Magnesium in PDB 7pm6: Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
(pdb code 7pm6). 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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER), PDB code: 7pm6:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7pm6
Go back to
Magnesium Binding Sites List in 7pm6
Magnesium binding site 1 out
of 5 in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1901
b:71.5
occ:1.00
|
O1B
|
A:ADP1902
|
1.9
|
78.4
|
1.0
|
OG1
|
A:THR170
|
2.6
|
74.2
|
1.0
|
OG
|
A:SER218
|
2.8
|
63.1
|
1.0
|
PB
|
A:ADP1902
|
3.2
|
78.4
|
1.0
|
O3B
|
A:ADP1902
|
3.6
|
78.4
|
1.0
|
CB
|
A:THR170
|
3.9
|
74.2
|
1.0
|
CB
|
A:SER218
|
4.0
|
63.1
|
1.0
|
O3A
|
A:ADP1902
|
4.0
|
78.4
|
1.0
|
O2B
|
A:ADP1902
|
4.4
|
78.4
|
1.0
|
OD2
|
A:ASP437
|
4.4
|
66.0
|
1.0
|
ND2
|
A:ASN208
|
4.5
|
65.4
|
1.0
|
O
|
A:ASN216
|
4.5
|
66.9
|
1.0
|
OE2
|
A:GLU204
|
4.6
|
73.1
|
1.0
|
CG2
|
A:THR170
|
4.7
|
74.2
|
1.0
|
N
|
A:SER218
|
4.7
|
63.1
|
1.0
|
N
|
A:THR170
|
4.8
|
74.2
|
1.0
|
PA
|
A:ADP1902
|
4.8
|
78.4
|
1.0
|
O1A
|
A:ADP1902
|
4.9
|
78.4
|
1.0
|
ND2
|
A:ASN216
|
4.9
|
66.9
|
1.0
|
CA
|
A:THR170
|
4.9
|
74.2
|
1.0
|
NZ
|
A:LYS169
|
4.9
|
70.9
|
1.0
|
CA
|
A:SER218
|
4.9
|
63.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7pm6
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Magnesium Binding Sites List in 7pm6
Magnesium binding site 2 out
of 5 in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:53.5
occ:1.00
|
O2B
|
C:ADP401
|
2.3
|
54.8
|
1.0
|
PB
|
C:ADP401
|
3.5
|
54.8
|
1.0
|
O2A
|
C:ADP401
|
3.6
|
54.8
|
1.0
|
O3B
|
C:ADP401
|
3.7
|
54.8
|
1.0
|
OD1
|
C:ASP154
|
4.0
|
52.2
|
1.0
|
CA
|
C:GLY156
|
4.0
|
50.6
|
1.0
|
O3A
|
C:ADP401
|
4.1
|
54.8
|
1.0
|
OD2
|
C:ASP154
|
4.3
|
52.2
|
1.0
|
PA
|
C:ADP401
|
4.4
|
54.8
|
1.0
|
CA
|
C:GLY301
|
4.5
|
50.2
|
1.0
|
OE1
|
C:GLN137
|
4.5
|
54.7
|
1.0
|
NE2
|
C:GLN137
|
4.5
|
54.7
|
1.0
|
N
|
C:GLY156
|
4.6
|
50.6
|
1.0
|
CG
|
C:ASP154
|
4.6
|
52.2
|
1.0
|
CD
|
C:GLN137
|
4.6
|
54.7
|
1.0
|
O1B
|
C:ADP401
|
4.7
|
54.8
|
1.0
|
O
|
C:SER155
|
4.7
|
50.6
|
1.0
|
CG2
|
C:VAL339
|
4.8
|
47.0
|
1.0
|
C
|
C:SER155
|
4.8
|
50.6
|
1.0
|
OD2
|
C:ASP11
|
4.9
|
57.5
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7pm6
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Magnesium Binding Sites List in 7pm6
Magnesium binding site 3 out
of 5 in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1901
b:75.5
occ:1.00
|
O1B
|
D:ADP1902
|
2.0
|
84.0
|
1.0
|
OG1
|
D:THR170
|
2.3
|
79.5
|
1.0
|
OG
|
D:SER218
|
2.9
|
68.2
|
1.0
|
PB
|
D:ADP1902
|
3.4
|
84.0
|
1.0
|
CB
|
D:THR170
|
3.6
|
79.5
|
1.0
|
O3B
|
D:ADP1902
|
3.8
|
84.0
|
1.0
|
CB
|
D:SER218
|
4.1
|
68.2
|
1.0
|
O3A
|
D:ADP1902
|
4.2
|
84.0
|
1.0
|
ND2
|
D:ASN208
|
4.2
|
70.6
|
1.0
|
CG2
|
D:THR170
|
4.2
|
79.5
|
1.0
|
OD2
|
D:ASP437
|
4.2
|
71.7
|
1.0
|
O2B
|
D:ADP1902
|
4.5
|
84.0
|
1.0
|
OE2
|
D:GLU204
|
4.5
|
80.6
|
1.0
|
CA
|
D:THR170
|
4.7
|
79.5
|
1.0
|
N
|
D:THR170
|
4.7
|
79.5
|
1.0
|
O
|
D:ASN216
|
4.7
|
73.0
|
1.0
|
CD
|
D:GLU204
|
4.9
|
80.6
|
1.0
|
ND2
|
D:ASN216
|
4.9
|
73.0
|
1.0
|
O2A
|
D:ADP1902
|
4.9
|
84.0
|
1.0
|
N
|
D:SER218
|
5.0
|
68.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7pm6
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Magnesium Binding Sites List in 7pm6
Magnesium binding site 4 out
of 5 in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:52.3
occ:1.00
|
O2B
|
F:ADP401
|
2.0
|
54.1
|
1.0
|
PB
|
F:ADP401
|
3.4
|
54.1
|
1.0
|
O2A
|
F:ADP401
|
3.5
|
54.1
|
1.0
|
O3B
|
F:ADP401
|
3.8
|
54.1
|
1.0
|
OD1
|
F:ASP154
|
4.1
|
50.4
|
1.0
|
O3A
|
F:ADP401
|
4.1
|
54.1
|
1.0
|
CA
|
F:GLY156
|
4.1
|
49.3
|
1.0
|
CA
|
F:GLY301
|
4.3
|
49.1
|
1.0
|
PA
|
F:ADP401
|
4.3
|
54.1
|
1.0
|
OD2
|
F:ASP154
|
4.4
|
50.4
|
1.0
|
O1B
|
F:ADP401
|
4.5
|
54.1
|
1.0
|
CG2
|
F:VAL339
|
4.6
|
45.8
|
1.0
|
CG
|
F:ASP154
|
4.6
|
50.4
|
1.0
|
OE1
|
F:GLN137
|
4.7
|
53.2
|
1.0
|
NE2
|
F:GLN137
|
4.7
|
53.2
|
1.0
|
N
|
F:GLY156
|
4.7
|
49.3
|
1.0
|
CD
|
F:GLN137
|
4.7
|
53.2
|
1.0
|
NZ
|
F:LYS18
|
4.7
|
49.9
|
1.0
|
O
|
F:SER155
|
4.8
|
49.6
|
1.0
|
OD2
|
F:ASP11
|
4.9
|
57.2
|
1.0
|
C
|
F:SER155
|
4.9
|
49.6
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7pm6
Go back to
Magnesium Binding Sites List in 7pm6
Magnesium binding site 5 out
of 5 in the Cryo-Em Structure of the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER)
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 the Actomyosin-V Complex in the Strong-Adp State (Central 3ER/2ER) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg402
b:53.7
occ:1.00
|
O2B
|
G:ADP401
|
2.0
|
52.6
|
1.0
|
PB
|
G:ADP401
|
3.3
|
52.6
|
1.0
|
O2A
|
G:ADP401
|
3.6
|
52.6
|
1.0
|
O3B
|
G:ADP401
|
3.7
|
52.6
|
1.0
|
O3A
|
G:ADP401
|
4.0
|
52.6
|
1.0
|
CA
|
G:GLY156
|
4.2
|
49.9
|
1.0
|
OD1
|
G:ASP154
|
4.3
|
52.9
|
1.0
|
NE2
|
G:GLN137
|
4.3
|
55.8
|
1.0
|
OD2
|
G:ASP11
|
4.3
|
58.5
|
1.0
|
PA
|
G:ADP401
|
4.4
|
52.6
|
1.0
|
O1B
|
G:ADP401
|
4.5
|
52.6
|
1.0
|
NZ
|
G:LYS18
|
4.5
|
50.4
|
1.0
|
CD
|
G:GLN137
|
4.5
|
55.8
|
1.0
|
OE1
|
G:GLN137
|
4.6
|
55.8
|
1.0
|
OD2
|
G:ASP154
|
4.6
|
52.9
|
1.0
|
CA
|
G:GLY301
|
4.8
|
48.6
|
1.0
|
CG2
|
G:VAL339
|
4.8
|
47.6
|
1.0
|
CA
|
G:GLY13
|
4.9
|
56.8
|
1.0
|
N
|
G:GLY156
|
4.9
|
49.9
|
1.0
|
CG
|
G:ASP154
|
4.9
|
52.9
|
1.0
|
|
Reference:
S.Pospich,
H.L.Sweeney,
A.Houdusse,
S.Raunser.
High-Resolution Structures of the Actomyosin-V Complex in Three Nucleotide States Provide Insights Into the Force Generation Mechanism. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34812732
DOI: 10.7554/ELIFE.73724
Page generated: Thu Oct 3 04:39:38 2024
|