Magnesium in PDB 7uuw: Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
(pdb code 7uuw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1, PDB code: 7uuw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 1 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:14.2
occ:1.00
|
O2B
|
A:ADP401
|
2.4
|
19.1
|
1.0
|
PB
|
A:ADP401
|
3.3
|
19.1
|
1.0
|
O3A
|
A:ADP401
|
3.5
|
19.1
|
1.0
|
O3B
|
A:ADP401
|
3.5
|
19.1
|
1.0
|
OE1
|
A:GLN137
|
3.6
|
19.0
|
1.0
|
OD2
|
A:ASP154
|
4.1
|
17.5
|
1.0
|
O
|
A:SER155
|
4.1
|
16.9
|
1.0
|
CD
|
A:GLN137
|
4.2
|
19.0
|
1.0
|
OD1
|
A:ASP154
|
4.3
|
17.5
|
1.0
|
NE2
|
A:GLN137
|
4.4
|
19.0
|
1.0
|
CG2
|
A:VAL339
|
4.5
|
18.9
|
1.0
|
CA
|
A:GLY301
|
4.6
|
16.8
|
1.0
|
CG
|
A:ASP154
|
4.6
|
17.5
|
1.0
|
O2A
|
A:ADP401
|
4.7
|
19.1
|
1.0
|
PA
|
A:ADP401
|
4.7
|
19.1
|
1.0
|
O1B
|
A:ADP401
|
4.7
|
19.1
|
1.0
|
OD2
|
A:ASP11
|
4.7
|
22.5
|
1.0
|
CA
|
A:GLY156
|
4.8
|
16.2
|
1.0
|
CB
|
A:VAL339
|
5.0
|
18.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 2 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:8.3
occ:1.00
|
O2B
|
B:ADP401
|
2.4
|
11.9
|
1.0
|
PB
|
B:ADP401
|
3.3
|
11.9
|
1.0
|
O3A
|
B:ADP401
|
3.4
|
11.9
|
1.0
|
O3B
|
B:ADP401
|
3.5
|
11.9
|
1.0
|
OE1
|
B:GLN137
|
3.7
|
10.7
|
1.0
|
OD2
|
B:ASP154
|
4.1
|
10.1
|
1.0
|
O
|
B:SER155
|
4.1
|
9.9
|
1.0
|
CD
|
B:GLN137
|
4.3
|
10.7
|
1.0
|
OD1
|
B:ASP154
|
4.3
|
10.1
|
1.0
|
NE2
|
B:GLN137
|
4.4
|
10.7
|
1.0
|
CG2
|
B:VAL339
|
4.5
|
11.3
|
1.0
|
CA
|
B:GLY301
|
4.5
|
10.1
|
1.0
|
O2A
|
B:ADP401
|
4.6
|
11.9
|
1.0
|
CG
|
B:ASP154
|
4.6
|
10.1
|
1.0
|
PA
|
B:ADP401
|
4.7
|
11.9
|
1.0
|
O1B
|
B:ADP401
|
4.7
|
11.9
|
1.0
|
OD2
|
B:ASP11
|
4.7
|
13.7
|
1.0
|
CA
|
B:GLY156
|
4.8
|
9.7
|
1.0
|
CB
|
B:VAL339
|
5.0
|
11.3
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 3 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:13.5
occ:1.00
|
O2B
|
C:ADP401
|
2.3
|
10.0
|
1.0
|
PB
|
C:ADP401
|
3.2
|
10.0
|
1.0
|
O3A
|
C:ADP401
|
3.4
|
10.0
|
1.0
|
O3B
|
C:ADP401
|
3.4
|
10.0
|
1.0
|
OE1
|
C:GLN137
|
3.7
|
9.9
|
1.0
|
OD2
|
C:ASP154
|
4.1
|
10.3
|
1.0
|
O
|
C:SER155
|
4.2
|
11.0
|
1.0
|
CD
|
C:GLN137
|
4.2
|
9.9
|
1.0
|
NE2
|
C:GLN137
|
4.3
|
9.9
|
1.0
|
OD1
|
C:ASP154
|
4.4
|
10.3
|
1.0
|
CG2
|
C:VAL339
|
4.5
|
9.3
|
1.0
|
CA
|
C:GLY301
|
4.6
|
9.6
|
1.0
|
O2A
|
C:ADP401
|
4.6
|
10.0
|
1.0
|
O1B
|
C:ADP401
|
4.7
|
10.0
|
1.0
|
PA
|
C:ADP401
|
4.7
|
10.0
|
1.0
|
CG
|
C:ASP154
|
4.7
|
10.3
|
1.0
|
OD2
|
C:ASP11
|
4.7
|
10.9
|
1.0
|
CA
|
C:GLY156
|
4.8
|
11.0
|
1.0
|
CB
|
C:VAL339
|
5.0
|
9.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 4 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:13.5
occ:1.00
|
O2B
|
D:ADP401
|
2.5
|
9.0
|
1.0
|
PB
|
D:ADP401
|
3.3
|
9.0
|
1.0
|
O3A
|
D:ADP401
|
3.4
|
9.0
|
1.0
|
O3B
|
D:ADP401
|
3.5
|
9.0
|
1.0
|
OE1
|
D:GLN137
|
3.8
|
9.3
|
1.0
|
O
|
D:SER155
|
4.0
|
8.3
|
1.0
|
OD2
|
D:ASP154
|
4.0
|
8.7
|
1.0
|
OD1
|
D:ASP154
|
4.2
|
8.7
|
1.0
|
CA
|
D:GLY301
|
4.4
|
8.1
|
1.0
|
CD
|
D:GLN137
|
4.4
|
9.3
|
1.0
|
CG2
|
D:VAL339
|
4.5
|
8.5
|
1.0
|
NE2
|
D:GLN137
|
4.5
|
9.3
|
1.0
|
O2A
|
D:ADP401
|
4.5
|
9.0
|
1.0
|
CG
|
D:ASP154
|
4.6
|
8.7
|
1.0
|
PA
|
D:ADP401
|
4.6
|
9.0
|
1.0
|
O1B
|
D:ADP401
|
4.8
|
9.0
|
1.0
|
CA
|
D:GLY156
|
4.8
|
8.1
|
1.0
|
OD2
|
D:ASP11
|
4.8
|
10.8
|
1.0
|
CB
|
D:VAL339
|
4.9
|
8.5
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 5 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg402
b:8.8
occ:1.00
|
O2B
|
E:ADP401
|
2.4
|
10.0
|
1.0
|
PB
|
E:ADP401
|
3.2
|
10.0
|
1.0
|
O3B
|
E:ADP401
|
3.3
|
10.0
|
1.0
|
O3A
|
E:ADP401
|
3.3
|
10.0
|
1.0
|
OE1
|
E:GLN137
|
3.9
|
10.1
|
1.0
|
O
|
E:SER155
|
4.3
|
8.6
|
1.0
|
OD2
|
E:ASP154
|
4.3
|
9.0
|
1.0
|
CD
|
E:GLN137
|
4.4
|
10.1
|
1.0
|
O2A
|
E:ADP401
|
4.4
|
10.0
|
1.0
|
NE2
|
E:GLN137
|
4.5
|
10.1
|
1.0
|
OD1
|
E:ASP154
|
4.5
|
9.0
|
1.0
|
PA
|
E:ADP401
|
4.5
|
10.0
|
1.0
|
CG2
|
E:VAL339
|
4.5
|
9.0
|
1.0
|
CA
|
E:GLY301
|
4.6
|
9.0
|
1.0
|
OD2
|
E:ASP11
|
4.6
|
11.8
|
1.0
|
O1B
|
E:ADP401
|
4.6
|
10.0
|
1.0
|
CG
|
E:ASP154
|
4.8
|
9.0
|
1.0
|
CA
|
E:GLY156
|
4.9
|
8.4
|
1.0
|
CB
|
E:VAL339
|
4.9
|
9.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7uuw
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Magnesium Binding Sites List in 7uuw
Magnesium binding site 6 out
of 6 in the Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryogenic Electron Microscopy 3D Map of F-Actin Bound By the Actin Binding Domain of Alpha-Catenin Ortholog, HMP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:7.6
occ:1.00
|
O2B
|
F:ADP401
|
2.3
|
10.9
|
1.0
|
PB
|
F:ADP401
|
3.2
|
10.9
|
1.0
|
O3B
|
F:ADP401
|
3.4
|
10.9
|
1.0
|
O3A
|
F:ADP401
|
3.4
|
10.9
|
1.0
|
OE1
|
F:GLN137
|
3.6
|
9.9
|
1.0
|
OD2
|
F:ASP154
|
4.1
|
8.5
|
1.0
|
O
|
F:SER155
|
4.2
|
9.1
|
1.0
|
CD
|
F:GLN137
|
4.2
|
9.9
|
1.0
|
NE2
|
F:GLN137
|
4.3
|
9.9
|
1.0
|
OD1
|
F:ASP154
|
4.5
|
8.5
|
1.0
|
O1B
|
F:ADP401
|
4.6
|
10.9
|
1.0
|
CG2
|
F:VAL339
|
4.6
|
9.2
|
1.0
|
O2A
|
F:ADP401
|
4.7
|
10.9
|
1.0
|
PA
|
F:ADP401
|
4.7
|
10.9
|
1.0
|
CA
|
F:GLY301
|
4.7
|
9.2
|
1.0
|
OD2
|
F:ASP11
|
4.7
|
11.9
|
1.0
|
CG
|
F:ASP154
|
4.7
|
8.5
|
1.0
|
CA
|
F:GLY156
|
4.8
|
9.3
|
1.0
|
|
Reference:
E.S.Rangarajan,
E.W.Smith,
T.Izard.
The Nematode HMP1/ Alpha-Catenin Has An Extended Alpha-Helix When Bound to Actin Filaments. J.Biol.Chem. 02817 2022.
ISSN: ESSN 1083-351X
PubMed: 36539037
DOI: 10.1016/J.JBC.2022.102817
Page generated: Thu Oct 3 10:13:40 2024
|