Magnesium in PDB 8oi8: Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
(pdb code 8oi8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation, PDB code: 8oi8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 8oi8
Go back to
Magnesium Binding Sites List in 8oi8
Magnesium binding site 1 out
of 5 in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:23.4
occ:1.00
|
O
|
C:HOH525
|
1.8
|
19.6
|
1.0
|
O
|
C:HOH533
|
1.9
|
22.2
|
1.0
|
O3B
|
C:ADP401
|
2.0
|
24.4
|
1.0
|
O
|
C:HOH509
|
2.0
|
23.0
|
1.0
|
O2A
|
C:ADP401
|
2.1
|
24.4
|
1.0
|
O
|
C:HOH590
|
2.2
|
23.8
|
1.0
|
PA
|
C:ADP401
|
3.3
|
24.4
|
1.0
|
PB
|
C:ADP401
|
3.3
|
24.4
|
1.0
|
O3A
|
C:ADP401
|
3.6
|
24.4
|
1.0
|
O1A
|
C:ADP401
|
4.1
|
24.4
|
1.0
|
CA
|
C:GLY301
|
4.1
|
22.5
|
1.0
|
NZ
|
C:LYS18
|
4.2
|
28.7
|
1.0
|
O
|
C:HOH548
|
4.2
|
23.4
|
1.0
|
CA
|
C:GLY156
|
4.2
|
22.9
|
1.0
|
O
|
C:HOH612
|
4.2
|
20.9
|
1.0
|
O1B
|
C:ADP401
|
4.3
|
24.4
|
1.0
|
O2B
|
C:ADP401
|
4.3
|
24.4
|
1.0
|
OD1
|
C:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
C:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
C:ASP11
|
4.5
|
30.4
|
1.0
|
O5'
|
C:ADP401
|
4.5
|
24.4
|
1.0
|
N
|
C:GLY302
|
4.6
|
22.8
|
1.0
|
N
|
C:GLY156
|
4.8
|
22.9
|
1.0
|
CG
|
C:ASP154
|
4.8
|
23.6
|
1.0
|
O
|
C:HOH510
|
4.8
|
21.7
|
1.0
|
C
|
C:GLY301
|
5.0
|
22.5
|
1.0
|
O
|
C:HOH591
|
5.0
|
22.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 8oi8
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Magnesium Binding Sites List in 8oi8
Magnesium binding site 2 out
of 5 in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:23.4
occ:1.00
|
O
|
A:HOH541
|
1.8
|
19.6
|
1.0
|
O
|
A:HOH510
|
1.9
|
23.0
|
1.0
|
O
|
A:HOH534
|
1.9
|
22.2
|
1.0
|
O3B
|
A:ADP401
|
2.0
|
24.4
|
1.0
|
O2A
|
A:ADP401
|
2.1
|
24.4
|
1.0
|
O
|
A:HOH557
|
2.2
|
23.8
|
1.0
|
PA
|
A:ADP401
|
3.3
|
24.4
|
1.0
|
PB
|
A:ADP401
|
3.3
|
24.4
|
1.0
|
O3A
|
A:ADP401
|
3.6
|
24.4
|
1.0
|
O
|
A:HOH535
|
3.9
|
23.4
|
1.0
|
O1A
|
A:ADP401
|
4.1
|
24.4
|
1.0
|
CA
|
A:GLY301
|
4.1
|
22.5
|
1.0
|
NZ
|
A:LYS18
|
4.2
|
28.7
|
1.0
|
CA
|
A:GLY156
|
4.2
|
22.9
|
1.0
|
O
|
A:HOH576
|
4.3
|
20.9
|
1.0
|
O1B
|
A:ADP401
|
4.3
|
24.4
|
1.0
|
O2B
|
A:ADP401
|
4.3
|
24.4
|
1.0
|
OD1
|
A:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
A:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
A:ASP11
|
4.5
|
30.4
|
1.0
|
O5'
|
A:ADP401
|
4.5
|
24.4
|
1.0
|
N
|
A:GLY302
|
4.6
|
22.8
|
1.0
|
N
|
A:GLY156
|
4.8
|
22.9
|
1.0
|
CG
|
A:ASP154
|
4.8
|
23.6
|
1.0
|
O
|
A:HOH588
|
4.8
|
22.3
|
1.0
|
O
|
A:HOH533
|
4.9
|
21.7
|
1.0
|
C
|
A:GLY301
|
5.0
|
22.5
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 8oi8
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Magnesium Binding Sites List in 8oi8
Magnesium binding site 3 out
of 5 in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:23.4
occ:1.00
|
O
|
B:HOH530
|
1.8
|
19.6
|
1.0
|
O
|
B:HOH534
|
1.9
|
22.2
|
1.0
|
O3B
|
B:ADP401
|
2.0
|
24.4
|
1.0
|
O
|
B:HOH510
|
2.0
|
23.0
|
1.0
|
O2A
|
B:ADP401
|
2.1
|
24.4
|
1.0
|
O
|
B:HOH604
|
2.1
|
23.8
|
1.0
|
PA
|
B:ADP401
|
3.3
|
24.4
|
1.0
|
PB
|
B:ADP401
|
3.3
|
24.4
|
1.0
|
O3A
|
B:ADP401
|
3.6
|
24.4
|
1.0
|
O
|
B:HOH549
|
4.0
|
23.4
|
1.0
|
O1A
|
B:ADP401
|
4.1
|
24.4
|
1.0
|
CA
|
B:GLY301
|
4.1
|
22.5
|
1.0
|
NZ
|
B:LYS18
|
4.2
|
28.7
|
1.0
|
O
|
B:HOH608
|
4.2
|
20.9
|
1.0
|
CA
|
B:GLY156
|
4.2
|
22.9
|
1.0
|
O1B
|
B:ADP401
|
4.3
|
24.4
|
1.0
|
O2B
|
B:ADP401
|
4.3
|
24.4
|
1.0
|
OD1
|
B:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
B:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
B:ASP11
|
4.5
|
30.4
|
1.0
|
O5'
|
B:ADP401
|
4.5
|
24.4
|
1.0
|
N
|
B:GLY302
|
4.6
|
22.8
|
1.0
|
O
|
B:HOH521
|
4.8
|
21.7
|
1.0
|
N
|
B:GLY156
|
4.8
|
22.9
|
1.0
|
CG
|
B:ASP154
|
4.8
|
23.6
|
1.0
|
C
|
B:GLY301
|
5.0
|
22.5
|
1.0
|
O
|
B:HOH592
|
5.0
|
22.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 8oi8
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Magnesium Binding Sites List in 8oi8
Magnesium binding site 4 out
of 5 in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:23.4
occ:1.00
|
O
|
D:HOH512
|
1.8
|
19.6
|
1.0
|
O
|
D:HOH511
|
1.8
|
22.2
|
1.0
|
O3B
|
D:ADP401
|
2.0
|
24.4
|
1.0
|
O
|
D:HOH611
|
2.1
|
23.8
|
1.0
|
O2A
|
D:ADP401
|
2.1
|
24.4
|
1.0
|
O
|
D:HOH516
|
2.2
|
23.0
|
1.0
|
PA
|
D:ADP401
|
3.3
|
24.4
|
1.0
|
PB
|
D:ADP401
|
3.3
|
24.4
|
1.0
|
O3A
|
D:ADP401
|
3.6
|
24.4
|
1.0
|
O1A
|
D:ADP401
|
4.1
|
24.4
|
1.0
|
CA
|
D:GLY301
|
4.1
|
22.5
|
1.0
|
O
|
D:HOH593
|
4.1
|
20.9
|
1.0
|
NZ
|
D:LYS18
|
4.2
|
28.7
|
1.0
|
CA
|
D:GLY156
|
4.2
|
22.9
|
1.0
|
O1B
|
D:ADP401
|
4.3
|
24.4
|
1.0
|
O2B
|
D:ADP401
|
4.3
|
24.4
|
1.0
|
OD1
|
D:ASP154
|
4.4
|
23.6
|
1.0
|
O
|
D:HOH531
|
4.4
|
23.4
|
1.0
|
OD2
|
D:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
D:ASP11
|
4.5
|
30.4
|
1.0
|
O5'
|
D:ADP401
|
4.5
|
24.4
|
1.0
|
N
|
D:GLY302
|
4.6
|
22.8
|
1.0
|
N
|
D:GLY156
|
4.8
|
22.9
|
1.0
|
O
|
D:HOH507
|
4.8
|
21.7
|
1.0
|
CG
|
D:ASP154
|
4.8
|
23.6
|
1.0
|
C
|
D:GLY301
|
5.0
|
22.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 8oi8
Go back to
Magnesium Binding Sites List in 8oi8
Magnesium binding site 5 out
of 5 in the Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of Adp-Bound, Filamentous Beta-Actin Harboring the R183W Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg402
b:23.4
occ:1.00
|
O
|
E:HOH507
|
1.8
|
19.6
|
1.0
|
O
|
E:HOH504
|
1.9
|
22.2
|
1.0
|
O3B
|
E:ADP401
|
2.0
|
24.4
|
1.0
|
O
|
E:HOH557
|
2.0
|
23.8
|
1.0
|
O2A
|
E:ADP401
|
2.1
|
24.4
|
1.0
|
O
|
E:HOH501
|
2.1
|
23.0
|
1.0
|
PA
|
E:ADP401
|
3.3
|
24.4
|
1.0
|
PB
|
E:ADP401
|
3.3
|
24.4
|
1.0
|
O3A
|
E:ADP401
|
3.6
|
24.4
|
1.0
|
O
|
E:HOH567
|
4.0
|
20.9
|
1.0
|
O1A
|
E:ADP401
|
4.1
|
24.4
|
1.0
|
CA
|
E:GLY301
|
4.1
|
22.5
|
1.0
|
NZ
|
E:LYS18
|
4.2
|
28.7
|
1.0
|
CA
|
E:GLY156
|
4.2
|
22.9
|
1.0
|
O1B
|
E:ADP401
|
4.3
|
24.4
|
1.0
|
O2B
|
E:ADP401
|
4.3
|
24.4
|
1.0
|
OD1
|
E:ASP154
|
4.4
|
23.6
|
1.0
|
OD2
|
E:ASP154
|
4.4
|
23.6
|
1.0
|
O
|
E:HOH523
|
4.5
|
23.4
|
1.0
|
OD2
|
E:ASP11
|
4.5
|
30.4
|
1.0
|
O5'
|
E:ADP401
|
4.5
|
24.4
|
1.0
|
N
|
E:GLY302
|
4.6
|
22.8
|
1.0
|
O
|
E:HOH502
|
4.6
|
21.7
|
1.0
|
N
|
E:GLY156
|
4.8
|
22.9
|
1.0
|
CG
|
E:ASP154
|
4.8
|
23.6
|
1.0
|
C
|
E:GLY301
|
5.0
|
22.5
|
1.0
|
|
Reference:
W.Oosterheert,
F.E.C.Blanc,
A.Roy,
A.Belyy,
O.Hofnagel,
G.Hummer,
P.Bieling,
S.Raunser.
Molecular Mechanisms of Inorganic-Phosphate Release From the Core and Barbed End of Actin Filaments To Be Published.
Page generated: Fri Oct 4 14:49:33 2024
|