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Magnesium in PDB 9jvp: Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3

Enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3

All present enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3:
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 3 (pdb code 9jvp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3, PDB code: 9jvp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9jvp

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Magnesium binding site 1 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:90.5
occ:1.00
 O3G A:ATP901 1.8 45.2 1.0
OG1 A:THR223 2.1 53.6 1.0
O2B A:ATP901 2.2 45.2 1.0
PG A:ATP901 3.0 45.2 1.0
O3B A:ATP901 3.1 45.2 1.0
PB A:ATP901 3.2 45.2 1.0
CB A:THR223 3.3 53.6 1.0
OD1 A:ASP287 3.6 63.0 1.0
NH2 B:ARG341 3.7 51.9 1.0
O2A A:ATP901 3.9 45.2 1.0
O2G A:ATP901 4.0 45.2 1.0
N A:THR223 4.0 53.6 1.0
O1G A:ATP901 4.0 45.2 1.0
O3A A:ATP901 4.1 45.2 1.0
CA A:THR223 4.2 53.6 1.0
CG2 A:THR223 4.2 53.6 1.0
OD2 A:ASP287 4.3 63.0 1.0
PA A:ATP901 4.3 45.2 1.0
CG A:ASP287 4.3 63.0 1.0
NH2 B:ARG340 4.3 53.2 1.0
O1A A:ATP901 4.4 45.2 1.0
O1B A:ATP901 4.4 45.2 1.0
CZ B:ARG341 4.7 51.9 1.0

Magnesium binding site 2 out of 8 in 9jvp

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Magnesium binding site 2 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:40.2
occ:1.00
 OG1 A:THR560 1.9 60.7 1.0
O2G A:ATP902 2.7 20.0 1.0
O2B A:ATP902 2.8 20.0 1.0
O3B A:ATP902 3.0 20.0 1.0
CB A:THR560 3.1 60.7 1.0
OD1 A:ASP625 3.4 64.4 1.0
PG A:ATP902 3.4 20.0 1.0
OD2 A:ASP625 3.4 64.4 1.0
NH2 B:ARG712 3.4 58.1 1.0
PB A:ATP902 3.5 20.0 1.0
O1A A:ATP902 3.5 20.0 1.0
N A:THR560 3.8 60.7 1.0
CG A:ASP625 3.8 64.4 1.0
CA A:THR560 4.0 60.7 1.0
CG2 A:THR560 4.1 60.7 1.0
O3G A:ATP902 4.2 20.0 1.0
O3A A:ATP902 4.3 20.0 1.0
NH2 A:ARG771 4.3 60.4 1.0
NZ A:LYS559 4.3 61.6 1.0
CG2 A:THR665 4.4 63.1 1.0
PA A:ATP902 4.4 20.0 1.0
CZ B:ARG712 4.6 58.1 1.0
O1G A:ATP902 4.6 20.0 1.0
O1B A:ATP902 4.7 20.0 1.0
CB A:LYS559 4.8 61.6 1.0
C A:LYS559 4.8 61.6 1.0

Magnesium binding site 3 out of 8 in 9jvp

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Magnesium binding site 3 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:49.7
occ:1.00
 OG1 B:THR223 1.8 47.7 1.0
O2G B:ATP902 1.9 35.1 1.0
O2B B:ATP902 2.1 35.1 1.0
CB B:THR223 3.1 47.7 1.0
PG B:ATP902 3.2 35.1 1.0
PB B:ATP902 3.3 35.1 1.0
O3B B:ATP902 3.3 35.1 1.0
OD2 B:ASP287 3.9 55.1 1.0
N B:THR223 3.9 47.7 1.0
O1G B:ATP902 3.9 35.1 1.0
OD1 B:ASP287 3.9 55.1 1.0
O2A B:ATP902 4.0 35.1 1.0
CG2 B:THR223 4.0 47.7 1.0
CA B:THR223 4.0 47.7 1.0
NH2 C:ARG341 4.1 48.7 1.0
O3A B:ATP902 4.1 35.1 1.0
NH2 C:ARG340 4.2 49.6 1.0
CG B:ASP287 4.3 55.1 1.0
PA B:ATP902 4.3 35.1 1.0
O3G B:ATP902 4.3 35.1 1.0
O1A B:ATP902 4.4 35.1 1.0
O1B B:ATP902 4.5 35.1 1.0
C B:LYS222 5.0 47.2 1.0
CZ C:ARG341 5.0 48.7 1.0

Magnesium binding site 4 out of 8 in 9jvp

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Magnesium binding site 4 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:47.9
occ:1.00
 OG1 B:THR560 1.8 53.3 1.0
O3G B:ATP901 1.9 41.8 1.0
O2B B:ATP901 2.5 41.8 1.0
CB B:THR560 3.0 53.3 1.0
PG B:ATP901 3.1 41.8 1.0
OD1 B:ASP625 3.3 56.7 1.0
NH2 C:ARG712 3.4 56.7 1.0
O3B B:ATP901 3.5 41.8 1.0
PB B:ATP901 3.5 41.8 1.0
O2G B:ATP901 3.6 41.8 1.0
OD2 B:ASP625 3.6 56.7 1.0
N B:THR560 3.8 53.3 1.0
O2A B:ATP901 3.8 41.8 1.0
CG B:ASP625 3.9 56.7 1.0
CA B:THR560 4.0 53.3 1.0
CG2 B:THR560 4.0 53.3 1.0
O1G B:ATP901 4.3 41.8 1.0
NZ B:LYS559 4.3 51.5 1.0
NH2 B:ARG771 4.4 58.1 1.0
O3A B:ATP901 4.4 41.8 1.0
OG1 B:THR665 4.5 53.9 1.0
CZ C:ARG712 4.5 56.7 1.0
PA B:ATP901 4.6 41.8 1.0
O1B B:ATP901 4.7 41.8 1.0
CB B:LYS559 4.9 51.5 1.0
C B:LYS559 4.9 51.5 1.0
NH1 C:ARG712 5.0 56.7 1.0
CB B:THR665 5.0 53.9 1.0

Magnesium binding site 5 out of 8 in 9jvp

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Magnesium binding site 5 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:46.4
occ:1.00
 OG1 C:THR223 2.0 46.1 1.0
O2B C:ATP902 2.0 30.2 1.0
O3G C:ATP902 2.1 30.2 1.0
PG C:ATP902 3.2 30.2 1.0
CB C:THR223 3.2 46.1 1.0
PB C:ATP902 3.2 30.2 1.0
O2G C:ATP902 3.4 30.2 1.0
O3B C:ATP902 3.5 30.2 1.0
OD1 C:ASP287 3.7 53.8 1.0
N C:THR223 3.8 46.1 1.0
O3A C:ATP902 3.8 30.2 1.0
CA C:THR223 4.1 46.1 1.0
NZ C:LYS222 4.1 44.8 1.0
CG2 C:THR223 4.2 46.1 1.0
NH2 D:ARG341 4.5 50.8 1.0
O1A C:ATP902 4.5 30.2 1.0
O1G C:ATP902 4.5 30.2 1.0
PA C:ATP902 4.5 30.2 1.0
O1B C:ATP902 4.6 30.2 1.0
CG C:ASP287 4.6 53.8 1.0
O2A C:ATP902 4.6 30.2 1.0
CB C:LYS222 4.7 44.8 1.0
OD2 C:ASP287 4.7 53.8 1.0
C C:LYS222 4.8 44.8 1.0
O C:ASP287 4.9 53.8 1.0

Magnesium binding site 6 out of 8 in 9jvp

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Magnesium binding site 6 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:53.4
occ:1.00
 OG1 C:THR560 1.6 54.1 1.0
O2B C:ATP901 2.0 40.7 1.0
O3G C:ATP901 2.2 40.7 1.0
CB C:THR560 2.7 54.1 1.0
PB C:ATP901 3.1 40.7 1.0
O3B C:ATP901 3.2 40.7 1.0
PG C:ATP901 3.2 40.7 1.0
OD1 C:ASP625 3.3 59.4 1.0
NH2 D:ARG712 3.5 63.5 1.0
N C:THR560 3.5 54.1 1.0
O2A C:ATP901 3.6 40.7 1.0
CA C:THR560 3.7 54.1 1.0
CG2 C:THR560 3.8 54.1 1.0
O2G C:ATP901 3.8 40.7 1.0
OD2 C:ASP625 4.0 59.4 1.0
CG C:ASP625 4.1 59.4 1.0
O3A C:ATP901 4.1 40.7 1.0
NZ C:LYS559 4.2 53.8 1.0
NH2 C:ARG771 4.2 62.0 1.0
O1B C:ATP901 4.3 40.7 1.0
PA C:ATP901 4.3 40.7 1.0
OG1 C:THR665 4.5 54.8 1.0
O1G C:ATP901 4.5 40.7 1.0
CZ D:ARG712 4.6 63.5 1.0
O1A C:ATP901 4.7 40.7 1.0
C C:LYS559 4.7 53.8 1.0
CB C:LYS559 4.7 53.8 1.0
CB C:THR665 4.9 54.8 1.0
C C:THR560 5.0 54.1 1.0

Magnesium binding site 7 out of 8 in 9jvp

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Magnesium binding site 7 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:130.5
occ:1.00
 O2B D:ATP902 1.9 64.4 1.0
OG1 D:THR560 2.1 76.4 1.0
O3G D:ATP902 2.6 64.4 1.0
O2G D:ATP902 2.7 64.4 1.0
PB D:ATP902 3.0 64.4 1.0
PG D:ATP902 3.0 64.4 1.0
CB D:THR560 3.2 76.4 1.0
O3B D:ATP902 3.3 64.4 1.0
O3A D:ATP902 3.3 64.4 1.0
OD1 D:ASP625 3.4 77.6 1.0
N D:THR560 3.7 76.4 1.0
NZ D:LYS559 3.8 76.2 1.0
O2A D:ATP902 4.0 64.4 1.0
CA D:THR560 4.1 76.4 1.0
OD2 D:ASP625 4.1 77.6 1.0
CG D:ASP625 4.1 77.6 1.0
NH2 D:ARG771 4.2 97.0 1.0
CG2 D:THR560 4.3 76.4 1.0
PA D:ATP902 4.3 64.4 1.0
O1B D:ATP902 4.4 64.4 1.0
O1G D:ATP902 4.4 64.4 1.0
CB D:LYS559 4.5 76.2 1.0
C D:LYS559 4.7 76.2 1.0
OG1 D:THR665 4.8 71.6 1.0

Magnesium binding site 8 out of 8 in 9jvp

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Magnesium binding site 8 out of 8 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:30.0
occ:1.00
 OG1 D:THR223 1.9 49.0 1.0
O3G D:ATP901 2.3 40.7 1.0
O2B D:ATP901 2.5 40.7 1.0
CB D:THR223 2.9 49.0 1.0
O3B D:ATP901 3.3 40.7 1.0
PG D:ATP901 3.4 40.7 1.0
PB D:ATP901 3.5 40.7 1.0
NH2 E:ARG341 3.5 54.1 1.0
O2A D:ATP901 3.6 40.7 1.0
CG2 D:THR223 3.8 49.0 1.0
N D:THR223 4.0 49.0 1.0
OD2 D:ASP287 4.0 53.1 1.0
PA D:ATP901 4.0 40.7 1.0
CA D:THR223 4.1 49.0 1.0
O1A D:ATP901 4.1 40.7 1.0
O3A D:ATP901 4.1 40.7 1.0
O2G D:ATP901 4.2 40.7 1.0
OD1 D:ASP287 4.4 53.1 1.0
O1G D:ATP901 4.5 40.7 1.0
NH2 E:ARG340 4.6 54.6 1.0
CG D:ASP287 4.6 53.1 1.0
CZ E:ARG341 4.6 54.1 1.0
O1B D:ATP901 4.8 40.7 1.0
NH2 E:ARG314 4.9 53.9 1.0
CB E:ALA313 5.0 53.9 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.
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