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Magnesium in PDB 8bmo: Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions

Enzymatic activity of Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions

All present enzymatic activity of Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions:
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 Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions (pdb code 8bmo). 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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions, PDB code: 8bmo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 8bmo

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Magnesium binding site 1 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:30.8
occ:1.00
 O1A C:ATP602 2.0 31.1 1.0
O1G C:ATP602 2.0 31.1 1.0
O1B C:ATP602 2.1 31.1 1.0
O3A C:ATP602 2.2 31.1 1.0
PB C:ATP602 2.2 31.1 1.0
O3B C:ATP602 2.4 31.1 1.0
PA C:ATP602 2.5 31.1 1.0
PG C:ATP602 2.7 31.1 1.0
OD2 C:ASP87 3.3 44.1 1.0
O5' C:ATP602 3.5 31.1 1.0
O3G C:ATP602 3.6 31.1 1.0
OD1 C:ASP87 3.7 44.1 1.0
C5' C:ATP602 3.7 31.1 1.0
CG C:ASP87 3.7 44.1 1.0
O2B C:ATP602 3.7 31.1 1.0
O2A C:ATP602 3.8 31.1 1.0
O2G C:ATP602 3.9 31.1 1.0
ND2 C:ASN153 4.1 74.8 1.0
N C:GLY88 4.2 29.5 1.0
CA C:GLY88 4.9 29.5 1.0
C4' C:ATP602 4.9 31.1 1.0
CB C:ASP87 5.0 44.1 1.0

Magnesium binding site 2 out of 14 in 8bmo

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Magnesium binding site 2 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:23.7
occ:1.00
 OD1 I:ASP87 2.1 23.5 1.0
O1B I:ATP602 2.2 24.3 1.0
OD2 I:ASP87 2.3 23.5 1.0
CG I:ASP87 2.5 23.5 1.0
O1G I:ATP602 2.5 24.3 1.0
O1A I:ATP602 2.5 24.3 1.0
PB I:ATP602 3.2 24.3 1.0
O3B I:ATP602 3.4 24.3 1.0
PG I:ATP602 3.5 24.3 1.0
PA I:ATP602 3.6 24.3 1.0
O3A I:ATP602 3.6 24.3 1.0
OG I:SER151 3.9 27.5 1.0
CB I:ASP87 4.0 23.5 1.0
O I:SER151 4.0 27.5 1.0
N I:GLY88 4.2 22.3 1.0
OD2 I:ASP398 4.4 29.7 1.0
O5' I:ATP602 4.5 24.3 1.0
O2G I:ATP602 4.5 24.3 1.0
CA I:SER151 4.5 27.5 1.0
CB I:ASP398 4.6 29.7 1.0
O2B I:ATP602 4.6 24.3 1.0
O3G I:ATP602 4.7 24.3 1.0
CB I:SER151 4.7 27.5 1.0
CA I:ASP87 4.7 23.5 1.0
C I:SER151 4.7 27.5 1.0
O2A I:ATP602 4.8 24.3 1.0
CG I:ASP398 4.9 29.7 1.0

Magnesium binding site 3 out of 14 in 8bmo

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Magnesium binding site 3 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:41.0
occ:1.00
 O1A A:ATP602 2.0 41.3 1.0
O1G A:ATP602 2.0 41.3 1.0
O3A A:ATP602 2.2 41.3 1.0
O1B A:ATP602 2.2 41.3 1.0
PB A:ATP602 2.2 41.3 1.0
O3B A:ATP602 2.3 41.3 1.0
PA A:ATP602 2.5 41.3 1.0
PG A:ATP602 2.6 41.3 1.0
O3G A:ATP602 3.5 41.3 1.0
O5' A:ATP602 3.5 41.3 1.0
O2A A:ATP602 3.7 41.3 1.0
O2B A:ATP602 3.7 41.3 1.0
OD1 A:ASP87 3.7 62.4 1.0
C5' A:ATP602 3.8 41.3 1.0
O2G A:ATP602 3.8 41.3 1.0
CG A:ASP87 3.9 62.4 1.0
OD2 A:ASP87 3.9 62.4 1.0
N A:GLY88 4.3 42.4 1.0
CB A:ASP87 4.7 62.4 1.0
CA A:ASP87 5.0 62.4 1.0

Magnesium binding site 4 out of 14 in 8bmo

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Magnesium binding site 4 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:18.8
occ:1.00
 O1B B:ATP602 2.2 21.3 1.0
OD1 B:ASP87 2.2 19.3 1.0
O1G B:ATP602 2.3 21.3 1.0
O1A B:ATP602 2.4 21.3 1.0
OD2 B:ASP87 2.7 19.3 1.0
CG B:ASP87 2.8 19.3 1.0
PB B:ATP602 3.1 21.3 1.0
PG B:ATP602 3.4 21.3 1.0
O3B B:ATP602 3.4 21.3 1.0
PA B:ATP602 3.5 21.3 1.0
O3A B:ATP602 3.5 21.3 1.0
O B:SER151 4.1 23.7 1.0
CB B:ASP87 4.3 19.3 1.0
O2G B:ATP602 4.3 21.3 1.0
OD2 B:ASP398 4.4 26.3 1.0
N B:GLY88 4.4 17.7 1.0
O5' B:ATP602 4.4 21.3 1.0
CA B:SER151 4.5 23.7 1.0
O3G B:ATP602 4.5 21.3 1.0
O2B B:ATP602 4.5 21.3 1.0
CB B:ASP398 4.6 26.3 1.0
O2A B:ATP602 4.7 21.3 1.0
C B:SER151 4.7 23.7 1.0
CB B:SER151 4.8 23.7 1.0
CA B:ASP87 4.9 19.3 1.0
CG B:ASP398 4.9 26.3 1.0

Magnesium binding site 5 out of 14 in 8bmo

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Magnesium binding site 5 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:36.3
occ:1.00
 O1G E:ATP602 2.0 32.2 1.0
O1A E:ATP602 2.2 32.2 1.0
OD1 E:ASP87 2.2 50.1 1.0
O1B E:ATP602 3.0 32.2 1.0
PG E:ATP602 3.2 32.2 1.0
CG E:ASP87 3.2 50.1 1.0
PA E:ATP602 3.2 32.2 1.0
O3A E:ATP602 3.3 32.2 1.0
O3B E:ATP602 3.3 32.2 1.0
PB E:ATP602 3.3 32.2 1.0
OD2 E:ASP87 3.5 50.1 1.0
O E:SER151 4.0 87.0 1.0
O2G E:ATP602 4.2 32.2 1.0
O3G E:ATP602 4.2 32.2 1.0
O5' E:ATP602 4.3 32.2 1.0
C5' E:ATP602 4.3 32.2 1.0
O2A E:ATP602 4.4 32.2 1.0
CB E:ASP87 4.6 50.1 1.0
N E:GLY88 4.8 37.0 1.0
C E:SER151 4.8 87.0 1.0
O2B E:ATP602 4.9 32.2 1.0
CA E:ASP87 5.0 50.1 1.0

Magnesium binding site 6 out of 14 in 8bmo

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Magnesium binding site 6 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:22.3
occ:1.00
 O1B F:ATP602 2.1 22.1 1.0
OD1 F:ASP87 2.2 21.3 1.0
O1G F:ATP602 2.4 22.1 1.0
OD2 F:ASP87 2.5 21.3 1.0
O1A F:ATP602 2.5 22.1 1.0
CG F:ASP87 2.7 21.3 1.0
PB F:ATP602 3.2 22.1 1.0
PG F:ATP602 3.5 22.1 1.0
O3B F:ATP602 3.5 22.1 1.0
O3A F:ATP602 3.6 22.1 1.0
PA F:ATP602 3.6 22.1 1.0
O F:SER151 4.0 25.9 1.0
OG F:SER151 4.0 25.9 1.0
CB F:ASP87 4.2 21.3 1.0
OD2 F:ASP398 4.2 27.8 1.0
N F:GLY88 4.3 19.6 1.0
O2G F:ATP602 4.4 22.1 1.0
CA F:SER151 4.5 25.9 1.0
O5' F:ATP602 4.5 22.1 1.0
CB F:ASP398 4.5 27.8 1.0
O2B F:ATP602 4.6 22.1 1.0
O3G F:ATP602 4.6 22.1 1.0
C F:SER151 4.7 25.9 1.0
CB F:SER151 4.7 25.9 1.0
CG F:ASP398 4.8 27.8 1.0
O2A F:ATP602 4.8 22.1 1.0
CA F:ASP87 4.8 21.3 1.0

Magnesium binding site 7 out of 14 in 8bmo

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Magnesium binding site 7 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:41.5
occ:1.00
 O1A H:ATP602 2.0 39.3 1.0
O1G H:ATP602 2.0 39.3 1.0
O1B H:ATP602 2.1 39.3 1.0
PB H:ATP602 2.2 39.3 1.0
O3A H:ATP602 2.2 39.3 1.0
O3B H:ATP602 2.3 39.3 1.0
PA H:ATP602 2.5 39.3 1.0
PG H:ATP602 2.6 39.3 1.0
OD1 H:ASP87 2.9 53.1 1.0
CG H:ASP87 3.5 53.1 1.0
O5' H:ATP602 3.5 39.3 1.0
O3G H:ATP602 3.5 39.3 1.0
OD2 H:ASP87 3.6 53.1 1.0
C5' H:ATP602 3.7 39.3 1.0
O2B H:ATP602 3.7 39.3 1.0
O2A H:ATP602 3.8 39.3 1.0
O2G H:ATP602 3.8 39.3 1.0
N H:GLY88 4.2 37.4 1.0
ND2 H:ASN153 4.3 129.3 1.0
CB H:ASP87 4.8 53.1 1.0
CA H:GLY88 4.8 37.4 1.0
C4' H:ATP602 4.9 39.3 1.0
CA H:ASP87 5.0 53.1 1.0

Magnesium binding site 8 out of 14 in 8bmo

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Magnesium binding site 8 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:9.2
occ:1.00
 OD1 J:ASP87 2.2 10.2 1.0
O1A J:ATP602 2.2 11.6 1.0
O1G J:ATP602 2.2 11.6 1.0
O1B J:ATP602 2.4 11.6 1.0
OD2 J:ASP87 2.6 10.2 1.0
CG J:ASP87 2.7 10.2 1.0
PB J:ATP602 3.2 11.6 1.0
PG J:ATP602 3.4 11.6 1.0
PA J:ATP602 3.4 11.6 1.0
O3B J:ATP602 3.4 11.6 1.0
O3A J:ATP602 3.5 11.6 1.0
O J:SER151 4.0 13.4 1.0
OG J:SER151 4.1 13.4 1.0
CB J:ASP87 4.2 10.2 1.0
OD2 J:ASP398 4.3 14.4 1.0
O2G J:ATP602 4.3 11.6 1.0
N J:GLY88 4.3 9.4 1.0
O5' J:ATP602 4.4 11.6 1.0
O3G J:ATP602 4.5 11.6 1.0
O2A J:ATP602 4.5 11.6 1.0
CB J:ASP398 4.5 14.4 1.0
CA J:SER151 4.6 13.4 1.0
O2B J:ATP602 4.7 11.6 1.0
C J:SER151 4.8 13.4 1.0
CG J:ASP398 4.8 14.4 1.0
CA J:ASP87 4.8 10.2 1.0
CB J:SER151 4.9 13.4 1.0

Magnesium binding site 9 out of 14 in 8bmo

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Magnesium binding site 9 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:37.7
occ:1.00
 O1A L:ATP602 1.9 40.2 1.0
O1G L:ATP602 2.0 40.2 1.0
O3B L:ATP602 2.2 40.2 1.0
PB L:ATP602 2.2 40.2 1.0
O3A L:ATP602 2.2 40.2 1.0
O1B L:ATP602 2.2 40.2 1.0
OD1 L:ASP87 2.4 50.5 1.0
PG L:ATP602 2.5 40.2 1.0
PA L:ATP602 2.5 40.2 1.0
O3G L:ATP602 3.4 40.2 1.0
CG L:ASP87 3.5 50.5 1.0
O5' L:ATP602 3.6 40.2 1.0
O2A L:ATP602 3.7 40.2 1.0
O2B L:ATP602 3.7 40.2 1.0
O2G L:ATP602 3.7 40.2 1.0
C5' L:ATP602 3.8 40.2 1.0
OD2 L:ASP87 3.8 50.5 1.0
N L:GLY88 4.2 36.9 1.0
CB L:ASP87 4.8 50.5 1.0
CA L:GLY88 4.9 36.9 1.0
CA L:ASP87 4.9 50.5 1.0

Magnesium binding site 10 out of 14 in 8bmo

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Magnesium binding site 10 out of 14 in the Structure of Groel:Groes Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions


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 Complex Exhibiting Adp-Conformation in Trans Ring Obtained Under the Continuous Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg601

b:20.2
occ:1.00
 O1G M:ATP602 2.1 22.2 1.0
O1A M:ATP602 2.1 22.2 1.0
OD1 M:ASP87 2.2 20.6 1.0
O1B M:ATP602 2.4 22.2 1.0
OD2 M:ASP87 2.8 20.6 1.0
CG M:ASP87 2.8 20.6 1.0
PB M:ATP602 3.2 22.2 1.0
PG M:ATP602 3.2 22.2 1.0
PA M:ATP602 3.3 22.2 1.0
O3B M:ATP602 3.4 22.2 1.0
O3A M:ATP602 3.5 22.2 1.0
O M:SER151 4.1 26.1 1.0
OG M:SER151 4.2 26.1 1.0
O2G M:ATP602 4.2 22.2 1.0
OD2 M:ASP398 4.3 27.5 1.0
O5' M:ATP602 4.3 22.2 1.0
CB M:ASP87 4.3 20.6 1.0
O3G M:ATP602 4.4 22.2 1.0
O2A M:ATP602 4.4 22.2 1.0
N M:GLY88 4.4 19.9 1.0
CB M:ASP398 4.6 27.5 1.0
CA M:SER151 4.6 26.1 1.0
O2B M:ATP602 4.7 22.2 1.0
C M:SER151 4.8 26.1 1.0
CG M:ASP398 4.8 27.5 1.0
CA M:ASP87 4.9 20.6 1.0
CB M:SER151 4.9 26.1 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 19:44:54 2024

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