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Magnesium in PDB 8bly: Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp

Enzymatic activity of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp

All present enzymatic activity of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp:
5.6.1.7;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp (pdb code 8bly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp, PDB code: 8bly:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 8bly

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Magnesium binding site 1 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:30.8
occ:0.00
 O3G A:ATP602 2.1 31.1 1.0
OD1 A:ASP87 2.3 38.4 1.0
O2A A:ATP602 2.4 36.1 1.0
O1B A:ATP602 2.5 37.2 1.0
CG A:ASP87 2.9 36.3 1.0
OD2 A:ASP87 3.0 35.3 1.0
O3B A:ATP602 3.1 14.0 1.0
PB A:ATP602 3.1 25.9 1.0
PG A:ATP602 3.2 30.8 1.0
O3A A:ATP602 3.6 25.3 1.0
PA A:ATP602 3.6 36.2 1.0
O1G A:ATP602 4.2 28.4 1.0
O A:SER151 4.2 34.8 1.0
O2G A:ATP602 4.2 35.4 1.0
OD2 A:ASP398 4.3 51.9 1.0
OG A:SER151 4.3 46.5 1.0
N A:GLY88 4.4 27.8 1.0
CB A:ASP87 4.4 26.4 1.0
C5' A:ATP602 4.4 26.0 1.0
O5' A:ATP602 4.5 23.6 1.0
CG A:ASP398 4.6 46.5 1.0
O2B A:ATP602 4.6 29.7 1.0
CB A:ASP398 4.6 40.8 1.0
O1A A:ATP602 4.7 30.6 1.0
CA A:ASP87 4.8 22.1 1.0
CA A:SER151 4.9 34.4 1.0

Magnesium binding site 2 out of 14 in 8bly

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Magnesium binding site 2 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:28.8
occ:0.00
 O2A B:ATP602 2.0 32.8 1.0
O3G B:ATP602 2.0 33.5 1.0
O3B B:ATP602 2.0 22.2 1.0
O1B B:ATP602 2.2 29.3 1.0
PB B:ATP602 2.3 26.6 1.0
PG B:ATP602 2.5 33.8 1.0
O3A B:ATP602 2.6 23.3 1.0
OD1 B:ASP87 2.7 31.6 1.0
PA B:ATP602 2.8 34.5 1.0
O1G B:ATP602 3.4 28.2 1.0
CG B:ASP87 3.5 37.1 1.0
O2G B:ATP602 3.7 32.4 1.0
N B:GLY88 3.8 34.1 1.0
O2B B:ATP602 3.8 28.9 1.0
OD2 B:ASP87 3.8 39.3 1.0
O1A B:ATP602 3.8 28.5 1.0
O5' B:ATP602 4.0 25.5 1.0
C5' B:ATP602 4.1 28.1 1.0
CA B:GLY88 4.4 29.5 1.0
CB B:ASP87 4.7 29.0 1.0
CA B:ASP87 4.8 25.4 1.0
C B:ASP87 4.8 36.2 1.0
OD2 B:ASP398 4.9 52.7 1.0

Magnesium binding site 3 out of 14 in 8bly

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Magnesium binding site 3 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:26.2
occ:0.00
 O2A C:ATP602 2.0 33.9 1.0
O3G C:ATP602 2.0 38.9 1.0
O3B C:ATP602 2.0 19.6 1.0
O1B C:ATP602 2.2 31.3 1.0
PB C:ATP602 2.3 29.6 1.0
PG C:ATP602 2.5 36.0 1.0
O3A C:ATP602 2.6 30.0 1.0
OD1 C:ASP87 2.8 37.5 1.0
PA C:ATP602 2.8 33.0 1.0
O1G C:ATP602 3.3 28.5 1.0
CG C:ASP87 3.6 37.9 1.0
O2G C:ATP602 3.7 35.1 1.0
O2B C:ATP602 3.8 32.5 1.0
N C:GLY88 3.8 31.4 1.0
O1A C:ATP602 3.9 35.7 1.0
O5' C:ATP602 3.9 26.3 1.0
OD2 C:ASP87 3.9 42.0 1.0
C5' C:ATP602 4.0 27.6 1.0
CA C:GLY88 4.3 27.9 1.0
CB C:ASP87 4.8 27.1 1.0
C C:ASP87 4.9 34.7 1.0
CA C:ASP87 4.9 24.0 1.0

Magnesium binding site 4 out of 14 in 8bly

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Magnesium binding site 4 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:22.4
occ:0.00
 OD1 D:ASP87 2.1 37.0 1.0
O2A D:ATP602 2.4 36.2 1.0
O1B D:ATP602 2.6 18.1 1.0
OD2 D:ASP87 2.7 36.2 1.0
CG D:ASP87 2.8 36.0 1.0
PA D:ATP602 3.8 46.6 1.0
PB D:ATP602 3.8 27.1 1.0
O3G D:ATP602 3.9 33.3 1.0
O D:SER151 4.0 41.4 1.0
O3A D:ATP602 4.1 32.7 1.0
CB D:ASP87 4.2 28.3 1.0
CA D:SER151 4.2 37.3 1.0
CB D:SER151 4.3 34.6 1.0
N D:GLY88 4.4 35.1 1.0
CB D:ASP398 4.4 43.8 1.0
OD2 D:ASP398 4.4 51.1 1.0
CG D:ASP398 4.5 49.5 1.0
C5' D:ATP602 4.5 25.6 1.0
O3B D:ATP602 4.6 31.3 1.0
C D:SER151 4.6 37.9 1.0
O5' D:ATP602 4.7 23.0 1.0
O1A D:ATP602 4.7 33.5 1.0
OG D:SER151 4.7 40.4 1.0
PG D:ATP602 4.8 50.2 1.0
CA D:ASP87 4.8 19.4 1.0
O2G D:ATP602 4.8 33.1 1.0

Magnesium binding site 5 out of 14 in 8bly

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Magnesium binding site 5 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:36.2
occ:0.00
 OD1 E:ASP87 2.1 41.8 1.0
O2A E:ATP602 2.4 45.9 1.0
O1B E:ATP602 2.5 29.1 1.0
OD2 E:ASP87 2.6 35.2 1.0
CG E:ASP87 2.6 38.4 1.0
OG E:SER151 3.7 50.1 1.0
PB E:ATP602 3.8 34.5 1.0
PA E:ATP602 3.8 45.8 1.0
O E:SER151 3.8 40.2 1.0
O3G E:ATP602 3.9 32.9 1.0
O3A E:ATP602 4.1 34.2 1.0
CB E:ASP87 4.1 27.3 1.0
OD2 E:ASP398 4.3 52.5 1.0
CB E:ASP398 4.3 40.5 1.0
CG E:ASP398 4.3 47.4 1.0
N E:GLY88 4.4 35.8 1.0
CA E:SER151 4.4 38.5 1.0
O3B E:ATP602 4.5 38.3 1.0
C E:SER151 4.6 38.2 1.0
CB E:SER151 4.6 39.6 1.0
C5' E:ATP602 4.7 32.5 1.0
CA E:ASP87 4.7 22.8 1.0
O1A E:ATP602 4.7 40.6 1.0
PG E:ATP602 4.7 57.8 1.0
O2G E:ATP602 4.8 38.4 1.0
O5' E:ATP602 4.8 23.8 1.0
OD1 E:ASP398 4.9 49.9 1.0
O2B E:ATP602 5.0 30.0 1.0

Magnesium binding site 6 out of 14 in 8bly

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Magnesium binding site 6 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:22.5
occ:0.00
 OD1 F:ASP87 2.2 30.3 1.0
O1B F:ATP602 2.3 34.9 1.0
O2A F:ATP602 2.8 47.5 1.0
CG F:ASP87 3.0 27.1 1.0
OD2 F:ASP87 3.1 27.4 1.0
PB F:ATP602 3.6 36.0 1.0
O3G F:ATP602 3.7 48.1 1.0
OG F:SER151 3.8 41.3 1.0
O F:SER151 3.8 32.5 1.0
PA F:ATP602 4.0 48.3 1.0
O3A F:ATP602 4.1 48.3 1.0
OD2 F:ASP398 4.2 49.9 1.0
CB F:ASP398 4.3 40.5 1.0
O3B F:ATP602 4.3 39.6 1.0
CG F:ASP398 4.4 47.1 1.0
CB F:ASP87 4.4 16.8 1.0
CA F:SER151 4.4 34.2 1.0
PG F:ATP602 4.5 51.9 1.0
O2G F:ATP602 4.5 42.2 1.0
C5' F:ATP602 4.6 41.5 1.0
C F:SER151 4.6 31.8 1.0
N F:GLY88 4.6 24.2 1.0
CB F:SER151 4.7 33.1 1.0
O2B F:ATP602 4.8 34.0 1.0
O5' F:ATP602 4.8 38.0 1.0
CA F:ASP87 4.9 10.8 1.0

Magnesium binding site 7 out of 14 in 8bly

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Magnesium binding site 7 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:34.1
occ:0.00
 OD1 G:ASP87 2.1 41.5 1.0
O1B G:ATP602 2.1 23.5 1.0
O2A G:ATP602 2.3 43.8 1.0
CG G:ASP87 2.9 37.2 1.0
OD2 G:ASP87 3.0 33.3 1.0
PB G:ATP602 3.4 29.9 1.0
O3G G:ATP602 3.6 35.5 1.0
PA G:ATP602 3.6 51.4 1.0
O3A G:ATP602 3.7 37.4 1.0
O3B G:ATP602 4.0 36.4 1.0
O G:SER151 4.2 37.0 1.0
OG G:SER151 4.2 46.9 1.0
OD2 G:ASP398 4.2 54.3 1.0
CB G:ASP87 4.3 27.2 1.0
N G:GLY88 4.3 33.5 1.0
PG G:ATP602 4.3 55.4 1.0
O2G G:ATP602 4.4 38.6 1.0
CG G:ASP398 4.5 47.4 1.0
CB G:ASP398 4.5 41.4 1.0
O1A G:ATP602 4.5 40.9 1.0
C5' G:ATP602 4.5 32.4 1.0
O5' G:ATP602 4.6 27.2 1.0
O2B G:ATP602 4.6 29.0 1.0
CA G:ASP87 4.7 21.9 1.0
CA G:SER151 4.8 34.2 1.0
C G:SER151 4.9 33.7 1.0

Magnesium binding site 8 out of 14 in 8bly

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Magnesium binding site 8 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:26.0
occ:0.00
 OD1 H:ASP87 2.4 39.5 1.0
O1B H:ATP602 2.4 38.5 1.0
O2A H:ATP602 2.9 51.2 1.0
OD2 H:ASP87 2.9 31.0 1.0
CG H:ASP87 3.0 34.9 1.0
OG H:SER151 3.5 49.1 1.0
O H:SER151 3.5 46.1 1.0
PB H:ATP602 3.8 42.5 1.0
O3G H:ATP602 4.0 50.8 1.0
CA H:SER151 4.0 41.3 1.0
PA H:ATP602 4.2 49.0 1.0
CB H:ASP398 4.2 45.0 1.0
C H:SER151 4.2 43.4 1.0
O3A H:ATP602 4.3 45.0 1.0
OD2 H:ASP398 4.3 54.7 1.0
CB H:SER151 4.3 39.8 1.0
CG H:ASP398 4.4 52.8 1.0
CB H:ASP87 4.5 24.8 1.0
O3B H:ATP602 4.5 45.9 1.0
C5' H:ATP602 4.6 41.1 1.0
N H:GLY88 4.8 38.8 1.0
PG H:ATP602 4.9 61.1 1.0
O5' H:ATP602 4.9 41.9 1.0
O2B H:ATP602 4.9 33.6 1.0

Magnesium binding site 9 out of 14 in 8bly

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Magnesium binding site 9 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:23.2
occ:0.00
 OD1 I:ASP87 2.4 36.8 1.0
O1B I:ATP602 2.4 27.0 1.0
O2A I:ATP602 2.8 38.7 1.0
OD2 I:ASP87 2.9 29.8 1.0
CG I:ASP87 3.0 32.9 1.0
O I:SER151 3.5 40.7 1.0
OG I:SER151 3.5 46.6 1.0
PB I:ATP602 3.8 32.0 1.0
O3G I:ATP602 4.0 39.8 1.0
CA I:SER151 4.0 39.5 1.0
PA I:ATP602 4.1 41.5 1.0
CB I:ASP398 4.2 39.7 1.0
O3A I:ATP602 4.2 35.6 1.0
C I:SER151 4.2 39.7 1.0
OD2 I:ASP398 4.3 49.4 1.0
CB I:SER151 4.3 37.6 1.0
CG I:ASP398 4.4 47.2 1.0
CB I:ASP87 4.5 25.7 1.0
O3B I:ATP602 4.5 36.2 1.0
C5' I:ATP602 4.6 28.7 1.0
N I:GLY88 4.8 34.5 1.0
O5' I:ATP602 4.9 30.7 1.0
PG I:ATP602 4.9 53.2 1.0
O2B I:ATP602 5.0 23.6 1.0

Magnesium binding site 10 out of 14 in 8bly

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Magnesium binding site 10 out of 14 in the Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Groel-Atp Complex Plunge-Frozen 13 Ms After Mixing with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:31.8
occ:0.00
 OD1 J:ASP87 2.2 35.1 1.0
O1B J:ATP602 2.3 20.6 1.0
O2A J:ATP602 2.8 37.8 1.0
CG J:ASP87 2.9 32.2 1.0
OD2 J:ASP87 3.0 33.5 1.0
PB J:ATP602 3.6 28.6 1.0
O3G J:ATP602 3.7 36.0 1.0
OG J:SER151 3.8 46.1 1.0
O J:SER151 3.8 37.4 1.0
PA J:ATP602 4.1 40.3 1.0
O3A J:ATP602 4.1 35.7 1.0
OD2 J:ASP398 4.2 50.5 1.0
O3B J:ATP602 4.3 30.8 1.0
CB J:ASP398 4.3 38.3 1.0
CG J:ASP398 4.4 46.5 1.0
CB J:ASP87 4.4 23.1 1.0
CA J:SER151 4.4 36.1 1.0
PG J:ATP602 4.5 52.9 1.0
O2G J:ATP602 4.5 33.4 1.0
N J:GLY88 4.6 27.5 1.0
C5' J:ATP602 4.6 25.6 1.0
C J:SER151 4.6 36.0 1.0
CB J:SER151 4.7 35.7 1.0
O2B J:ATP602 4.8 24.4 1.0
O5' J:ATP602 4.9 22.0 1.0
CA J:ASP87 4.9 19.4 1.0

Reference:

S.Torino, M.Dhurandhar, A.Stroobants, R.Claessens, R.Efremov. Time-Resolved Cryo-Em Using A Combination of Droplet Microfluidics with on-Demand Jetting Nat.Methods 2023.
ISSN: ESSN 1548-7105
DOI: 10.1038/S41592-023-01967-Z
Page generated: Thu Oct 3 19:43:09 2024

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