Atomistry » Magnesium » PDB 8bi7-8bw1 » 8bm0
Atomistry »
  Magnesium »
    PDB 8bi7-8bw1 »
      8bm0 »

Magnesium in PDB 8bm0: Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation

Enzymatic activity of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation

All present enzymatic activity of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation:
5.6.1.7;

Other elements in 8bm0:

The structure of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation also contains other interesting chemical elements:

Potassium (K) 14 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation (pdb code 8bm0). 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 Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation, PDB code: 8bm0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 1 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:45.3
occ:1.00
 O1G I:ATP603 2.0 56.7 1.0
O1B I:ATP603 2.1 57.3 1.0
O3B I:ATP603 2.1 38.0 1.0
PB I:ATP603 2.4 39.5 1.0
PG I:ATP603 2.4 62.7 1.0
OD1 I:ASP87 2.5 46.6 1.0
O1A I:ATP603 2.6 57.5 1.0
O3A I:ATP603 2.9 47.4 1.0
O2G I:ATP603 3.1 61.0 1.0
PA I:ATP603 3.2 66.7 1.0
CG I:ASP87 3.4 47.6 1.0
OD2 I:ASP87 3.8 47.4 1.0
O3G I:ATP603 3.8 54.8 1.0
O2B I:ATP603 3.8 41.9 1.0
N I:GLY88 4.0 41.6 1.0
O2A I:ATP603 4.1 59.6 1.0
OD2 I:ASP398 4.3 61.2 1.0
K I:K602 4.3 61.4 1.0
O5' I:ATP603 4.5 45.4 1.0
CB I:ASP87 4.7 41.4 1.0
CA I:GLY88 4.7 38.9 1.0
CA I:ASP87 4.8 35.7 1.0
O I:SER151 4.8 51.7 1.0
C I:ASP87 4.9 45.5 1.0

Magnesium binding site 2 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 2 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:56.6
occ:0.00
 O3B G:ATP602 2.0 47.0 1.0
O3G G:ATP602 2.0 55.1 1.0
OD1 G:ASP87 2.1 59.9 1.0
O2A G:ATP602 2.2 57.1 1.0
PB G:ATP602 2.5 59.0 1.0
O1B G:ATP602 2.5 58.4 1.0
PG G:ATP602 2.5 58.0 1.0
O3A G:ATP602 2.8 55.6 1.0
PA G:ATP602 3.0 70.0 1.0
CG G:ASP87 3.2 63.9 1.0
OD2 G:ASP87 3.6 66.6 1.0
O1G G:ATP602 3.6 47.7 1.0
O2G G:ATP602 3.6 61.3 1.0
N G:GLY88 3.8 53.8 1.0
O2B G:ATP602 3.9 56.2 1.0
O1A G:ATP602 4.1 59.1 1.0
O5' G:ATP602 4.1 51.9 1.0
C5' G:ATP602 4.3 51.1 1.0
CB G:ASP87 4.4 57.9 1.0
CA G:GLY88 4.5 46.1 1.0
CA G:ASP87 4.6 57.9 1.0
C G:ASP87 4.7 63.7 1.0
OD2 G:ASP398 4.8 72.3 1.0
OG G:SER151 4.9 73.2 1.0
O G:SER151 5.0 68.2 1.0

Magnesium binding site 3 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 3 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:23.9
occ:1.00
 O1G A:ATP603 2.0 46.6 1.0
OD1 A:ASP87 2.1 41.6 1.0
O1A A:ATP603 2.5 50.3 1.0
CG A:ASP87 2.8 42.9 1.0
OD2 A:ASP87 2.9 41.1 1.0
O3B A:ATP603 2.9 34.9 1.0
O1B A:ATP603 3.0 48.0 1.0
PG A:ATP603 3.0 46.9 1.0
PB A:ATP603 3.2 37.5 1.0
O3A A:ATP603 3.2 46.2 1.0
PA A:ATP603 3.3 64.8 1.0
O2G A:ATP603 3.9 55.4 1.0
OG A:SER151 4.0 54.5 1.0
O A:SER151 4.0 49.0 1.0
O3G A:ATP603 4.1 39.9 1.0
O5' A:ATP603 4.1 36.7 1.0
N A:GLY88 4.2 32.6 1.0
CB A:ASP87 4.2 38.8 1.0
OD2 A:ASP398 4.3 62.0 1.0
CB A:ASP398 4.6 55.8 1.0
O2A A:ATP603 4.6 53.6 1.0
CA A:ASP87 4.6 33.3 1.0
O2B A:ATP603 4.7 40.2 1.0
CA A:SER151 4.8 48.9 1.0
C A:SER151 4.8 48.8 1.0
CG A:ASP398 4.9 62.7 1.0
C A:ASP87 5.0 37.5 1.0
CB A:SER151 5.0 47.0 1.0

Magnesium binding site 4 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 4 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:37.2
occ:0.00
 O3B C:ATP602 2.0 37.4 1.0
O3G C:ATP602 2.0 42.7 1.0
OD1 C:ASP87 2.1 51.2 1.0
O2A C:ATP602 2.2 45.2 1.0
PB C:ATP602 2.5 43.7 1.0
O1B C:ATP602 2.5 43.7 1.0
PG C:ATP602 2.5 43.2 1.0
O3A C:ATP602 2.7 42.0 1.0
PA C:ATP602 3.0 54.9 1.0
CG C:ASP87 3.2 54.5 1.0
OD2 C:ASP87 3.6 58.5 1.0
O1G C:ATP602 3.6 36.5 1.0
O2G C:ATP602 3.6 47.4 1.0
N C:GLY88 3.8 44.2 1.0
O2B C:ATP602 3.9 42.1 1.0
O1A C:ATP602 4.1 45.3 1.0
O5' C:ATP602 4.1 39.1 1.0
C5' C:ATP602 4.3 41.3 1.0
CB C:ASP87 4.5 50.2 1.0
CA C:GLY88 4.5 36.2 1.0
CA C:ASP87 4.6 48.2 1.0
OD2 C:ASP398 4.7 75.2 1.0
C C:ASP87 4.7 53.8 1.0
O C:SER151 4.9 65.3 1.0
OG C:SER151 4.9 69.4 1.0

Magnesium binding site 5 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 5 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:31.8
occ:1.00
 O1G D:ATP603 2.1 54.0 1.0
OD1 D:ASP87 2.1 42.2 1.0
O1A D:ATP603 2.5 60.0 1.0
CG D:ASP87 2.9 43.6 1.0
OD2 D:ASP87 3.0 43.5 1.0
O1B D:ATP603 3.0 58.2 1.0
O3B D:ATP603 3.0 45.7 1.0
PG D:ATP603 3.1 53.4 1.0
O3A D:ATP603 3.2 53.2 1.0
PB D:ATP603 3.2 44.9 1.0
PA D:ATP603 3.4 67.1 1.0
O D:SER151 3.9 51.1 1.0
OG D:SER151 4.0 60.5 1.0
O2G D:ATP603 4.1 61.7 1.0
O5' D:ATP603 4.2 44.1 1.0
O3G D:ATP603 4.2 44.7 1.0
N D:GLY88 4.3 34.5 1.0
CB D:ASP87 4.3 38.5 1.0
OD2 D:ASP398 4.3 62.6 1.0
CB D:ASP398 4.5 57.9 1.0
O2A D:ATP603 4.7 62.0 1.0
CA D:ASP87 4.7 34.5 1.0
CA D:SER151 4.7 51.7 1.0
C D:SER151 4.7 50.6 1.0
O2B D:ATP603 4.8 45.1 1.0
CG D:ASP398 4.8 63.5 1.0
CB D:SER151 4.9 53.4 1.0

Magnesium binding site 6 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 6 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:32.5
occ:0.00
 O3B F:ATP602 2.0 53.4 1.0
O3G F:ATP602 2.0 59.9 1.0
OD1 F:ASP87 2.1 48.2 1.0
O2A F:ATP602 2.2 61.6 1.0
PB F:ATP602 2.5 56.5 1.0
O1B F:ATP602 2.5 62.2 1.0
PG F:ATP602 2.5 56.4 1.0
O3A F:ATP602 2.8 60.1 1.0
PA F:ATP602 3.1 64.2 1.0
CG F:ASP87 3.1 50.5 1.0
OD2 F:ASP87 3.5 53.0 1.0
O1G F:ATP602 3.6 55.6 1.0
O2G F:ATP602 3.6 60.7 1.0
N F:GLY88 3.8 40.9 1.0
O2B F:ATP602 3.9 56.4 1.0
O1A F:ATP602 4.1 61.5 1.0
O5' F:ATP602 4.1 58.1 1.0
C5' F:ATP602 4.3 60.1 1.0
CB F:ASP87 4.4 44.8 1.0
CA F:GLY88 4.5 33.0 1.0
CA F:ASP87 4.6 43.5 1.0
C F:ASP87 4.7 48.1 1.0
OD2 F:ASP398 4.7 65.3 1.0
OG F:SER151 4.9 67.1 1.0
O F:SER151 4.9 64.8 1.0

Magnesium binding site 7 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 7 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:32.6
occ:1.00
 O1G H:ATP603 2.0 58.2 1.0
OD1 H:ASP87 2.1 42.6 1.0
O1A H:ATP603 2.6 59.0 1.0
O3B H:ATP603 2.8 49.0 1.0
O1B H:ATP603 2.9 59.3 1.0
CG H:ASP87 2.9 46.7 1.0
PG H:ATP603 2.9 54.8 1.0
OD2 H:ASP87 3.0 45.4 1.0
PB H:ATP603 3.1 45.1 1.0
O3A H:ATP603 3.1 56.1 1.0
PA H:ATP603 3.3 71.9 1.0
O2G H:ATP603 4.0 65.1 1.0
O3G H:ATP603 4.0 48.3 1.0
O H:SER151 4.1 52.7 1.0
O5' H:ATP603 4.1 50.2 1.0
N H:GLY88 4.1 38.9 1.0
OG H:SER151 4.1 57.9 1.0
CB H:ASP87 4.3 40.7 1.0
OD2 H:ASP398 4.3 58.0 1.0
O2B H:ATP603 4.6 49.7 1.0
CB H:ASP398 4.6 54.3 1.0
O2A H:ATP603 4.6 65.3 1.0
CA H:ASP87 4.6 36.1 1.0
CG H:ASP398 4.8 60.3 1.0
CA H:SER151 4.9 49.3 1.0
C H:SER151 4.9 49.9 1.0
C H:ASP87 4.9 41.7 1.0
CA H:GLY88 5.0 40.1 1.0

Magnesium binding site 8 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 8 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:52.2
occ:0.00
 O3G K:ATP602 2.0 52.6 1.0
O3B K:ATP602 2.0 38.8 1.0
OD1 K:ASP87 2.1 58.1 1.0
O2A K:ATP602 2.3 53.3 1.0
O1B K:ATP602 2.4 50.4 1.0
PB K:ATP602 2.4 53.7 1.0
PG K:ATP602 2.5 50.1 1.0
O3A K:ATP602 2.7 53.6 1.0
PA K:ATP602 3.0 65.8 1.0
CG K:ASP87 3.1 61.8 1.0
OD2 K:ASP87 3.5 66.1 1.0
O2G K:ATP602 3.6 62.0 1.0
O1G K:ATP602 3.6 42.3 1.0
N K:GLY88 3.8 47.2 1.0
O2B K:ATP602 3.9 55.6 1.0
O1A K:ATP602 4.1 56.3 1.0
O5' K:ATP602 4.1 47.1 1.0
C5' K:ATP602 4.3 49.6 1.0
CB K:ASP87 4.4 53.4 1.0
CA K:ASP87 4.5 54.8 1.0
CA K:GLY88 4.5 42.2 1.0
C K:ASP87 4.7 58.9 1.0
OD2 K:ASP398 4.7 71.1 1.0
OG K:SER151 4.9 68.4 1.0
O K:SER151 4.9 64.8 1.0
K K:K603 5.0 56.1 1.0

Magnesium binding site 9 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 9 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:41.8
occ:1.00
 O1G L:ATP603 2.0 55.8 1.0
O1B L:ATP603 2.0 57.8 1.0
O3B L:ATP603 2.2 35.7 1.0
PB L:ATP603 2.4 37.4 1.0
PG L:ATP603 2.4 63.3 1.0
OD1 L:ASP87 2.5 42.9 1.0
O1A L:ATP603 2.6 54.9 1.0
O3A L:ATP603 2.9 50.5 1.0
O2G L:ATP603 3.1 61.9 1.0
PA L:ATP603 3.2 66.8 1.0
CG L:ASP87 3.4 45.0 1.0
OD2 L:ASP87 3.8 42.5 1.0
O3G L:ATP603 3.8 54.1 1.0
O2B L:ATP603 3.9 35.6 1.0
N L:GLY88 4.0 40.1 1.0
O2A L:ATP603 4.1 60.3 1.0
K L:K602 4.3 67.3 1.0
OD2 L:ASP398 4.3 63.4 1.0
O5' L:ATP603 4.5 40.8 1.0
CB L:ASP87 4.7 39.5 1.0
CA L:GLY88 4.7 39.0 1.0
CA L:ASP87 4.7 32.2 1.0
O L:SER151 4.8 55.8 1.0
C L:ASP87 4.9 41.4 1.0

Magnesium binding site 10 out of 14 in 8bm0

Go back to Magnesium Binding Sites List in 8bm0
Magnesium binding site 10 out of 14 in the Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Groel:Groes-Atp Complex Plunge Frozen 200 Ms After Reaction Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg601

b:50.0
occ:0.00
 O3B N:ATP602 2.0 40.2 1.0
O3G N:ATP602 2.0 50.9 1.0
OD1 N:ASP87 2.2 54.4 1.0
O2A N:ATP602 2.2 53.8 1.0
O1B N:ATP602 2.4 50.7 1.0
PB N:ATP602 2.4 47.6 1.0
PG N:ATP602 2.5 48.9 1.0
O3A N:ATP602 2.7 50.1 1.0
PA N:ATP602 3.0 65.0 1.0
CG N:ASP87 3.1 57.9 1.0
OD2 N:ASP87 3.5 61.8 1.0
O2G N:ATP602 3.6 54.7 1.0
O1G N:ATP602 3.6 42.8 1.0
N N:GLY88 3.7 47.2 1.0
O2B N:ATP602 3.9 47.8 1.0
O1A N:ATP602 4.1 53.0 1.0
O5' N:ATP602 4.1 47.4 1.0
C5' N:ATP602 4.2 47.9 1.0
CB N:ASP87 4.4 50.9 1.0
CA N:GLY88 4.5 39.6 1.0
CA N:ASP87 4.6 50.4 1.0
C N:ASP87 4.7 56.9 1.0
OD2 N:ASP398 4.8 71.7 1.0
OG N:SER151 4.8 67.0 1.0
O N:SER151 5.0 63.6 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 19:43:04 2024

Last articles

Sr in 3BNQ
Sr in 2X53
Sr in 2SPT
Sr in 2QJY
Sr in 2XRM
Sr in 2WOH
Sr in 2RIO
Sr in 2PN4
Sr in 2QJP
Sr in 2HMP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy