Magnesium in PDB 8tym: Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
Enzymatic activity of Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
All present enzymatic activity of Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State:
3.6.5.5;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
(pdb code 8tym). 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 (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State, PDB code: 8tym:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8tym
Go back to
Magnesium Binding Sites List in 8tym
Magnesium binding site 1 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
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 (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Mg902
b:30.0
occ:1.00
|
HG
|
c:SER45
|
1.8
|
484.5
|
1.0
|
HG1
|
c:THR65
|
1.8
|
386.8
|
1.0
|
OG1
|
c:THR65
|
2.0
|
322.4
|
1.0
|
OG
|
c:SER45
|
2.0
|
403.8
|
1.0
|
CB
|
c:SER45
|
3.0
|
403.8
|
1.0
|
HB2
|
c:SER45
|
3.0
|
484.5
|
1.0
|
O
|
c:PRO58
|
3.1
|
336.4
|
1.0
|
O2B
|
c:GDP901
|
3.2
|
3.8
|
1.0
|
HB3
|
c:SER45
|
3.2
|
484.5
|
1.0
|
CB
|
c:THR65
|
3.4
|
322.4
|
1.0
|
HA
|
c:ARG59
|
3.7
|
338.6
|
1.0
|
HB
|
c:THR65
|
3.9
|
386.8
|
1.0
|
H
|
c:THR65
|
3.9
|
386.8
|
1.0
|
OD2
|
c:ASP136
|
3.9
|
506.9
|
1.0
|
HB
|
c:VAL64
|
3.9
|
367.7
|
1.0
|
HA
|
c:THR65
|
4.1
|
386.8
|
1.0
|
HG12
|
c:VAL64
|
4.1
|
367.7
|
1.0
|
N
|
c:THR65
|
4.1
|
322.4
|
1.0
|
CA
|
c:THR65
|
4.1
|
322.4
|
1.0
|
O2A
|
c:GDP901
|
4.1
|
5.9
|
1.0
|
HG21
|
c:THR65
|
4.2
|
386.8
|
1.0
|
CG2
|
c:THR65
|
4.2
|
322.4
|
1.0
|
HG2
|
c:PRO58
|
4.2
|
403.6
|
1.0
|
C
|
c:PRO58
|
4.2
|
336.4
|
1.0
|
HG23
|
c:THR65
|
4.2
|
386.8
|
1.0
|
H
|
c:SER45
|
4.3
|
484.5
|
1.0
|
CA
|
c:SER45
|
4.3
|
403.8
|
1.0
|
HB3
|
c:ARG59
|
4.4
|
338.6
|
1.0
|
CA
|
c:ARG59
|
4.5
|
282.2
|
1.0
|
HA
|
c:SER45
|
4.5
|
484.5
|
1.0
|
HG11
|
c:VAL64
|
4.6
|
367.7
|
1.0
|
O1A
|
c:GDP901
|
4.6
|
6.0
|
1.0
|
PB
|
c:GDP901
|
4.6
|
4.0
|
1.0
|
CG1
|
c:VAL64
|
4.6
|
306.4
|
1.0
|
N
|
c:SER45
|
4.7
|
403.8
|
1.0
|
CB
|
c:VAL64
|
4.7
|
306.4
|
1.0
|
OD1
|
c:ASP136
|
4.7
|
506.9
|
1.0
|
PA
|
c:GDP901
|
4.8
|
5.5
|
1.0
|
CG
|
c:ASP136
|
4.8
|
506.9
|
1.0
|
HB3
|
c:LEU57
|
4.8
|
503.0
|
1.0
|
N
|
c:ARG59
|
4.9
|
282.2
|
1.0
|
C
|
c:VAL64
|
4.9
|
306.4
|
1.0
|
CB
|
c:ARG59
|
4.9
|
282.2
|
1.0
|
HB2
|
c:ARG59
|
5.0
|
338.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8tym
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Magnesium Binding Sites List in 8tym
Magnesium binding site 2 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
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 (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Mg902
b:30.0
occ:1.00
|
HG
|
f:SER45
|
1.6
|
580.1
|
1.0
|
HG1
|
f:THR65
|
1.9
|
567.8
|
1.0
|
OG1
|
f:THR65
|
2.0
|
473.2
|
1.0
|
O3B
|
f:GDP901
|
2.1
|
7.0
|
1.0
|
HB
|
f:THR65
|
2.2
|
567.8
|
1.0
|
OG
|
f:SER45
|
2.3
|
483.4
|
1.0
|
CB
|
f:THR65
|
2.5
|
473.2
|
1.0
|
HG21
|
f:THR65
|
3.1
|
567.8
|
1.0
|
HB2
|
f:SER45
|
3.3
|
580.1
|
1.0
|
CB
|
f:SER45
|
3.4
|
483.4
|
1.0
|
CG2
|
f:THR65
|
3.4
|
473.2
|
1.0
|
PB
|
f:GDP901
|
3.6
|
6.5
|
1.0
|
H
|
f:THR65
|
3.7
|
567.8
|
1.0
|
CA
|
f:THR65
|
3.8
|
473.2
|
1.0
|
H
|
f:SER45
|
3.9
|
580.1
|
1.0
|
HB3
|
f:SER45
|
3.9
|
580.1
|
1.0
|
O3A
|
f:GDP901
|
3.9
|
6.2
|
1.0
|
N
|
f:THR65
|
3.9
|
473.2
|
1.0
|
HG23
|
f:THR65
|
4.0
|
567.8
|
1.0
|
HG22
|
f:THR65
|
4.1
|
567.8
|
1.0
|
OD1
|
f:ASP136
|
4.2
|
750.4
|
1.0
|
HA
|
f:THR65
|
4.3
|
567.8
|
1.0
|
HA
|
f:PRO138
|
4.4
|
648.2
|
1.0
|
O1B
|
f:GDP901
|
4.4
|
6.7
|
1.0
|
N
|
f:SER45
|
4.4
|
483.4
|
1.0
|
CA
|
f:SER45
|
4.5
|
483.4
|
1.0
|
OD2
|
f:ASP136
|
4.5
|
750.4
|
1.0
|
O2B
|
f:GDP901
|
4.5
|
6.6
|
1.0
|
HB
|
f:VAL64
|
4.5
|
499.8
|
1.0
|
O
|
f:LEU137
|
4.5
|
639.2
|
1.0
|
H
|
f:GLY139
|
4.6
|
608.3
|
1.0
|
HA
|
f:SER45
|
4.7
|
580.1
|
1.0
|
CG
|
f:ASP136
|
4.8
|
750.4
|
1.0
|
O
|
f:THR65
|
4.8
|
473.2
|
1.0
|
C
|
f:THR65
|
4.8
|
473.2
|
1.0
|
C
|
f:VAL64
|
4.9
|
416.5
|
1.0
|
HB3
|
f:ALA44
|
4.9
|
36.0
|
1.0
|
H
|
f:VAL64
|
4.9
|
499.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8tym
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Magnesium Binding Sites List in 8tym
Magnesium binding site 3 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
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 (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg902
b:30.0
occ:1.00
|
HG
|
B:SER45
|
1.6
|
484.5
|
1.0
|
HG1
|
B:THR65
|
1.8
|
386.8
|
1.0
|
OG
|
B:SER45
|
2.0
|
403.8
|
1.0
|
OG1
|
B:THR65
|
2.0
|
322.4
|
1.0
|
O2B
|
B:GDP901
|
2.7
|
3.8
|
1.0
|
HB2
|
B:SER45
|
2.9
|
484.5
|
1.0
|
CB
|
B:SER45
|
2.9
|
403.8
|
1.0
|
HB3
|
B:SER45
|
3.2
|
484.5
|
1.0
|
CB
|
B:THR65
|
3.4
|
322.4
|
1.0
|
O
|
B:PRO58
|
3.4
|
336.4
|
1.0
|
HB
|
B:THR65
|
3.8
|
386.8
|
1.0
|
HA
|
B:ARG59
|
3.9
|
338.6
|
1.0
|
H
|
B:THR65
|
3.9
|
386.8
|
1.0
|
OD2
|
B:ASP136
|
4.0
|
506.9
|
1.0
|
HB
|
B:VAL64
|
4.1
|
367.7
|
1.0
|
HG21
|
B:THR65
|
4.1
|
386.8
|
1.0
|
H
|
B:SER45
|
4.1
|
484.5
|
1.0
|
PB
|
B:GDP901
|
4.2
|
4.0
|
1.0
|
CG2
|
B:THR65
|
4.2
|
322.4
|
1.0
|
N
|
B:THR65
|
4.2
|
322.4
|
1.0
|
CA
|
B:THR65
|
4.2
|
322.4
|
1.0
|
O1A
|
B:GDP901
|
4.2
|
6.0
|
1.0
|
CA
|
B:SER45
|
4.2
|
403.8
|
1.0
|
HA
|
B:THR65
|
4.2
|
386.8
|
1.0
|
HG23
|
B:THR65
|
4.3
|
386.8
|
1.0
|
HG12
|
B:VAL64
|
4.4
|
367.7
|
1.0
|
O2A
|
B:GDP901
|
4.4
|
5.9
|
1.0
|
HA
|
B:SER45
|
4.5
|
484.5
|
1.0
|
HB3
|
B:ARG59
|
4.5
|
338.6
|
1.0
|
N
|
B:SER45
|
4.5
|
403.8
|
1.0
|
HG2
|
B:PRO58
|
4.5
|
403.6
|
1.0
|
C
|
B:PRO58
|
4.6
|
336.4
|
1.0
|
OD1
|
B:ASP136
|
4.7
|
506.9
|
1.0
|
PA
|
B:GDP901
|
4.7
|
5.5
|
1.0
|
CA
|
B:ARG59
|
4.8
|
282.2
|
1.0
|
CG
|
B:ASP136
|
4.8
|
506.9
|
1.0
|
HG11
|
B:VAL64
|
4.8
|
367.7
|
1.0
|
CB
|
B:VAL64
|
4.9
|
306.4
|
1.0
|
O3A
|
B:GDP901
|
4.9
|
4.7
|
1.0
|
HB3
|
B:LEU57
|
4.9
|
503.0
|
1.0
|
O3B
|
B:GDP901
|
4.9
|
4.0
|
1.0
|
CG1
|
B:VAL64
|
4.9
|
306.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8tym
Go back to
Magnesium Binding Sites List in 8tym
Magnesium binding site 4 out
of 4 in the Cryo-Em of the Gdp-Bound Human Dynamin (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State
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 (Full-Length) Polymer Assembled on the Membrane in the Super Constricted State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg902
b:30.0
occ:1.00
|
HG
|
C:SER45
|
1.6
|
580.1
|
1.0
|
HG1
|
C:THR65
|
1.8
|
567.8
|
1.0
|
O3B
|
C:GDP901
|
2.0
|
7.0
|
1.0
|
OG1
|
C:THR65
|
2.0
|
473.2
|
1.0
|
OG
|
C:SER45
|
2.3
|
483.4
|
1.0
|
HB
|
C:THR65
|
2.3
|
567.8
|
1.0
|
CB
|
C:THR65
|
2.6
|
473.2
|
1.0
|
HG21
|
C:THR65
|
3.3
|
567.8
|
1.0
|
HB2
|
C:SER45
|
3.3
|
580.1
|
1.0
|
CB
|
C:SER45
|
3.4
|
483.4
|
1.0
|
PB
|
C:GDP901
|
3.4
|
6.5
|
1.0
|
CG2
|
C:THR65
|
3.5
|
473.2
|
1.0
|
H
|
C:THR65
|
3.7
|
567.8
|
1.0
|
H
|
C:SER45
|
3.8
|
580.1
|
1.0
|
CA
|
C:THR65
|
3.9
|
473.2
|
1.0
|
HB3
|
C:SER45
|
4.0
|
580.1
|
1.0
|
N
|
C:THR65
|
4.0
|
473.2
|
1.0
|
O3A
|
C:GDP901
|
4.0
|
6.2
|
1.0
|
HG23
|
C:THR65
|
4.1
|
567.8
|
1.0
|
O2B
|
C:GDP901
|
4.1
|
6.6
|
1.0
|
HG22
|
C:THR65
|
4.2
|
567.8
|
1.0
|
HA
|
C:THR65
|
4.4
|
567.8
|
1.0
|
N
|
C:SER45
|
4.4
|
483.4
|
1.0
|
O1B
|
C:GDP901
|
4.4
|
6.7
|
1.0
|
HB
|
C:VAL64
|
4.4
|
499.8
|
1.0
|
OD1
|
C:ASP136
|
4.4
|
750.4
|
1.0
|
CA
|
C:SER45
|
4.5
|
483.4
|
1.0
|
HA
|
C:PRO138
|
4.6
|
648.2
|
1.0
|
OD2
|
C:ASP136
|
4.6
|
750.4
|
1.0
|
H
|
C:GLY139
|
4.6
|
608.3
|
1.0
|
HA
|
C:SER45
|
4.8
|
580.1
|
1.0
|
O
|
C:LEU137
|
4.8
|
639.2
|
1.0
|
C
|
C:VAL64
|
4.8
|
416.5
|
1.0
|
HB3
|
C:ALA44
|
4.9
|
36.0
|
1.0
|
H
|
C:VAL64
|
4.9
|
499.8
|
1.0
|
C
|
C:THR65
|
5.0
|
473.2
|
1.0
|
O1A
|
C:GDP901
|
5.0
|
7.1
|
1.0
|
CG
|
C:ASP136
|
5.0
|
750.4
|
1.0
|
O
|
C:THR65
|
5.0
|
473.2
|
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 21:07:50 2024
|