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

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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 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 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

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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

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