Magnesium in PDB 8ww7: Structure of Amppnp-Form Asfvprimpol Dodecamer
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Amppnp-Form Asfvprimpol Dodecamer
(pdb code 8ww7). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Structure of Amppnp-Form Asfvprimpol Dodecamer, PDB code: 8ww7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 1 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1002
b:143.2
occ:1.00
|
OG1
|
A:THR643
|
1.9
|
124.9
|
1.0
|
|
O2B
|
A:ANP1001
|
2.0
|
136.1
|
1.0
|
|
O
|
A:LYS642
|
2.0
|
133.4
|
1.0
|
|
O2A
|
A:ANP1001
|
2.0
|
136.1
|
1.0
|
|
O1A
|
A:ANP1001
|
2.0
|
136.1
|
1.0
|
|
PA
|
A:ANP1001
|
2.2
|
136.1
|
1.0
|
|
O3A
|
A:ANP1001
|
2.9
|
136.1
|
1.0
|
|
PB
|
A:ANP1001
|
3.0
|
136.1
|
1.0
|
|
C
|
A:LYS642
|
3.1
|
133.4
|
1.0
|
|
CB
|
A:THR643
|
3.2
|
124.9
|
1.0
|
|
C
|
A:THR643
|
3.3
|
124.9
|
1.0
|
|
O1G
|
A:ANP1001
|
3.5
|
136.1
|
1.0
|
|
O
|
A:THR643
|
3.5
|
124.9
|
1.0
|
|
CA
|
A:THR643
|
3.6
|
124.9
|
1.0
|
|
N
|
A:PHE644
|
3.7
|
105.6
|
1.0
|
|
O
|
A:ASN640
|
3.7
|
134.9
|
1.0
|
|
O5'
|
A:ANP1001
|
3.7
|
136.1
|
1.0
|
|
N
|
A:THR643
|
3.8
|
124.9
|
1.0
|
|
N3B
|
A:ANP1001
|
3.8
|
136.1
|
1.0
|
|
PG
|
A:ANP1001
|
4.0
|
136.1
|
1.0
|
|
CG2
|
A:THR643
|
4.1
|
124.9
|
1.0
|
|
O1B
|
A:ANP1001
|
4.2
|
136.1
|
1.0
|
|
O3G
|
A:ANP1001
|
4.2
|
136.1
|
1.0
|
|
CB
|
A:PHE644
|
4.3
|
105.6
|
1.0
|
|
CA
|
A:LYS642
|
4.4
|
133.4
|
1.0
|
|
CA
|
A:PHE644
|
4.4
|
105.6
|
1.0
|
|
N
|
A:LYS642
|
4.5
|
133.4
|
1.0
|
|
O
|
A:GLY641
|
4.6
|
127.4
|
1.0
|
|
C
|
A:GLY641
|
4.6
|
127.4
|
1.0
|
|
CG
|
A:LYS642
|
4.7
|
133.4
|
1.0
|
|
C5'
|
A:ANP1001
|
4.8
|
136.1
|
1.0
|
|
C
|
A:ASN640
|
4.8
|
134.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 2 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:119.1
occ:1.00
|
O
|
B:LYS642
|
1.8
|
110.4
|
1.0
|
|
O2B
|
B:ANP1001
|
1.8
|
116.1
|
1.0
|
|
O2A
|
B:ANP1001
|
1.9
|
116.1
|
1.0
|
|
PB
|
B:ANP1001
|
2.2
|
116.1
|
1.0
|
|
PA
|
B:ANP1001
|
2.3
|
116.1
|
1.0
|
|
O1B
|
B:ANP1001
|
2.3
|
116.1
|
1.0
|
|
O1A
|
B:ANP1001
|
2.4
|
116.1
|
1.0
|
|
OG1
|
B:THR643
|
2.6
|
106.8
|
1.0
|
|
O3A
|
B:ANP1001
|
2.6
|
116.1
|
1.0
|
|
C
|
B:LYS642
|
3.0
|
110.4
|
1.0
|
|
CB
|
B:THR643
|
3.7
|
106.8
|
1.0
|
|
CG
|
B:LYS642
|
3.7
|
110.4
|
1.0
|
|
O5'
|
B:ANP1001
|
3.8
|
116.1
|
1.0
|
|
C
|
B:THR643
|
3.8
|
106.8
|
1.0
|
|
O3G
|
B:ANP1001
|
3.8
|
116.1
|
1.0
|
|
N3B
|
B:ANP1001
|
3.8
|
116.1
|
1.0
|
|
N
|
B:LYS642
|
3.9
|
110.4
|
1.0
|
|
N
|
B:THR643
|
3.9
|
106.8
|
1.0
|
|
CA
|
B:LYS642
|
3.9
|
110.4
|
1.0
|
|
CA
|
B:THR643
|
4.0
|
106.8
|
1.0
|
|
O
|
B:THR643
|
4.0
|
106.8
|
1.0
|
|
O
|
B:ASN640
|
4.1
|
113.0
|
1.0
|
|
N
|
B:PHE644
|
4.2
|
99.7
|
1.0
|
|
CG2
|
B:THR643
|
4.2
|
106.8
|
1.0
|
|
C
|
B:GLY641
|
4.3
|
112.8
|
1.0
|
|
CB
|
B:PHE644
|
4.3
|
99.7
|
1.0
|
|
PG
|
B:ANP1001
|
4.4
|
116.1
|
1.0
|
|
CB
|
B:LYS642
|
4.4
|
110.4
|
1.0
|
|
C
|
B:ASN640
|
4.5
|
113.0
|
1.0
|
|
N
|
B:ASN640
|
4.5
|
113.0
|
1.0
|
|
C5'
|
B:ANP1001
|
4.5
|
116.1
|
1.0
|
|
O
|
B:GLY641
|
4.6
|
112.8
|
1.0
|
|
O1G
|
B:ANP1001
|
4.8
|
116.1
|
1.0
|
|
CA
|
B:PHE644
|
4.8
|
99.7
|
1.0
|
|
NZ
|
B:LYS642
|
4.8
|
110.4
|
1.0
|
|
N
|
B:GLY641
|
4.9
|
112.8
|
1.0
|
|
CD
|
B:LYS642
|
5.0
|
110.4
|
1.0
|
|
CA
|
B:GLY641
|
5.0
|
112.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 3 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:134.6
occ:1.00
|
O
|
C:ASN640
|
2.0
|
126.3
|
1.0
|
|
O
|
C:LYS642
|
2.0
|
129.4
|
1.0
|
|
O2A
|
C:ANP1001
|
2.1
|
133.3
|
1.0
|
|
O3A
|
C:ANP1001
|
2.1
|
133.3
|
1.0
|
|
O1B
|
C:ANP1001
|
2.2
|
133.3
|
1.0
|
|
PB
|
C:ANP1001
|
2.3
|
133.3
|
1.0
|
|
PA
|
C:ANP1001
|
2.3
|
133.3
|
1.0
|
|
O5'
|
C:ANP1001
|
2.6
|
133.3
|
1.0
|
|
O2B
|
C:ANP1001
|
2.6
|
133.3
|
1.0
|
|
C
|
C:ASN640
|
3.1
|
126.3
|
1.0
|
|
C
|
C:LYS642
|
3.2
|
129.4
|
1.0
|
|
OG1
|
C:THR643
|
3.2
|
128.2
|
1.0
|
|
N
|
C:LYS642
|
3.5
|
129.4
|
1.0
|
|
C
|
C:GLY641
|
3.6
|
126.6
|
1.0
|
|
O1A
|
C:ANP1001
|
3.8
|
133.3
|
1.0
|
|
N
|
C:ASN640
|
3.8
|
126.3
|
1.0
|
|
C5'
|
C:ANP1001
|
3.9
|
133.3
|
1.0
|
|
CA
|
C:LYS642
|
3.9
|
129.4
|
1.0
|
|
N3B
|
C:ANP1001
|
3.9
|
133.3
|
1.0
|
|
CG
|
C:LYS642
|
4.0
|
129.4
|
1.0
|
|
N
|
C:GLY641
|
4.0
|
126.6
|
1.0
|
|
CA
|
C:GLY641
|
4.0
|
126.6
|
1.0
|
|
O
|
C:GLY641
|
4.1
|
126.6
|
1.0
|
|
CA
|
C:ASN640
|
4.1
|
126.3
|
1.0
|
|
N
|
C:THR643
|
4.3
|
128.2
|
1.0
|
|
CB
|
C:THR643
|
4.4
|
128.2
|
1.0
|
|
N
|
C:PHE644
|
4.4
|
119.3
|
1.0
|
|
C
|
C:CYS639
|
4.5
|
130.5
|
1.0
|
|
CB
|
C:LYS642
|
4.5
|
129.4
|
1.0
|
|
CA
|
C:THR643
|
4.7
|
128.2
|
1.0
|
|
C
|
C:THR643
|
4.7
|
128.2
|
1.0
|
|
O1G
|
C:ANP1001
|
4.8
|
133.3
|
1.0
|
|
PG
|
C:ANP1001
|
4.9
|
133.3
|
1.0
|
|
NZ
|
C:LYS642
|
4.9
|
129.4
|
1.0
|
|
CG2
|
C:THR643
|
4.9
|
128.2
|
1.0
|
|
CB
|
C:PHE644
|
4.9
|
119.3
|
1.0
|
|
CB
|
C:ASN640
|
4.9
|
126.3
|
1.0
|
|
CA
|
C:CYS639
|
5.0
|
130.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 4 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:156.1
occ:1.00
|
O
|
D:ASN640
|
2.0
|
162.3
|
1.0
|
|
O2A
|
D:ANP1001
|
2.2
|
160.8
|
1.0
|
|
PA
|
D:ANP1001
|
2.4
|
160.8
|
1.0
|
|
O1A
|
D:ANP1001
|
2.4
|
160.8
|
1.0
|
|
C5'
|
D:ANP1001
|
2.4
|
160.8
|
1.0
|
|
O
|
D:LYS642
|
2.5
|
155.8
|
1.0
|
|
O5'
|
D:ANP1001
|
2.6
|
160.8
|
1.0
|
|
C
|
D:ASN640
|
3.3
|
162.3
|
1.0
|
|
OG1
|
D:THR643
|
3.4
|
145.1
|
1.0
|
|
C
|
D:GLY641
|
3.6
|
160.0
|
1.0
|
|
C
|
D:LYS642
|
3.7
|
155.8
|
1.0
|
|
O
|
D:GLY641
|
3.8
|
160.0
|
1.0
|
|
CA
|
D:GLY641
|
3.9
|
160.0
|
1.0
|
|
C4'
|
D:ANP1001
|
3.9
|
160.8
|
1.0
|
|
O3A
|
D:ANP1001
|
3.9
|
160.8
|
1.0
|
|
N
|
D:LYS642
|
4.0
|
155.8
|
1.0
|
|
N
|
D:GLY641
|
4.0
|
160.0
|
1.0
|
|
N
|
D:ASN640
|
4.2
|
162.3
|
1.0
|
|
N
|
D:PHE644
|
4.3
|
141.8
|
1.0
|
|
CB
|
D:PHE644
|
4.3
|
141.8
|
1.0
|
|
C
|
D:CYS639
|
4.3
|
162.6
|
1.0
|
|
O2B
|
D:ANP1001
|
4.3
|
160.8
|
1.0
|
|
CA
|
D:ASN640
|
4.4
|
162.3
|
1.0
|
|
C8
|
D:ANP1001
|
4.5
|
160.8
|
1.0
|
|
CA
|
D:LYS642
|
4.5
|
155.8
|
1.0
|
|
O
|
D:CYS639
|
4.5
|
162.6
|
1.0
|
|
O4'
|
D:ANP1001
|
4.6
|
160.8
|
1.0
|
|
C3'
|
D:ANP1001
|
4.6
|
160.8
|
1.0
|
|
CB
|
D:THR643
|
4.6
|
145.1
|
1.0
|
|
N
|
D:THR643
|
4.7
|
145.1
|
1.0
|
|
C
|
D:THR643
|
4.7
|
145.1
|
1.0
|
|
PB
|
D:ANP1001
|
4.8
|
160.8
|
1.0
|
|
CA
|
D:PHE644
|
4.9
|
141.8
|
1.0
|
|
CA
|
D:CYS639
|
4.9
|
162.6
|
1.0
|
|
CA
|
D:THR643
|
4.9
|
145.1
|
1.0
|
|
C2'
|
D:ANP1001
|
5.0
|
160.8
|
1.0
|
|
O2G
|
D:ANP1001
|
5.0
|
160.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 5 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1002
b:155.3
occ:1.00
|
O1A
|
E:ANP1001
|
2.0
|
161.9
|
1.0
|
|
O3A
|
E:ANP1001
|
2.0
|
161.9
|
1.0
|
|
N
|
E:LYS642
|
2.1
|
149.7
|
1.0
|
|
N
|
E:THR643
|
2.1
|
145.1
|
1.0
|
|
PA
|
E:ANP1001
|
2.4
|
161.9
|
1.0
|
|
C
|
E:GLY641
|
2.6
|
154.9
|
1.0
|
|
CA
|
E:LYS642
|
2.8
|
149.7
|
1.0
|
|
C
|
E:LYS642
|
2.8
|
149.7
|
1.0
|
|
OG1
|
E:THR643
|
2.9
|
145.1
|
1.0
|
|
CA
|
E:GLY641
|
3.1
|
154.9
|
1.0
|
|
CA
|
E:THR643
|
3.1
|
145.1
|
1.0
|
|
N
|
E:GLY641
|
3.2
|
154.9
|
1.0
|
|
O
|
E:THR643
|
3.3
|
145.1
|
1.0
|
|
O5'
|
E:ANP1001
|
3.3
|
161.9
|
1.0
|
|
CB
|
E:LYS642
|
3.4
|
149.7
|
1.0
|
|
PB
|
E:ANP1001
|
3.4
|
161.9
|
1.0
|
|
O
|
E:GLY641
|
3.4
|
154.9
|
1.0
|
|
C
|
E:THR643
|
3.5
|
145.1
|
1.0
|
|
CB
|
E:THR643
|
3.5
|
145.1
|
1.0
|
|
O2A
|
E:ANP1001
|
3.7
|
161.9
|
1.0
|
|
O2B
|
E:ANP1001
|
3.9
|
161.9
|
1.0
|
|
O
|
E:LYS642
|
4.0
|
149.7
|
1.0
|
|
O1B
|
E:ANP1001
|
4.1
|
161.9
|
1.0
|
|
C
|
E:ASN640
|
4.2
|
156.7
|
1.0
|
|
C5'
|
E:ANP1001
|
4.2
|
161.9
|
1.0
|
|
CG2
|
E:THR643
|
4.2
|
145.1
|
1.0
|
|
N
|
E:ASN640
|
4.2
|
156.7
|
1.0
|
|
N3B
|
E:ANP1001
|
4.6
|
161.9
|
1.0
|
|
N
|
E:PHE644
|
4.6
|
134.2
|
1.0
|
|
CG
|
E:LYS642
|
4.7
|
149.7
|
1.0
|
|
CA
|
E:ASN640
|
4.7
|
156.7
|
1.0
|
|
C
|
E:CYS639
|
4.8
|
162.1
|
1.0
|
|
O
|
E:ASN640
|
4.9
|
156.7
|
1.0
|
|
CA
|
E:CYS639
|
5.0
|
162.1
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8ww7
Go back to
Magnesium Binding Sites List in 8ww7
Magnesium binding site 6 out
of 6 in the Structure of Amppnp-Form Asfvprimpol Dodecamer
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Amppnp-Form Asfvprimpol Dodecamer within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1002
b:145.5
occ:1.00
|
O1A
|
F:ANP1001
|
2.0
|
145.7
|
1.0
|
|
O
|
F:LYS642
|
2.0
|
140.5
|
1.0
|
|
N
|
F:PHE644
|
2.1
|
122.1
|
1.0
|
|
OG1
|
F:THR643
|
2.1
|
137.5
|
1.0
|
|
C
|
F:THR643
|
2.2
|
137.5
|
1.0
|
|
O
|
F:THR643
|
2.7
|
137.5
|
1.0
|
|
CA
|
F:PHE644
|
2.8
|
122.1
|
1.0
|
|
CA
|
F:THR643
|
2.9
|
137.5
|
1.0
|
|
CB
|
F:PHE644
|
2.9
|
122.1
|
1.0
|
|
C
|
F:LYS642
|
2.9
|
140.5
|
1.0
|
|
PA
|
F:ANP1001
|
3.0
|
145.7
|
1.0
|
|
CB
|
F:THR643
|
3.0
|
137.5
|
1.0
|
|
N
|
F:THR643
|
3.2
|
137.5
|
1.0
|
|
O2A
|
F:ANP1001
|
3.4
|
145.7
|
1.0
|
|
O3A
|
F:ANP1001
|
3.4
|
145.7
|
1.0
|
|
O
|
F:GLY641
|
3.9
|
139.0
|
1.0
|
|
O
|
F:ASN640
|
4.2
|
138.5
|
1.0
|
|
CG2
|
F:THR643
|
4.2
|
137.5
|
1.0
|
|
C
|
F:PHE644
|
4.3
|
122.1
|
1.0
|
|
O1B
|
F:ANP1001
|
4.3
|
145.7
|
1.0
|
|
CA
|
F:LYS642
|
4.3
|
140.5
|
1.0
|
|
CG
|
F:PHE644
|
4.3
|
122.1
|
1.0
|
|
O5'
|
F:ANP1001
|
4.3
|
145.7
|
1.0
|
|
C
|
F:GLY641
|
4.4
|
139.0
|
1.0
|
|
PB
|
F:ANP1001
|
4.5
|
145.7
|
1.0
|
|
N
|
F:LYS642
|
4.6
|
140.5
|
1.0
|
|
C5'
|
F:ANP1001
|
4.7
|
145.7
|
1.0
|
|
N
|
F:LEU645
|
4.8
|
115.7
|
1.0
|
|
CD1
|
F:ILE781
|
5.0
|
137.1
|
1.0
|
|
Reference:
T.H.Shi,
Y.Y.Guo,
R.H.Yan.
Structure of Adp-Form Asfvprimpol Hexamer To Be Published.
Page generated: Fri Aug 15 20:04:30 2025
|
