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Magnesium in PDB 9ok5: 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16

Enzymatic activity of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16

All present enzymatic activity of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16:
3.6.4.6;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 (pdb code 9ok5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16, PDB code: 9ok5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 9ok5

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Magnesium binding site 1 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:15.9
occ:1.00
 HG1 A:THR550 2.4 32.1 1.0
O2B A:ATP802 2.4 49.6 1.0
O2G A:ATP802 2.5 57.3 1.0
OG1 A:THR550 2.6 33.8 1.0
PB A:ATP802 3.7 48.5 1.0
PG A:ATP802 3.8 62.7 1.0
O3B A:ATP802 4.0 53.3 1.0
HG21 A:THR645 4.0 30.7 1.0
CB A:THR550 4.0 24.3 1.0
OD2 A:ASP604 4.1 45.7 1.0
H A:THR550 4.1 32.4 1.0
HG22 A:THR645 4.2 32.6 1.0
HB A:THR550 4.2 30.1 1.0
HE2 A:LYS549 4.3 34.1 1.0
OD1 A:ASP603 4.4 47.4 1.0
O1B A:ATP802 4.5 43.5 1.0
CG2 A:THR645 4.5 33.5 1.0
HG21 A:THR550 4.5 32.2 1.0
HB2 A:LYS549 4.7 33.3 1.0
N A:THR550 4.7 29.2 1.0
O3G A:ATP802 4.7 45.5 1.0
O1G A:ATP802 4.7 49.4 1.0
CG A:ASP604 4.8 39.1 1.0
CG2 A:THR550 4.8 30.8 1.0
O A:ASP603 4.8 44.2 1.0
HG23 A:THR645 4.8 32.0 1.0
O3A A:ATP802 4.9 43.9 1.0
CA A:THR550 4.9 25.0 1.0
HG23 A:THR550 5.0 31.4 1.0

Magnesium binding site 2 out of 9 in 9ok5

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Magnesium binding site 2 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:36.4
occ:1.00
 OG1 B:THR550 2.3 16.2 1.0
O2B B:ATP801 2.5 30.7 1.0
O1G B:ATP801 2.9 29.7 1.0
OD1 B:ASP603 3.5 23.6 1.0
CB B:THR550 3.6 10.2 1.0
HB B:THR550 3.8 14.8 1.0
PB B:ATP801 3.9 24.9 1.0
H B:THR550 4.0 17.0 1.0
HG21 B:THR550 4.1 16.2 1.0
PG B:ATP801 4.1 39.8 1.0
HG21 B:THR645 4.2 18.1 1.0
O3B B:ATP801 4.2 28.4 1.0
HG22 B:THR645 4.4 17.9 1.0
CG2 B:THR550 4.4 13.9 1.0
CG B:ASP603 4.4 20.7 1.0
OD2 B:ASP603 4.5 28.2 1.0
N B:THR550 4.5 14.2 1.0
HB2 B:LYS549 4.5 19.8 1.0
CA B:THR550 4.6 9.8 1.0
HB2 B:ASP604 4.6 18.8 1.0
OD2 B:ASP604 4.6 30.5 1.0
HE2 B:LYS549 4.6 19.1 1.0
HG23 B:THR550 4.7 15.8 1.0
O1B B:ATP801 4.7 20.1 1.0
O A:HOH935 4.7 29.2 1.0
CG2 B:THR645 4.8 22.0 1.0
HA B:THR550 4.8 15.1 1.0
CG B:ASP604 4.8 26.9 1.0
O3A B:ATP801 4.9 21.5 1.0

Magnesium binding site 3 out of 9 in 9ok5

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Magnesium binding site 3 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:32.6
occ:1.00
 HG1 C:THR267 1.9 35.6 1.0
OG1 C:THR267 2.4 36.7 1.0
O1B C:ADP802 2.8 55.1 1.0
O1 B:PO4804 2.9 117.8 1.0
HB C:THR267 3.6 35.2 1.0
CB C:THR267 3.6 32.0 1.0
O2A C:ADP802 3.7 54.9 1.0
O2B C:ADP802 3.7 55.0 1.0
PB C:ADP802 3.8 51.7 1.0
HG21 C:THR267 4.0 35.8 1.0
H C:THR267 4.2 36.1 1.0
O B:ASP359 4.3 52.5 1.0
CG2 C:THR267 4.4 35.7 1.0
OD1 C:ASP328 4.4 64.7 1.0
P B:PO4804 4.4 119.0 1.0
HA2 B:GLY360 4.6 52.2 1.0
CA C:THR267 4.7 31.9 1.0
PA C:ADP802 4.7 54.5 1.0
N C:THR267 4.7 36.4 1.0
O3A C:ADP802 4.8 52.5 1.0
HH22 B:ARG388 4.8 43.1 1.0
HG23 C:THR267 4.9 35.8 1.0
O3B C:ADP802 4.9 50.2 1.0
HA C:THR267 5.0 35.3 1.0

Magnesium binding site 4 out of 9 in 9ok5

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Magnesium binding site 4 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:26.2
occ:1.00
 OG1 C:THR550 2.2 48.1 1.0
O2B C:ATP801 2.9 45.2 1.0
O1G C:ATP801 2.9 48.8 1.0
CB C:THR550 3.5 43.7 1.0
HG1 C:THR645 3.6 45.1 1.0
OD1 C:ASP603 3.6 43.7 1.0
HG21 C:THR550 3.8 44.5 1.0
HB C:THR550 3.8 44.9 1.0
PG C:ATP801 4.2 54.0 1.0
CG2 C:THR550 4.2 41.7 1.0
HB2 C:ASP604 4.2 46.1 1.0
PB C:ATP801 4.2 40.6 1.0
OG1 C:THR645 4.2 46.9 1.0
HZ2 C:LYS549 4.2 59.2 1.0
HG2 C:LYS549 4.2 59.4 1.0
CG C:ASP603 4.4 42.0 1.0
HG3 C:LYS549 4.4 59.4 1.0
H C:ASP604 4.4 46.0 1.0
O3B C:ATP801 4.5 47.9 1.0
OD2 C:ASP603 4.5 42.3 1.0
HG23 C:THR550 4.5 44.6 1.0
H C:THR550 4.5 46.2 1.0
CA C:THR550 4.6 44.3 1.0
N C:THR550 4.6 46.4 1.0
HA C:THR550 4.6 45.0 1.0
CG C:ASP604 4.8 50.6 1.0
HA C:ASP604 4.8 45.9 1.0
CG C:LYS549 4.8 57.3 1.0
O3G C:ATP801 4.8 48.2 1.0
CB C:ASP604 4.8 46.3 1.0
N C:ASP604 4.9 44.5 1.0
O1B C:ATP801 4.9 48.1 1.0
OD1 C:ASP604 4.9 47.7 1.0
O C:HOH938 5.0 58.0 1.0

Magnesium binding site 5 out of 9 in 9ok5

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Magnesium binding site 5 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:47.6
occ:1.00
 OG1 D:THR550 2.3 42.9 1.0
O2B D:ATP801 2.4 55.5 1.0
O1G D:ATP801 2.7 57.5 1.0
CB D:THR550 3.7 36.4 1.0
PB D:ATP801 3.7 51.7 1.0
PG D:ATP801 3.9 62.3 1.0
H D:THR550 3.9 38.4 1.0
HB D:THR550 4.0 36.4 1.0
O3B D:ATP801 4.0 57.7 1.0
HG21 D:THR550 4.1 36.9 1.0
HG1 D:THR645 4.3 66.7 1.0
HB2 D:ASP604 4.3 60.5 1.0
HB2 D:ASP603 4.3 41.7 1.0
CG2 D:THR550 4.3 37.4 1.0
HG23 D:THR550 4.4 36.4 1.0
HB2 D:LYS549 4.5 67.8 1.0
N D:THR550 4.5 36.8 1.0
HE2 D:LYS549 4.5 67.6 1.0
O1B D:ATP801 4.5 60.3 1.0
CA D:THR550 4.6 34.2 1.0
OD2 D:ASP603 4.7 45.2 1.0
OD1 D:ASP604 4.7 60.7 1.0
O D:HOH965 4.7 56.8 1.0
O3A D:ATP801 4.8 53.5 1.0
HA D:THR550 4.8 36.5 1.0
CG D:ASP604 4.9 62.3 1.0
O1A D:ATP801 4.9 56.4 1.0
O2G D:ATP801 4.9 60.1 1.0
HE3 D:LYS549 4.9 67.7 1.0
OG1 D:THR645 4.9 65.3 1.0
H D:ASP604 4.9 60.6 1.0
O3G D:ATP801 4.9 59.1 1.0

Magnesium binding site 6 out of 9 in 9ok5

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Magnesium binding site 6 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:29.4
occ:1.00
 OG1 D:THR267 2.1 42.2 1.0
O3B D:ADP802 2.2 50.1 1.0
O1 D:PO4805 3.3 139.1 1.0
CB D:THR267 3.4 41.8 1.0
HB D:THR267 3.7 41.5 1.0
PB D:ADP802 3.7 55.3 1.0
HG21 D:THR267 3.8 41.9 1.0
H D:THR267 3.9 41.2 1.0
O2A D:ADP802 4.1 53.6 1.0
CG2 D:THR267 4.1 43.2 1.0
HH21 C:ARG388 4.4 55.6 1.0
HA2 C:GLY360 4.4 68.8 1.0
O C:ASP359 4.4 77.4 1.0
HG23 D:THR267 4.4 41.3 1.0
HH22 C:ARG388 4.4 55.4 1.0
O3A D:ADP802 4.4 51.2 1.0
P D:PO4805 4.4 139.2 1.0
O2B D:ADP802 4.5 56.2 1.0
N D:THR267 4.5 39.0 1.0
CA D:THR267 4.5 38.0 1.0
O1B D:ADP802 4.6 49.6 1.0
O4 D:PO4805 4.6 139.6 1.0
NH2 C:ARG388 4.7 57.4 1.0
HA D:THR267 4.7 40.5 1.0
O3 D:PO4805 4.7 138.2 1.0
HB2 D:LYS266 4.8 38.7 1.0
PA D:ADP802 4.9 48.0 1.0
HE3 D:LYS266 4.9 38.6 1.0
OD2 D:ASP328 4.9 60.2 1.0

Magnesium binding site 7 out of 9 in 9ok5

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Magnesium binding site 7 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg803

b:12.8
occ:1.00
 HG1 E:THR267 2.3 30.2 1.0
OG1 E:THR267 2.7 34.5 1.0
O2B E:ATP801 2.8 126.7 1.0
O1G E:ATP801 2.8 125.2 1.0
O3G E:ATP801 3.3 125.3 1.0
PG E:ATP801 3.4 124.6 1.0
O3B E:ATP801 3.4 125.8 1.0
PB E:ATP801 3.7 126.5 1.0
HB E:THR267 3.8 30.3 1.0
CB E:THR267 3.9 31.2 1.0
HH22 D:ARG388 3.9 58.4 1.0
O1A E:ATP801 4.0 125.8 1.0
H E:THR267 4.0 29.2 1.0
OD1 E:ASP328 4.3 32.0 1.0
HB2 E:LYS266 4.4 25.0 1.0
NH2 D:ARG388 4.6 59.0 1.0
HG21 E:THR267 4.6 29.9 1.0
N E:THR267 4.6 21.2 1.0
HH21 D:ARG388 4.6 58.5 1.0
O1B E:ATP801 4.7 126.3 1.0
OD2 E:ASP328 4.7 31.7 1.0
O3A E:ATP801 4.7 125.3 1.0
CA E:THR267 4.8 23.6 1.0
HA2 D:GLY360 4.8 88.4 1.0
O2G E:ATP801 4.8 125.0 1.0
CG2 E:THR267 4.9 28.4 1.0
PA E:ATP801 4.9 124.3 1.0
CG E:ASP328 5.0 29.8 1.0
HA E:THR267 5.0 28.2 1.0

Magnesium binding site 8 out of 9 in 9ok5

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Magnesium binding site 8 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg804

b:2.7
occ:1.00
 HG1 E:THR550 2.3 10.1 1.0
OG1 E:THR550 2.5 9.1 1.0
O3G E:ATP802 2.5 22.5 1.0
O2B E:ATP802 2.7 15.4 1.0
CB E:THR550 3.8 7.5 1.0
PG E:ATP802 3.9 16.4 1.0
PB E:ATP802 3.9 6.3 1.0
HB E:THR550 4.0 9.5 1.0
O3B E:ATP802 4.0 16.6 1.0
H E:THR550 4.1 12.8 1.0
HG21 E:THR550 4.2 9.3 1.0
HB2 E:ASP604 4.3 23.4 1.0
HB2 E:ASP603 4.4 8.6 1.0
CG2 E:THR550 4.6 7.2 1.0
O2G E:ATP802 4.7 9.0 1.0
N E:THR550 4.7 7.7 1.0
O1A E:ATP802 4.7 12.0 1.0
CA E:THR550 4.8 7.5 1.0
HG23 E:THR550 4.8 8.8 1.0
HG21 E:THR645 4.8 12.8 1.0
CG E:ASP604 4.8 28.4 1.0
O1B E:ATP802 4.9 17.9 1.0
HB2 E:LYS549 4.9 30.7 1.0
OD2 E:ASP603 4.9 13.4 1.0
OD1 E:ASP604 4.9 20.8 1.0
O1G E:ATP802 4.9 21.6 1.0
O3A E:ATP802 4.9 7.3 1.0
HE2 E:LYS549 5.0 29.2 1.0

Magnesium binding site 9 out of 9 in 9ok5

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Magnesium binding site 9 out of 9 in the 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 22BIN20S Complex (Nsf-Alphasnap-2:2 Syntaxin-1A:Snap-25), Hydrolyzing, Class 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg803

b:21.8
occ:1.00
 O2B F:ATP801 2.0 34.7 1.0
HG1 F:THR550 2.2 38.5 1.0
O2G F:ATP801 2.4 30.3 1.0
OG1 F:THR550 2.6 37.5 1.0
PB F:ATP801 3.3 23.3 1.0
PG F:ATP801 3.6 35.8 1.0
O3B F:ATP801 3.7 26.6 1.0
CB F:THR550 3.9 34.3 1.0
H F:THR550 3.9 37.7 1.0
HB F:THR550 4.0 37.7 1.0
O1B F:ATP801 4.1 31.9 1.0
OD1 F:ASP604 4.2 23.2 1.0
HB2 F:ASP603 4.4 37.5 1.0
O3A F:ATP801 4.4 26.6 1.0
CG F:ASP604 4.5 24.6 1.0
HG1 F:THR645 4.5 38.1 1.0
O1G F:ATP801 4.5 35.1 1.0
OD2 F:ASP604 4.5 25.3 1.0
HG21 F:THR550 4.6 38.1 1.0
N F:THR550 4.6 34.2 1.0
HB2 F:LYS549 4.6 37.8 1.0
HE2 F:LYS549 4.6 36.7 1.0
O3G F:ATP801 4.7 34.3 1.0
OD2 F:ASP603 4.8 40.5 1.0
CA F:THR550 4.8 33.5 1.0
CG2 F:THR550 4.8 35.7 1.0
O F:HOH920 4.9 21.4 1.0
O1A F:ATP801 5.0 28.1 1.0

Reference:

K.I.White, Y.A.Khan, K.Qiu, A.Balaji, S.Couoh-Cardel, L.Esquivies, R.A.Pfuetzner, J.Diao, A.T.Brunger. Pre-Fusion Aaa+ Remodeling of Target-Snare Protein Complexes Enables Synaptic Transmission. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39416070
DOI: 10.1101/2024.10.11.617886
Page generated: Sat Aug 23 06:07:52 2025

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