
|
1.0
|
|
O
|
H:ILE256
|
4.0
|
118.2
|
1.0
|
|
NE2
|
H:GLN116
|
4.1
|
102.8
|
1.0
|
|
CD
|
H:GLN116
|
4.3
|
102.8
|
1.0
|
|
C
|
H:ASN114
|
4.3
|
105.1
|
1.0
|
|
CB
|
H:ASN114
|
4.4
|
105.1
|
1.0
|
|
CA
|
H:ASN114
|
4.6
|
105.1
|
1.0
|
|
N
|
H:ASN117
|
4.6
|
97.1
|
1.0
|
|
CG2
|
H:VAL115
|
4.6
|
100.2
|
1.0
|
|
CB
|
H:VAL115
|
4.6
|
100.2
|
1.0
|
|
C
|
H:ASP257
|
4.6
|
114.6
|
1.0
|
|
C
|
H:THR258
|
4.7
|
113.6
|
1.0
|
|
N
|
H:GLY259
|
4.7
|
98.3
|
1.0
|
|
NZ
|
H:LYS124
|
4.8
|
97.5
|
1.0
|
|
CD1
|
H:LEU276
|
4.8
|
98.3
|
1.0
|
|
O
|
H:GLN116
|
4.8
|
102.8
|
1.0
|
|
CA
|
H:ASP257
|
5.0
|
114.6
|
1.0
|
|
Reference:
A.V.Parker,
D.Mann,
S.B.Tzokov,
L.C.Hwang,
J.R.C.Bergeron.
The Structure of the Bacterial Dna Segregation Atpase Filament Reveals the Conformational Plasticity of Para Upon Dna Binding. Nat Commun V. 12 5166 2021.
ISSN: ESSN 2041-1723
PubMed: 34453062
DOI: 10.1038/S41467-021-25429-2
Page generated: Thu Oct 3 02:10:58 2024
|
