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Magnesium in PDB 8xoo: Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis

Enzymatic activity of Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis

All present enzymatic activity of Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis:
3.4.21.92;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis (pdb code 8xoo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis, PDB code: 8xoo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8xoo

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg903

b:55.0
occ:1.00
 O2G R:ATP902 2.1 56.7 1.0
O1B R:ATP902 2.1 56.7 1.0
OG1 R:THR556 2.1 56.2 1.0
PB R:ATP902 3.3 56.7 1.0
CB R:THR556 3.3 56.2 1.0
PG R:ATP902 3.4 56.7 1.0
O3B R:ATP902 3.5 56.7 1.0
OD1 R:ASP621 3.8 59.8 1.0
O3G R:ATP902 3.9 56.7 1.0
OD2 R:ASP621 4.0 59.8 1.0
O3A R:ATP902 4.1 56.7 1.0
N R:THR556 4.2 56.2 1.0
CG2 R:THR556 4.2 56.2 1.0
NH2 Q:ARG709 4.2 53.3 1.0
O1A R:ATP902 4.3 56.7 1.0
CG R:ASP621 4.4 59.8 1.0
CA R:THR556 4.4 56.2 1.0
O2B R:ATP902 4.6 56.7 1.0
O1G R:ATP902 4.6 56.7 1.0
PA R:ATP902 4.6 56.7 1.0
NH2 R:ARG768 4.7 54.6 1.0
O2A R:ATP902 4.8 56.7 1.0

Magnesium binding site 2 out of 7 in 8xoo

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg904

b:84.1
occ:1.00
 O2G R:ATP901 2.1 83.8 1.0
O1A R:ATP901 2.1 83.8 1.0
O1B R:ATP901 2.3 83.8 1.0
PB R:ATP901 2.4 83.8 1.0
O3B R:ATP901 2.4 83.8 1.0
O3A R:ATP901 2.4 83.8 1.0
PG R:ATP901 2.6 83.8 1.0
PA R:ATP901 2.6 83.8 1.0
O1G R:ATP901 3.1 83.8 1.0
OG1 R:THR219 3.2 86.0 1.0
O2A R:ATP901 3.4 83.8 1.0
NH2 Q:ARG336 3.5 73.1 1.0
CB R:THR219 3.9 86.0 1.0
O2B R:ATP901 3.9 83.8 1.0
O3G R:ATP901 4.0 83.8 1.0
O5' R:ATP901 4.0 83.8 1.0
NH2 Q:ARG337 4.3 71.9 1.0
N R:THR219 4.5 86.0 1.0
CZ Q:ARG336 4.5 73.1 1.0
C5' R:ATP901 4.6 83.8 1.0
NE Q:ARG336 4.8 73.1 1.0
CA R:THR219 4.8 86.0 1.0
CG2 R:THR219 5.0 86.0 1.0

Magnesium binding site 3 out of 7 in 8xoo

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg903

b:62.1
occ:1.00
 OG1 Q:THR556 2.1 58.6 1.0
O2G Q:ATP902 2.2 60.0 1.0
O1B Q:ATP902 2.2 60.0 1.0
CB Q:THR556 3.4 58.6 1.0
PB Q:ATP902 3.4 60.0 1.0
PG Q:ATP902 3.5 60.0 1.0
OD1 Q:ASP621 3.7 56.8 1.0
O3B Q:ATP902 3.7 60.0 1.0
OD2 Q:ASP621 3.7 56.8 1.0
CG Q:ASP621 4.1 56.8 1.0
O3A Q:ATP902 4.1 60.0 1.0
NH2 P:ARG709 4.2 58.7 1.0
O1A Q:ATP902 4.2 60.0 1.0
CG2 Q:THR556 4.2 58.6 1.0
N Q:THR556 4.3 58.6 1.0
O3G Q:ATP902 4.3 60.0 1.0
CA Q:THR556 4.4 58.6 1.0
O1G Q:ATP902 4.5 60.0 1.0
O2B Q:ATP902 4.7 60.0 1.0
PA Q:ATP902 4.7 60.0 1.0
NH2 Q:ARG768 4.9 59.1 1.0

Magnesium binding site 4 out of 7 in 8xoo

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg903

b:78.9
occ:1.00
 O1B P:ATP902 2.1 82.8 1.0
O2G P:ATP902 2.1 82.8 1.0
OG1 P:THR556 2.2 74.0 1.0
PB P:ATP902 3.3 82.8 1.0
CB P:THR556 3.3 74.0 1.0
PG P:ATP902 3.4 82.8 1.0
O3B P:ATP902 3.5 82.8 1.0
OD2 P:ASP621 3.8 72.7 1.0
OD1 P:ASP621 4.0 72.7 1.0
O3A P:ATP902 4.0 82.8 1.0
O1A P:ATP902 4.1 82.8 1.0
CG2 P:THR556 4.2 74.0 1.0
O3G P:ATP902 4.2 82.8 1.0
CG P:ASP621 4.3 72.7 1.0
N P:THR556 4.3 74.0 1.0
NH2 P:ARG768 4.4 95.2 1.0
CA P:THR556 4.4 74.0 1.0
O1G P:ATP902 4.5 82.8 1.0
O2B P:ATP902 4.6 82.8 1.0
PA P:ATP902 4.6 82.8 1.0

Magnesium binding site 5 out of 7 in 8xoo

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg903

b:138.6
occ:1.00
 O2B O:ATP902 2.1 145.4 1.0
O2G O:ATP902 2.1 145.4 1.0
PB O:ATP902 2.8 145.4 1.0
O3B O:ATP902 3.0 145.4 1.0
PG O:ATP902 3.0 145.4 1.0
O1B O:ATP902 3.2 145.4 1.0
NH2 O:ARG768 3.4 153.5 1.0
O1G O:ATP902 3.6 145.4 1.0
OG O:SER551 3.7 144.5 1.0
CA O:SER551 3.9 144.5 1.0
N O:GLY552 4.0 145.1 1.0
CB O:SER551 4.1 144.5 1.0
O3A O:ATP902 4.3 145.4 1.0
O3G O:ATP902 4.3 145.4 1.0
CZ O:ARG768 4.4 153.5 1.0
C O:SER551 4.5 144.5 1.0
NE O:ARG768 4.8 153.5 1.0
OG1 O:THR556 4.9 127.8 1.0

Magnesium binding site 6 out of 7 in 8xoo

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Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg903

b:161.7
occ:1.00
 O3B T:ATP902 2.1 160.6 1.0
O1B T:ATP902 2.2 160.6 1.0
O1G T:ATP902 2.3 160.6 1.0
PB T:ATP902 2.5 160.6 1.0
PG T:ATP902 2.5 160.6 1.0
OG1 T:THR556 3.0 164.1 1.0
O2G T:ATP902 3.2 160.6 1.0
O2B T:ATP902 3.4 160.6 1.0
O3A T:ATP902 3.8 160.6 1.0
O3G T:ATP902 3.9 160.6 1.0
CB T:THR556 4.3 164.1 1.0
N T:THR556 4.5 164.1 1.0
OD1 T:ASP621 4.6 180.5 1.0
CB T:LYS555 4.6 166.8 1.0
O1A T:ATP902 4.7 160.6 1.0
PA T:ATP902 4.8 160.6 1.0
OD2 T:ASP621 4.8 180.5 1.0
CD T:LYS555 4.9 166.8 1.0
CE T:LYS555 4.9 166.8 1.0
NH2 T:ARG768 5.0 147.3 1.0

Magnesium binding site 7 out of 7 in 8xoo

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Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis


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 the CLPC1:CLPP1P2 Degradation Complex in Streptomyces Hawaiiensis within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg903

b:78.1
occ:1.00
 O2G S:ATP902 2.1 81.4 1.0
O1B S:ATP902 2.1 81.4 1.0
OG1 S:THR556 2.2 83.9 1.0
PB S:ATP902 3.3 81.4 1.0
PG S:ATP902 3.4 81.4 1.0
CB S:THR556 3.4 83.9 1.0
O3B S:ATP902 3.5 81.4 1.0
O3A S:ATP902 4.0 81.4 1.0
O1A S:ATP902 4.1 81.4 1.0
OD2 S:ASP621 4.1 87.8 1.0
OD1 S:ASP621 4.2 87.8 1.0
N S:THR556 4.2 83.9 1.0
O1G S:ATP902 4.3 81.4 1.0
CG2 S:THR556 4.3 83.9 1.0
O3G S:ATP902 4.4 81.4 1.0
CA S:THR556 4.4 83.9 1.0
CG S:ASP621 4.5 87.8 1.0
O2B S:ATP902 4.6 81.4 1.0
PA S:ATP902 4.7 81.4 1.0
NH2 R:ARG709 4.9 66.8 1.0
CB S:LYS555 5.0 82.1 1.0

Reference:

X.Xu, Y.Wang, W.Huang, D.Li, Z.Deng, F.Long. Structural Insights Into the Clp Protein Degradation Machinery. Mbio 03124 2024.
ISSN: ESSN 2150-7511
PubMed: 38501868
DOI: 10.1128/MBIO.00031-24
Page generated: Sat Oct 5 07:48:21 2024

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