Magnesium in PDB 8wux: Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex

Enzymatic activity of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex

All present enzymatic activity of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex:
5.6.1.7;

Other elements in 8wux:

The structure of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex also contains other interesting chemical elements:

Potassium (K) 7 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex (pdb code 8wux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex, PDB code: 8wux:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 8wux

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Magnesium binding site 1 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:94.5
occ:1.00
 O3G A:ANP602 2.1 93.1 1.0
OD2 A:ASP87 2.1 101.1 1.0
O1B A:ANP602 2.3 87.1 1.0
O2A A:ANP602 2.3 89.0 1.0
OD1 A:ASP87 2.8 100.6 1.0
CG A:ASP87 2.8 95.6 1.0
PG A:ANP602 3.4 93.0 1.0
PB A:ANP602 3.5 85.9 1.0
PA A:ANP602 3.7 90.9 1.0
N3B A:ANP602 3.9 79.8 1.0
O3A A:ANP602 4.0 79.2 1.0
CB A:ASP87 4.2 83.1 1.0
O1G A:ANP602 4.2 86.2 1.0
N A:GLY88 4.2 77.3 1.0
O A:SER151 4.5 87.5 1.0
C5' A:ANP602 4.5 85.5 1.0
O2G A:ANP602 4.6 94.3 1.0
O5' A:ANP602 4.6 82.3 1.0
CA A:ASP87 4.7 77.5 1.0
O1A A:ANP602 4.7 89.4 1.0
CA A:SER151 4.8 82.7 1.0
O2B A:ANP602 4.8 85.7 1.0
CB A:SER151 4.9 86.9 1.0

Magnesium binding site 2 out of 14 in 8wux

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Magnesium binding site 2 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:101.5
occ:1.00
 O1G H:ANP603 2.0 108.8 1.0
O2A H:ANP603 2.1 104.3 1.0
O1B H:ANP603 2.4 97.8 1.0
OD1 H:ASP87 2.4 112.9 1.0
OD2 H:ASP87 2.9 119.3 1.0
CG H:ASP87 3.0 114.5 1.0
PG H:ANP603 3.4 108.5 1.0
PA H:ANP603 3.4 97.0 1.0
PB H:ANP603 3.5 92.6 1.0
N3B H:ANP603 3.7 94.3 1.0
O3A H:ANP603 3.8 92.3 1.0
O H:SER151 3.9 128.5 1.0
C5' H:ANP603 4.1 93.6 1.0
O2G H:ANP603 4.2 102.7 1.0
O5' H:ANP603 4.2 94.3 1.0
CB H:ASP87 4.4 105.4 1.0
O3G H:ANP603 4.4 98.8 1.0
O1A H:ANP603 4.6 88.0 1.0
O2B H:ANP603 4.9 91.5 1.0
C H:SER151 4.9 128.1 1.0
O H:ILE150 4.9 129.0 1.0
N H:GLY88 4.9 94.2 1.0
CA H:ASP87 5.0 101.3 1.0

Magnesium binding site 3 out of 14 in 8wux

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Magnesium binding site 3 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:90.0
occ:1.00
 OD1 B:ASP87 2.1 105.3 1.0
O2A B:ANP602 2.1 91.2 1.0
O3G B:ANP602 2.2 96.6 1.0
O1B B:ANP602 2.3 88.6 1.0
CG B:ASP87 2.9 101.9 1.0
OD2 B:ASP87 3.0 108.7 1.0
PA B:ANP602 3.5 90.3 1.0
PB B:ANP602 3.5 90.1 1.0
PG B:ANP602 3.5 95.7 1.0
O3A B:ANP602 3.9 80.0 1.0
N3B B:ANP602 3.9 82.8 1.0
O1G B:ANP602 4.3 89.0 1.0
CB B:ASP87 4.3 87.5 1.0
N B:GLY88 4.3 78.7 1.0
O B:SER151 4.4 89.6 1.0
C5' B:ANP602 4.4 87.7 1.0
O5' B:ANP602 4.5 83.2 1.0
O1A B:ANP602 4.6 91.0 1.0
CA B:SER151 4.7 82.7 1.0
O2G B:ANP602 4.7 99.5 1.0
CA B:ASP87 4.8 81.8 1.0
O2B B:ANP602 4.9 88.9 1.0
CB B:SER151 4.9 85.6 1.0

Magnesium binding site 4 out of 14 in 8wux

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Magnesium binding site 4 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:98.1
occ:1.00
 O1G I:ANP603 2.0 104.6 1.0
O2A I:ANP603 2.1 99.8 1.0
O1B I:ANP603 2.2 93.3 1.0
OD1 I:ASP87 2.3 113.2 1.0
OD2 I:ASP87 2.4 106.3 1.0
CG I:ASP87 2.6 108.6 1.0
PG I:ANP603 3.3 106.1 1.0
PB I:ANP603 3.4 90.0 1.0
PA I:ANP603 3.4 92.9 1.0
N3B I:ANP603 3.7 92.8 1.0
O3A I:ANP603 3.7 90.2 1.0
CB I:ASP87 4.1 99.9 1.0
O2G I:ANP603 4.1 99.2 1.0
O I:SER151 4.2 122.1 1.0
C5' I:ANP603 4.2 91.8 1.0
O5' I:ANP603 4.3 92.0 1.0
O3G I:ANP603 4.5 97.6 1.0
O1A I:ANP603 4.6 83.3 1.0
N I:GLY88 4.8 90.1 1.0
O2B I:ANP603 4.8 87.3 1.0
CA I:ASP87 4.8 96.9 1.0
O I:ILE150 4.9 121.0 1.0

Magnesium binding site 5 out of 14 in 8wux

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Magnesium binding site 5 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:80.8
occ:1.00
 OD1 C:ASP87 2.1 91.9 1.0
O2A C:ANP602 2.2 79.1 1.0
O1B C:ANP602 2.3 82.6 1.0
O3G C:ANP602 2.7 81.5 1.0
CG C:ASP87 2.8 86.0 1.0
OD2 C:ASP87 2.9 88.2 1.0
PB C:ANP602 3.4 78.9 1.0
PG C:ANP602 3.5 85.4 1.0
PA C:ANP602 3.5 84.1 1.0
O1G C:ANP602 3.6 86.2 1.0
N3B C:ANP602 3.7 74.3 1.0
O3A C:ANP602 3.8 75.9 1.0
CB C:ASP87 4.3 74.3 1.0
N C:GLY88 4.3 71.1 1.0
C5' C:ANP602 4.4 80.1 1.0
O5' C:ANP602 4.5 79.9 1.0
O C:SER151 4.5 85.7 1.0
O1A C:ANP602 4.6 81.7 1.0
CA C:SER151 4.7 76.1 1.0
CA C:ASP87 4.8 71.2 1.0
O2B C:ANP602 4.8 80.5 1.0
CB C:SER151 4.9 81.1 1.0
O2G C:ANP602 5.0 87.7 1.0

Magnesium binding site 6 out of 14 in 8wux

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Magnesium binding site 6 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:102.9
occ:1.00
 O1G J:ANP603 2.0 107.1 1.0
O2A J:ANP603 2.1 101.2 1.0
O1B J:ANP603 2.4 93.9 1.0
OD1 J:ASP87 2.4 110.9 1.0
OD2 J:ASP87 2.9 115.1 1.0
CG J:ASP87 3.0 111.1 1.0
PG J:ANP603 3.4 111.1 1.0
PA J:ANP603 3.5 95.5 1.0
PB J:ANP603 3.5 93.7 1.0
N3B J:ANP603 3.7 95.6 1.0
O3A J:ANP603 3.8 93.3 1.0
O J:SER151 4.0 127.7 1.0
C5' J:ANP603 4.1 92.9 1.0
O2G J:ANP603 4.3 102.1 1.0
O5' J:ANP603 4.3 94.1 1.0
O3G J:ANP603 4.5 100.3 1.0
CB J:ASP87 4.5 102.8 1.0
O1A J:ANP603 4.6 86.5 1.0
O J:ILE150 4.8 127.5 1.0
N J:GLY88 4.9 91.1 1.0
C J:SER151 4.9 127.2 1.0
O2B J:ANP603 4.9 90.3 1.0

Magnesium binding site 7 out of 14 in 8wux

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Magnesium binding site 7 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:84.7
occ:1.00
 OD2 D:ASP87 2.1 93.8 1.0
O3G D:ANP602 2.1 87.9 1.0
O2A D:ANP602 2.3 82.0 1.0
O1B D:ANP602 2.4 82.5 1.0
CG D:ASP87 2.9 90.7 1.0
OD1 D:ASP87 3.0 93.1 1.0
PG D:ANP602 3.5 90.2 1.0
PB D:ANP602 3.6 80.7 1.0
PA D:ANP602 3.7 84.2 1.0
N3B D:ANP602 3.9 74.7 1.0
O3A D:ANP602 4.0 74.6 1.0
N D:GLY88 4.2 74.4 1.0
O1G D:ANP602 4.3 82.7 1.0
CB D:ASP87 4.3 79.5 1.0
O D:SER151 4.4 84.6 1.0
C5' D:ANP602 4.5 80.3 1.0
O2G D:ANP602 4.6 90.5 1.0
O5' D:ANP602 4.6 77.1 1.0
CA D:SER151 4.7 76.6 1.0
O1A D:ANP602 4.8 83.0 1.0
CA D:ASP87 4.8 74.5 1.0
CB D:SER151 4.9 82.5 1.0
O2B D:ANP602 4.9 81.3 1.0

Magnesium binding site 8 out of 14 in 8wux

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Magnesium binding site 8 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:102.9
occ:1.00
 O1G K:ANP603 2.1 109.7 1.0
O2A K:ANP603 2.1 102.1 1.0
OD1 K:ASP87 2.2 111.4 1.0
O1B K:ANP603 2.4 94.9 1.0
CG K:ASP87 2.9 111.0 1.0
OD2 K:ASP87 2.9 112.1 1.0
PG K:ANP603 3.4 111.9 1.0
PA K:ANP603 3.4 96.6 1.0
PB K:ANP603 3.5 93.4 1.0
N3B K:ANP603 3.7 95.9 1.0
O3A K:ANP603 3.8 93.0 1.0
O K:SER151 4.1 130.7 1.0
C5' K:ANP603 4.2 94.7 1.0
O2G K:ANP603 4.2 103.3 1.0
O5' K:ANP603 4.3 94.8 1.0
CB K:ASP87 4.3 103.3 1.0
O3G K:ANP603 4.5 102.0 1.0
O1A K:ANP603 4.6 87.6 1.0
N K:GLY88 4.7 93.2 1.0
O K:ILE150 4.9 130.3 1.0
O2B K:ANP603 4.9 90.6 1.0
CA K:ASP87 5.0 100.5 1.0
C K:SER151 5.0 129.1 1.0

Magnesium binding site 9 out of 14 in 8wux

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Magnesium binding site 9 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:92.2
occ:1.00
 O3G E:ANP602 2.1 96.6 1.0
OD2 E:ASP87 2.1 101.7 1.0
O2A E:ANP602 2.3 92.1 1.0
O1B E:ANP602 2.5 90.8 1.0
CG E:ASP87 2.9 100.0 1.0
OD1 E:ASP87 3.0 101.0 1.0
PG E:ANP602 3.5 97.2 1.0
PB E:ANP602 3.7 90.1 1.0
PA E:ANP602 3.7 91.7 1.0
N3B E:ANP602 3.9 83.5 1.0
O3A E:ANP602 4.1 82.8 1.0
O1G E:ANP602 4.2 90.8 1.0
N E:GLY88 4.3 81.5 1.0
O E:SER151 4.3 91.3 1.0
CB E:ASP87 4.4 87.3 1.0
C5' E:ANP602 4.6 91.2 1.0
O2G E:ANP602 4.6 102.5 1.0
CA E:SER151 4.6 83.6 1.0
O5' E:ANP602 4.7 85.7 1.0
O1A E:ANP602 4.7 93.0 1.0
CB E:SER151 4.8 86.1 1.0
CA E:ASP87 4.9 82.5 1.0
C E:SER151 5.0 87.7 1.0
CB E:ASP398 5.0 100.7 1.0

Magnesium binding site 10 out of 14 in 8wux

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Magnesium binding site 10 out of 14 in the Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of H. Thermophilus Groel-Groes Bullet Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:102.3
occ:1.00
 O1G L:ANP603 2.1 109.8 1.0
O2A L:ANP603 2.1 101.7 1.0
O1B L:ANP603 2.3 96.7 1.0
OD1 L:ASP87 2.3 112.8 1.0
OD2 L:ASP87 2.4 116.5 1.0
CG L:ASP87 2.6 113.4 1.0
PG L:ANP603 3.3 111.2 1.0
PB L:ANP603 3.4 93.8 1.0
PA L:ANP603 3.4 95.2 1.0
N3B L:ANP603 3.6 97.1 1.0
O3A L:ANP603 3.7 92.8 1.0
O2G L:ANP603 4.1 102.7 1.0
CB L:ASP87 4.1 105.0 1.0
O L:SER151 4.1 130.2 1.0
C5' L:ANP603 4.2 93.3 1.0
O5' L:ANP603 4.3 95.0 1.0
O3G L:ANP603 4.5 101.1 1.0
O1A L:ANP603 4.6 85.5 1.0
N L:GLY88 4.7 94.2 1.0
O2B L:ANP603 4.8 90.5 1.0
CA L:ASP87 4.8 102.1 1.0
O L:ILE150 4.9 127.7 1.0

Reference:

Z.Liao, C.C.Gopalasingam, M.Kameya, C.Gerle, H.Shigematsu, M.Ishii, T.Arakawa, S.Fushinobu. Structural Insights Into Thermophilic Chaperonin Complexes. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38492570
DOI: 10.1016/J.STR.2024.02.012
Page generated: Sat Oct 5 00:56:22 2024

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