Magnesium in PDB 8tyn: Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
Enzymatic activity of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
All present enzymatic activity of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model):
3.6.5.5;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
(pdb code 8tyn). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model), PDB code: 8tyn:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8tyn
Go back to
Magnesium Binding Sites List in 8tyn
Magnesium binding site 1 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Mg802
b:30.0
occ:1.00
|
HG1
|
c:THR65
|
1.9
|
386.8
|
1.0
|
OG1
|
c:THR65
|
2.0
|
322.4
|
1.0
|
HG
|
c:SER45
|
2.2
|
484.5
|
1.0
|
O2B
|
c:GDP801
|
2.4
|
3.8
|
1.0
|
HB
|
c:THR65
|
2.7
|
386.8
|
1.0
|
OG
|
c:SER45
|
2.8
|
403.8
|
1.0
|
CB
|
c:THR65
|
2.8
|
322.4
|
1.0
|
PB
|
c:GDP801
|
3.3
|
4.0
|
1.0
|
O3B
|
c:GDP801
|
3.3
|
4.0
|
1.0
|
HG21
|
c:THR65
|
3.3
|
386.8
|
1.0
|
CG2
|
c:THR65
|
3.7
|
322.4
|
1.0
|
H
|
c:THR65
|
3.8
|
386.8
|
1.0
|
H
|
c:SER45
|
3.9
|
484.5
|
1.0
|
CB
|
c:SER45
|
4.0
|
403.8
|
1.0
|
HB2
|
c:SER45
|
4.1
|
484.5
|
1.0
|
O1B
|
c:GDP801
|
4.1
|
4.0
|
1.0
|
CA
|
c:THR65
|
4.1
|
322.4
|
1.0
|
N
|
c:THR65
|
4.2
|
322.4
|
1.0
|
HB2
|
c:ALA44
|
4.2
|
36.0
|
1.0
|
HG23
|
c:THR65
|
4.2
|
386.8
|
1.0
|
O2A
|
c:GDP801
|
4.3
|
5.9
|
1.0
|
HG22
|
c:THR65
|
4.4
|
386.8
|
1.0
|
OD1
|
c:ASP136
|
4.5
|
506.9
|
1.0
|
HA
|
c:THR65
|
4.5
|
386.8
|
1.0
|
N
|
c:SER45
|
4.5
|
403.8
|
1.0
|
O3A
|
c:GDP801
|
4.6
|
4.7
|
1.0
|
O
|
c:LEU137
|
4.6
|
442.7
|
1.0
|
HA
|
c:PRO138
|
4.7
|
436.4
|
1.0
|
HB3
|
c:SER45
|
4.7
|
484.5
|
1.0
|
HB
|
c:VAL64
|
4.7
|
367.7
|
1.0
|
H
|
c:GLY139
|
4.8
|
469.4
|
1.0
|
PA
|
c:GDP801
|
4.8
|
5.5
|
1.0
|
OD2
|
c:ASP136
|
4.8
|
506.9
|
1.0
|
CA
|
c:SER45
|
4.9
|
403.8
|
1.0
|
O1A
|
c:GDP801
|
5.0
|
6.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8tyn
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Magnesium Binding Sites List in 8tyn
Magnesium binding site 2 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Mg802
b:30.0
occ:1.00
|
HG1
|
f:THR65
|
1.8
|
567.8
|
1.0
|
O3B
|
f:GDP801
|
2.1
|
7.0
|
1.0
|
OG1
|
f:THR65
|
2.1
|
473.2
|
1.0
|
HG
|
f:SER45
|
2.4
|
580.1
|
1.0
|
PB
|
f:GDP801
|
2.9
|
6.5
|
1.0
|
HB
|
f:THR65
|
2.9
|
567.8
|
1.0
|
OG
|
f:SER45
|
3.0
|
483.4
|
1.0
|
CB
|
f:THR65
|
3.0
|
473.2
|
1.0
|
O2B
|
f:GDP801
|
3.1
|
6.6
|
1.0
|
H
|
f:THR65
|
3.4
|
567.8
|
1.0
|
O1B
|
f:GDP801
|
3.4
|
6.7
|
1.0
|
HG21
|
f:THR65
|
3.8
|
567.8
|
1.0
|
HB2
|
f:SER45
|
3.8
|
580.1
|
1.0
|
CB
|
f:SER45
|
4.0
|
483.4
|
1.0
|
CG2
|
f:THR65
|
4.0
|
473.2
|
1.0
|
H
|
f:SER45
|
4.0
|
580.1
|
1.0
|
N
|
f:THR65
|
4.0
|
473.2
|
1.0
|
CA
|
f:THR65
|
4.1
|
473.2
|
1.0
|
HB
|
f:VAL64
|
4.2
|
499.8
|
1.0
|
O3A
|
f:GDP801
|
4.3
|
6.2
|
1.0
|
O1A
|
f:GDP801
|
4.4
|
7.1
|
1.0
|
HG23
|
f:THR65
|
4.5
|
567.8
|
1.0
|
HB3
|
f:ALA44
|
4.5
|
36.0
|
1.0
|
HB3
|
f:SER45
|
4.6
|
580.1
|
1.0
|
OD2
|
f:ASP136
|
4.6
|
750.4
|
1.0
|
HA
|
f:PRO138
|
4.6
|
648.2
|
1.0
|
HA
|
f:THR65
|
4.7
|
567.8
|
1.0
|
N
|
f:SER45
|
4.7
|
483.4
|
1.0
|
OD1
|
f:ASP136
|
4.7
|
750.4
|
1.0
|
HG22
|
f:THR65
|
4.7
|
567.8
|
1.0
|
O
|
f:LEU137
|
4.7
|
639.2
|
1.0
|
PA
|
f:GDP801
|
4.8
|
6.7
|
1.0
|
H
|
f:VAL64
|
4.9
|
499.8
|
1.0
|
CA
|
f:SER45
|
5.0
|
483.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8tyn
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Magnesium Binding Sites List in 8tyn
Magnesium binding site 3 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg802
b:30.0
occ:1.00
|
HG
|
C:SER45
|
1.7
|
484.5
|
1.0
|
HG1
|
C:THR65
|
1.9
|
386.8
|
1.0
|
OG1
|
C:THR65
|
2.0
|
322.4
|
1.0
|
OG
|
C:SER45
|
2.1
|
403.8
|
1.0
|
O2B
|
C:GDP801
|
2.5
|
3.8
|
1.0
|
HB
|
C:THR65
|
3.1
|
386.8
|
1.0
|
CB
|
C:THR65
|
3.1
|
322.4
|
1.0
|
CB
|
C:SER45
|
3.3
|
403.8
|
1.0
|
HB2
|
C:SER45
|
3.4
|
484.5
|
1.0
|
HG21
|
C:THR65
|
3.5
|
386.8
|
1.0
|
PB
|
C:GDP801
|
3.7
|
4.0
|
1.0
|
H
|
C:SER45
|
3.8
|
484.5
|
1.0
|
CG2
|
C:THR65
|
3.8
|
322.4
|
1.0
|
HB3
|
C:SER45
|
3.9
|
484.5
|
1.0
|
H
|
C:THR65
|
4.1
|
386.8
|
1.0
|
O1B
|
C:GDP801
|
4.2
|
4.0
|
1.0
|
CA
|
C:THR65
|
4.3
|
322.4
|
1.0
|
OD1
|
C:ASP136
|
4.3
|
506.9
|
1.0
|
HG23
|
C:THR65
|
4.3
|
386.8
|
1.0
|
N
|
C:SER45
|
4.3
|
403.8
|
1.0
|
N
|
C:THR65
|
4.4
|
322.4
|
1.0
|
CA
|
C:SER45
|
4.4
|
403.8
|
1.0
|
O2A
|
C:GDP801
|
4.4
|
5.9
|
1.0
|
OD2
|
C:ASP136
|
4.4
|
506.9
|
1.0
|
O3B
|
C:GDP801
|
4.4
|
4.0
|
1.0
|
HB2
|
C:ALA44
|
4.6
|
36.0
|
1.0
|
HA
|
C:THR65
|
4.6
|
386.8
|
1.0
|
HA
|
C:SER45
|
4.6
|
484.5
|
1.0
|
HG22
|
C:THR65
|
4.6
|
386.8
|
1.0
|
HB
|
C:VAL64
|
4.7
|
367.7
|
1.0
|
O
|
C:PRO58
|
4.7
|
336.4
|
1.0
|
CG
|
C:ASP136
|
4.8
|
506.9
|
1.0
|
HA
|
C:ARG59
|
4.9
|
338.6
|
1.0
|
O3A
|
C:GDP801
|
4.9
|
4.7
|
1.0
|
O
|
C:LEU137
|
5.0
|
442.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8tyn
Go back to
Magnesium Binding Sites List in 8tyn
Magnesium binding site 4 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em of the Gdp-Bound Human Dynamin Polymer Assembled on the Membrane in the Super Constricted State (Tetramer Model) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg802
b:30.0
occ:1.00
|
HG1
|
F:THR65
|
1.6
|
567.8
|
1.0
|
OG1
|
F:THR65
|
1.9
|
473.2
|
1.0
|
O3B
|
F:GDP801
|
2.1
|
7.0
|
1.0
|
HG
|
F:SER45
|
2.2
|
580.1
|
1.0
|
OG
|
F:SER45
|
2.7
|
483.4
|
1.0
|
PB
|
F:GDP801
|
2.9
|
6.5
|
1.0
|
CB
|
F:THR65
|
3.0
|
473.2
|
1.0
|
HB
|
F:THR65
|
3.0
|
567.8
|
1.0
|
O2B
|
F:GDP801
|
3.3
|
6.6
|
1.0
|
O1B
|
F:GDP801
|
3.3
|
6.7
|
1.0
|
H
|
F:THR65
|
3.4
|
567.8
|
1.0
|
HB2
|
F:SER45
|
3.5
|
580.1
|
1.0
|
CB
|
F:SER45
|
3.7
|
483.4
|
1.0
|
HG21
|
F:THR65
|
3.7
|
567.8
|
1.0
|
CG2
|
F:THR65
|
3.9
|
473.2
|
1.0
|
H
|
F:SER45
|
4.0
|
580.1
|
1.0
|
N
|
F:THR65
|
4.0
|
473.2
|
1.0
|
CA
|
F:THR65
|
4.1
|
473.2
|
1.0
|
HB
|
F:VAL64
|
4.1
|
499.8
|
1.0
|
HB3
|
F:SER45
|
4.2
|
580.1
|
1.0
|
O1A
|
F:GDP801
|
4.3
|
7.1
|
1.0
|
HG23
|
F:THR65
|
4.3
|
567.8
|
1.0
|
O3A
|
F:GDP801
|
4.3
|
6.2
|
1.0
|
OD2
|
F:ASP136
|
4.4
|
750.4
|
1.0
|
HA
|
F:THR65
|
4.5
|
567.8
|
1.0
|
N
|
F:SER45
|
4.6
|
483.4
|
1.0
|
HB3
|
F:ALA44
|
4.6
|
36.0
|
1.0
|
OD1
|
F:ASP136
|
4.7
|
750.4
|
1.0
|
HG22
|
F:THR65
|
4.7
|
567.8
|
1.0
|
CA
|
F:SER45
|
4.8
|
483.4
|
1.0
|
PA
|
F:GDP801
|
4.8
|
6.7
|
1.0
|
HA
|
F:PRO138
|
4.9
|
648.2
|
1.0
|
CG
|
F:ASP136
|
5.0
|
750.4
|
1.0
|
HG12
|
F:VAL64
|
5.0
|
499.8
|
1.0
|
O
|
F:LEU137
|
5.0
|
639.2
|
1.0
|
|
Reference:
J.R.Jimah,
N.Kundu,
A.E.Stanton,
K.A.Sochacki,
B.Canagarajah,
L.Chan,
M.P.Strub,
H.Wang,
J.W.Taraska,
J.E.Hinshaw.
Cryo-Em Structures of Membrane-Bound Dynamin in A Post-Hydrolysis State Primed For Membrane Fission. Dev.Cell 2024.
ISSN: ISSN 1534-5807
PubMed: 38663399
DOI: 10.1016/J.DEVCEL.2024.04.008
Page generated: Fri Oct 4 21:07:43 2024
|