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Magnesium in PDB 8yd1: Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1

Enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1

All present enzymatic activity of Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1:
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 1 (pdb code 8yd1). 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 1, PDB code: 8yd1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8yd1

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:79.2
occ:1.00
 O2B A:ATP904 1.5 20.0 1.0
CG2 A:THR223 1.9 91.3 1.0
OG1 A:THR223 2.1 91.3 1.0
CB A:THR223 2.5 91.3 1.0
PB A:ATP904 3.0 20.0 1.0
O2G A:ATP904 3.1 20.0 1.0
N A:THR223 3.5 91.3 1.0
CA A:THR223 3.5 91.3 1.0
O3B A:ATP904 3.7 20.0 1.0
PG A:ATP904 3.8 20.0 1.0
O3A A:ATP904 3.8 20.0 1.0
O3G A:ATP904 3.9 20.0 1.0
O1B A:ATP904 4.0 20.0 1.0
NH2 B:ARG341 4.0 77.7 1.0
O1A A:ATP904 4.3 20.0 1.0
CD A:LYS222 4.4 91.8 1.0
PA A:ATP904 4.6 20.0 1.0
C A:THR223 4.6 91.3 1.0
C A:LYS222 4.7 91.8 1.0
CG A:LYS222 4.9 91.8 1.0
O2A A:ATP904 5.0 20.0 1.0

Magnesium binding site 2 out of 7 in 8yd1

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


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

b:88.6
occ:1.00
 O3G A:ATP902 1.8 89.7 1.0
CG2 A:THR560 2.2 86.8 1.0
O2B A:ATP902 2.4 89.7 1.0
OD1 A:ASP625 3.1 93.8 1.0
PG A:ATP902 3.2 89.7 1.0
CB A:THR560 3.4 86.8 1.0
PB A:ATP902 3.4 89.7 1.0
OG1 A:THR560 3.5 86.8 1.0
O3B A:ATP902 3.5 89.7 1.0
NH1 B:ARG712 3.6 84.0 1.0
O3A A:ATP902 3.9 89.7 1.0
O1G A:ATP902 4.1 89.7 1.0
N A:THR560 4.1 86.8 1.0
O2G A:ATP902 4.1 89.7 1.0
CG A:ASP625 4.2 93.8 1.0
CA A:THR560 4.4 86.8 1.0
CG2 A:THR665 4.5 92.1 1.0
NH2 A:ARG771 4.6 84.8 1.0
OD1 A:ASN667 4.7 100.6 1.0
OD2 A:ASP625 4.8 93.8 1.0
O2A A:ATP902 4.8 89.7 1.0
O1B A:ATP902 4.8 89.7 1.0
CZ B:ARG712 4.9 84.0 1.0
CB A:LYS559 4.9 90.3 1.0
PA A:ATP902 5.0 89.7 1.0

Magnesium binding site 3 out of 7 in 8yd1

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Magnesium binding site 3 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:71.5
occ:1.00
 OG1 B:THR223 1.4 66.2 1.0
O2B B:ATP904 2.4 67.0 1.0
O3G B:ATP904 2.5 67.0 1.0
CB B:THR223 2.7 66.2 1.0
O2A B:ATP904 3.0 67.0 1.0
CG2 B:THR223 3.4 66.2 1.0
OD2 B:ASP287 3.5 77.0 1.0
PB B:ATP904 3.7 67.0 1.0
PG B:ATP904 3.8 67.0 1.0
CA B:THR223 3.8 66.2 1.0
N B:THR223 3.9 66.2 1.0
NH2 C:ARG341 4.0 63.2 1.0
O3B B:ATP904 4.0 67.0 1.0
OD1 B:ASP287 4.1 77.0 1.0
PA B:ATP904 4.1 67.0 1.0
CG B:ASP287 4.2 77.0 1.0
O3A B:ATP904 4.2 67.0 1.0
NH2 C:ARG340 4.3 64.5 1.0
O2G B:ATP904 4.3 67.0 1.0
CD B:LYS222 4.4 66.4 1.0
O1A B:ATP904 4.8 67.0 1.0
CG B:LYS222 4.9 66.4 1.0
C B:LYS222 4.9 66.4 1.0
O1B B:ATP904 4.9 67.0 1.0
O1G B:ATP904 5.0 67.0 1.0

Magnesium binding site 4 out of 7 in 8yd1

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Magnesium binding site 4 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:30.0
occ:1.00
 O2G B:ATP903 1.8 79.3 1.0
O2B B:ATP903 2.0 79.3 1.0
OG1 B:THR560 2.6 67.1 1.0
PG B:ATP903 3.0 79.3 1.0
PB B:ATP903 3.0 79.3 1.0
O3B B:ATP903 3.2 79.3 1.0
NH2 C:ARG712 3.5 74.1 1.0
OD1 B:ASP625 3.5 76.9 1.0
O3A B:ATP903 3.6 79.3 1.0
CB B:THR560 3.8 67.1 1.0
O3G B:ATP903 3.8 79.3 1.0
NZ B:LYS559 3.8 70.4 1.0
NH1 B:ARG771 3.8 72.2 1.0
O1G B:ATP903 4.1 79.3 1.0
OD2 B:ASP625 4.2 76.9 1.0
O2A B:ATP903 4.3 79.3 1.0
CG B:ASP625 4.3 76.9 1.0
N B:THR560 4.3 67.1 1.0
O1B B:ATP903 4.4 79.3 1.0
PA B:ATP903 4.4 79.3 1.0
ND2 B:ASN667 4.4 84.4 1.0
CZ C:ARG712 4.7 74.1 1.0
CA B:THR560 4.7 67.1 1.0
CG2 B:THR560 4.7 67.1 1.0
O1A B:ATP903 4.7 79.3 1.0
CB B:LYS559 4.9 70.4 1.0
CZ B:ARG771 4.9 72.2 1.0

Magnesium binding site 5 out of 7 in 8yd1

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Magnesium binding site 5 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:30.0
occ:1.00
 O2B C:ATP901 1.7 67.2 1.0
O3G C:ATP901 1.7 67.2 1.0
PG C:ATP901 2.6 67.2 1.0
PB C:ATP901 2.7 67.2 1.0
O3B C:ATP901 2.9 67.2 1.0
O2G C:ATP901 2.9 67.2 1.0
CG2 C:THR223 3.0 62.3 1.0
CB C:THR223 3.5 62.3 1.0
O3A C:ATP901 3.6 67.2 1.0
NH2 D:ARG340 3.8 67.9 1.0
N C:THR223 3.8 62.3 1.0
NH2 D:ARG341 3.8 67.7 1.0
O1G C:ATP901 4.0 67.2 1.0
O1B C:ATP901 4.0 67.2 1.0
CA C:THR223 4.3 62.3 1.0
OD1 C:ASP287 4.4 66.8 1.0
CE C:LYS222 4.6 60.7 1.0
OG1 C:THR223 4.6 62.3 1.0
CB C:LYS222 4.6 60.7 1.0
CZ D:ARG341 4.7 67.7 1.0
OD2 C:ASP287 4.8 66.8 1.0
C C:LYS222 4.9 60.7 1.0
NZ C:LYS222 4.9 60.7 1.0
PA C:ATP901 4.9 67.2 1.0
O2A C:ATP901 4.9 67.2 1.0
N C:LYS222 4.9 60.7 1.0
CZ D:ARG340 5.0 67.9 1.0

Magnesium binding site 6 out of 7 in 8yd1

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Magnesium binding site 6 out of 7 in the Cryoem Structure of M. Tuberculosis CLPC1P1P2 Complex Bound to Bortezomib, Conformation 1


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

b:30.0
occ:1.00
 O3G C:ATP904 1.5 91.2 1.0
O2B C:ATP904 1.8 91.2 1.0
OG1 C:THR560 2.5 70.7 1.0
PG C:ATP904 2.7 91.2 1.0
PB C:ATP904 2.7 91.2 1.0
O3B C:ATP904 2.8 91.2 1.0
O3A C:ATP904 3.4 91.2 1.0
NZ C:LYS559 3.5 72.8 1.0
NH2 D:ARG712 3.6 92.5 1.0
O1G C:ATP904 3.6 91.2 1.0
CB C:THR560 3.7 70.7 1.0
OD1 C:ASP625 3.8 81.3 1.0
O2G C:ATP904 3.8 91.2 1.0
OD1 C:ASN667 3.9 85.2 1.0
N C:THR560 4.0 70.7 1.0
O1B C:ATP904 4.1 91.2 1.0
CB C:LYS559 4.1 72.8 1.0
OE1 D:GLU643 4.2 88.8 1.0
NH1 C:ARG771 4.5 84.6 1.0
CA C:THR560 4.5 70.7 1.0
CG2 C:THR560 4.7 70.7 1.0
PA C:ATP904 4.8 91.2 1.0
CE C:LYS559 4.8 72.8 1.0
C C:LYS559 4.8 72.8 1.0
CG C:ASP625 4.8 81.3 1.0
CG C:ASN667 4.8 85.2 1.0
CZ D:ARG712 4.8 92.5 1.0
OG1 C:THR665 4.9 76.6 1.0
ND2 C:ASN667 4.9 85.2 1.0
CA C:LYS559 4.9 72.8 1.0
OE2 D:GLU643 5.0 88.8 1.0
CD C:LYS559 5.0 72.8 1.0

Magnesium binding site 7 out of 7 in 8yd1

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:30.0
occ:1.00
 O3G D:ATP903 0.8 20.0 1.0
PG D:ATP903 1.9 20.0 1.0
O2B D:ATP903 2.3 20.0 1.0
O3B D:ATP903 2.4 20.0 1.0
O2G D:ATP903 2.8 20.0 1.0
PB D:ATP903 2.9 20.0 1.0
O1A D:ATP903 2.9 20.0 1.0
CG2 D:THR223 3.0 69.4 1.0
O1G D:ATP903 3.1 20.0 1.0
OG1 D:THR223 3.4 69.4 1.0
NH1 E:ARG341 3.6 80.5 1.0
O3A D:ATP903 3.7 20.0 1.0
NZ D:LYS222 3.8 69.0 1.0
CB D:THR223 3.8 69.4 1.0
PA D:ATP903 3.9 20.0 1.0
N D:THR223 4.1 69.4 1.0
O1B D:ATP903 4.1 20.0 1.0
CA D:THR223 4.6 69.4 1.0
NH1 E:ARG340 4.7 80.8 1.0
OD1 D:ASP287 4.7 76.2 1.0
CB D:LYS222 4.8 69.0 1.0
CZ E:ARG341 4.8 80.5 1.0
O2A D:ATP903 4.8 20.0 1.0
OD2 D:ASP287 4.8 76.2 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 21:22:10 2025

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