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Magnesium in PDB 8ycx: Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2

Enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2

All present enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2:
3.4.21.92;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 (pdb code 8ycx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2, PDB code: 8ycx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8ycx

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Magnesium binding site 1 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:57.0
occ:1.00
 OG1 A:THR223 1.4 62.0 1.0
O3G A:ATP902 2.2 108.7 1.0
O2B A:ATP902 2.7 108.7 1.0
CB A:THR223 2.7 62.0 1.0
O2A A:ATP902 3.2 108.7 1.0
PG A:ATP902 3.5 108.7 1.0
N A:THR223 3.5 62.0 1.0
O3B A:ATP902 3.6 108.7 1.0
CG2 A:THR223 3.6 62.0 1.0
CA A:THR223 3.7 62.0 1.0
PB A:ATP902 3.7 108.7 1.0
NH2 B:ARG341 4.1 57.3 1.0
PA A:ATP902 4.2 108.7 1.0
O1G A:ATP902 4.3 108.7 1.0
O3A A:ATP902 4.4 108.7 1.0
O2G A:ATP902 4.5 108.7 1.0
C A:LYS222 4.7 63.1 1.0
O1A A:ATP902 4.8 108.7 1.0
CB A:LYS222 4.9 63.1 1.0
C A:THR223 5.0 62.0 1.0

Magnesium binding site 2 out of 7 in 8ycx

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Magnesium binding site 2 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:57.0
occ:1.00
 O3G A:ATP904 1.7 86.4 1.0
CG2 A:THR560 2.3 63.0 1.0
O2B A:ATP904 2.6 86.4 1.0
PG A:ATP904 3.0 86.4 1.0
O3B A:ATP904 3.2 86.4 1.0
OG1 A:THR560 3.2 63.0 1.0
CB A:THR560 3.3 63.0 1.0
NH2 B:ARG712 3.3 59.9 1.0
OD1 A:ASP625 3.4 67.1 1.0
PB A:ATP904 3.5 86.4 1.0
NZ A:LYS559 3.8 63.3 1.0
N A:THR560 3.8 63.0 1.0
OD2 A:ASP625 3.9 67.1 1.0
O2A A:ATP904 3.9 86.4 1.0
O2G A:ATP904 3.9 86.4 1.0
CG A:ASP625 4.0 67.1 1.0
CG2 A:THR665 4.0 65.0 1.0
O1G A:ATP904 4.0 86.4 1.0
NH2 A:ARG771 4.1 61.1 1.0
CA A:THR560 4.2 63.0 1.0
O3A A:ATP904 4.3 86.4 1.0
CB A:LYS559 4.5 63.3 1.0
PA A:ATP904 4.5 86.4 1.0
CZ B:ARG712 4.5 59.9 1.0
O1B A:ATP904 4.7 86.4 1.0
O1A A:ATP904 4.7 86.4 1.0
C A:LYS559 4.8 63.3 1.0

Magnesium binding site 3 out of 7 in 8ycx

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Magnesium binding site 3 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:57.0
occ:1.00
 OG1 B:THR560 1.8 52.8 1.0
O1G B:ATP902 2.0 67.1 1.0
O2B B:ATP902 2.4 67.1 1.0
CB B:THR560 3.0 52.8 1.0
PG B:ATP902 3.2 67.1 1.0
OD1 B:ASP625 3.3 58.1 1.0
NH2 C:ARG712 3.3 57.2 1.0
O3B B:ATP902 3.4 67.1 1.0
PB B:ATP902 3.5 67.1 1.0
OD2 B:ASP625 3.6 58.1 1.0
N B:THR560 3.7 52.8 1.0
O2A B:ATP902 3.8 67.1 1.0
CG B:ASP625 3.8 58.1 1.0
CA B:THR560 3.9 52.8 1.0
CG2 B:THR560 4.0 52.8 1.0
CG2 B:THR665 4.1 55.9 1.0
O3G B:ATP902 4.2 67.1 1.0
O2G B:ATP902 4.3 67.1 1.0
O3A B:ATP902 4.3 67.1 1.0
PA B:ATP902 4.4 67.1 1.0
CZ C:ARG712 4.5 57.2 1.0
O1B B:ATP902 4.7 67.1 1.0
O1A B:ATP902 4.7 67.1 1.0
C B:LYS559 4.8 53.0 1.0
CB B:LYS559 4.8 53.0 1.0
NH1 B:ARG771 4.9 58.4 1.0
NH1 C:ARG712 4.9 57.2 1.0

Magnesium binding site 4 out of 7 in 8ycx

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Magnesium binding site 4 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:57.0
occ:1.00
 O3G B:ATP903 1.7 79.8 1.0
OG1 B:THR223 1.9 49.6 1.0
O2B B:ATP903 2.6 79.8 1.0
PG B:ATP903 3.2 79.8 1.0
CB B:THR223 3.2 49.6 1.0
OD2 B:ASP287 3.3 56.9 1.0
OD1 B:ASP287 3.5 56.9 1.0
O2A B:ATP903 3.6 79.8 1.0
NH2 C:ARG341 3.6 50.3 1.0
O3B B:ATP903 3.7 79.8 1.0
PB B:ATP903 3.7 79.8 1.0
CG B:ASP287 3.8 56.9 1.0
N B:THR223 3.9 49.6 1.0
O1G B:ATP903 4.1 79.8 1.0
O2G B:ATP903 4.1 79.8 1.0
CA B:THR223 4.1 49.6 1.0
CG2 B:THR223 4.1 49.6 1.0
O3A B:ATP903 4.2 79.8 1.0
NZ B:LYS222 4.4 49.8 1.0
PA B:ATP903 4.5 79.8 1.0
CZ C:ARG341 4.8 50.3 1.0
C B:LYS222 5.0 49.8 1.0
CB B:LYS222 5.0 49.8 1.0

Magnesium binding site 5 out of 7 in 8ycx

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Magnesium binding site 5 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:57.0
occ:1.00
 OG1 C:THR560 1.9 56.5 1.0
O2G C:ATP902 2.1 66.8 1.0
O2B C:ATP902 2.1 66.8 1.0
CB C:THR560 3.1 56.5 1.0
PG C:ATP902 3.3 66.8 1.0
PB C:ATP902 3.3 66.8 1.0
OD1 C:ASP625 3.3 63.6 1.0
O2A C:ATP902 3.4 66.8 1.0
O3B C:ATP902 3.4 66.8 1.0
NH2 D:ARG712 3.7 68.6 1.0
OE1 D:GLU643 3.7 70.8 1.0
N C:THR560 3.8 56.5 1.0
CG2 C:THR665 4.0 59.1 1.0
O1G C:ATP902 4.0 66.8 1.0
OD2 C:ASP625 4.0 63.6 1.0
OE2 D:GLU643 4.0 70.8 1.0
CA C:THR560 4.0 56.5 1.0
CG C:ASP625 4.1 63.6 1.0
NZ C:LYS559 4.1 55.2 1.0
CG2 C:THR560 4.1 56.5 1.0
O3A C:ATP902 4.2 66.8 1.0
NH2 C:ARG771 4.3 63.1 1.0
CD D:GLU643 4.3 70.8 1.0
PA C:ATP902 4.4 66.8 1.0
O3G C:ATP902 4.5 66.8 1.0
O1B C:ATP902 4.5 66.8 1.0
CB C:LYS559 4.6 55.2 1.0
C C:LYS559 4.8 55.2 1.0
CZ D:ARG712 4.9 68.6 1.0

Magnesium binding site 6 out of 7 in 8ycx

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Magnesium binding site 6 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:57.0
occ:1.00
 O3G C:ATP903 1.8 71.9 1.0
OG1 C:THR223 2.2 48.1 1.0
O2B C:ATP903 2.3 71.9 1.0
O2A C:ATP903 3.0 71.9 1.0
PG C:ATP903 3.1 71.9 1.0
CB C:THR223 3.3 48.1 1.0
PB C:ATP903 3.4 71.9 1.0
O3B C:ATP903 3.4 71.9 1.0
O2G C:ATP903 3.6 71.9 1.0
NH2 D:ARG341 3.8 50.8 1.0
OD2 C:ASP287 3.9 55.0 1.0
OD1 C:ASP287 4.0 55.0 1.0
O3A C:ATP903 4.0 71.9 1.0
N C:THR223 4.0 48.1 1.0
PA C:ATP903 4.1 71.9 1.0
CA C:THR223 4.3 48.1 1.0
NZ C:LYS222 4.3 47.6 1.0
O1G C:ATP903 4.3 71.9 1.0
CG2 C:THR223 4.3 48.1 1.0
CG C:ASP287 4.4 55.0 1.0
NH2 D:ARG340 4.4 50.5 1.0
O1B C:ATP903 4.7 71.9 1.0
CZ D:ARG341 4.8 50.8 1.0
O1A C:ATP903 4.8 71.9 1.0

Magnesium binding site 7 out of 7 in 8ycx

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Magnesium binding site 7 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:57.0
occ:1.00
 O2B E:ATP902 1.9 20.0 1.0
O2G E:ATP902 2.0 20.0 1.0
OG1 D:THR223 2.2 50.8 1.0
PB E:ATP902 3.1 20.0 1.0
PG E:ATP902 3.2 20.0 1.0
CB D:THR223 3.3 50.8 1.0
O1A E:ATP902 3.4 20.0 1.0
O3B E:ATP902 3.4 20.0 1.0
NH2 E:ARG341 3.6 58.5 1.0
O3A E:ATP902 3.7 20.0 1.0
OD2 D:ASP287 3.8 56.3 1.0
O3G E:ATP902 3.8 20.0 1.0
N D:THR223 3.9 50.8 1.0
OD1 D:ASP287 4.1 56.3 1.0
PA E:ATP902 4.2 20.0 1.0
CA D:THR223 4.2 50.8 1.0
CG2 D:THR223 4.3 50.8 1.0
CG D:ASP287 4.4 56.3 1.0
O1B E:ATP902 4.4 20.0 1.0
O1G E:ATP902 4.5 20.0 1.0
NH1 E:ARG314 4.7 58.6 1.0
NZ D:LYS222 4.7 50.4 1.0
CZ E:ARG341 4.8 58.5 1.0

Reference:

B.Zhou, H.Zhao, Y.Gao, X.Chen, T.Zhang, J.He, X.Xiong. Activation Mechanism of Caseinolytic Chaperone-Protease System in Mycobacterium Tuberculosis By the Anti-Cancer Drug Bortezomib To Be Published.
Page generated: Fri Aug 15 21:21:59 2025

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