Magnesium in PDB 8xon: 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 8xon). 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: 8xon:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8xon

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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
S:Mg903

b:156.4
occ:1.00
 O3B S:ATP901 2.1 150.9 1.0
O2G S:ATP901 2.2 150.9 1.0
OG1 S:THR219 2.4 156.8 1.0
PG S:ATP901 2.6 150.9 1.0
O1B S:ATP901 3.0 150.9 1.0
PB S:ATP901 3.0 150.9 1.0
O3G S:ATP901 3.1 150.9 1.0
CB S:THR219 3.7 156.8 1.0
O3A S:ATP901 3.8 150.9 1.0
O1A S:ATP901 3.9 150.9 1.0
O1G S:ATP901 3.9 150.9 1.0
O2B S:ATP901 4.3 150.9 1.0
PA S:ATP901 4.3 150.9 1.0
N S:THR219 4.4 156.8 1.0
O2A S:ATP901 4.5 150.9 1.0
CG2 S:THR219 4.6 156.8 1.0
CA S:THR219 4.7 156.8 1.0
NH2 R:ARG337 4.7 134.6 1.0
OD1 S:ASP283 4.8 184.6 1.0

Magnesium binding site 2 out of 7 in 8xon

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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
S:Mg904

b:94.0
occ:1.00
 O2B S:ATP902 2.1 76.7 1.0
O2G S:ATP902 2.1 76.7 1.0
OG1 S:THR556 2.1 97.0 1.0
CB S:THR556 3.2 97.0 1.0
PB S:ATP902 3.3 76.7 1.0
PG S:ATP902 3.3 76.7 1.0
O3B S:ATP902 3.4 76.7 1.0
O1A S:ATP902 3.8 76.7 1.0
O3A S:ATP902 4.1 76.7 1.0
CG2 S:THR556 4.2 97.0 1.0
N S:THR556 4.2 97.0 1.0
NH2 R:ARG709 4.2 91.8 1.0
O1G S:ATP902 4.2 76.7 1.0
CA S:THR556 4.3 97.0 1.0
O3G S:ATP902 4.4 76.7 1.0
O1B S:ATP902 4.4 76.7 1.0
PA S:ATP902 4.5 76.7 1.0
NH2 S:ARG768 4.7 95.0 1.0

Magnesium binding site 3 out of 7 in 8xon

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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
R:Mg903

b:112.0
occ:1.00
 O2G R:ATP901 2.1 106.1 1.0
OG1 R:THR219 2.1 106.6 1.0
O1B R:ATP901 2.2 106.1 1.0
PB R:ATP901 3.4 106.1 1.0
PG R:ATP901 3.5 106.1 1.0
CB R:THR219 3.5 106.6 1.0
O3B R:ATP901 3.6 106.1 1.0
OD1 R:ASP283 3.7 124.7 1.0
N R:THR219 4.2 106.6 1.0
CG2 R:THR219 4.3 106.6 1.0
OD2 R:ASP283 4.4 124.7 1.0
O1G R:ATP901 4.4 106.1 1.0
O3A R:ATP901 4.4 106.1 1.0
O3G R:ATP901 4.4 106.1 1.0
CA R:THR219 4.4 106.6 1.0
NH2 Q:ARG337 4.4 102.8 1.0
CG R:ASP283 4.5 124.7 1.0
O2B R:ATP901 4.5 106.1 1.0
O1A R:ATP901 4.5 106.1 1.0
PA R:ATP901 4.9 106.1 1.0
O2A R:ATP901 5.0 106.1 1.0

Magnesium binding site 4 out of 7 in 8xon

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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
R:Mg904

b:78.6
occ:1.00
 O2G R:ATP902 2.1 86.2 1.0
O1B R:ATP902 2.1 86.2 1.0
OG1 R:THR556 2.2 84.9 1.0
CB R:THR556 3.3 84.9 1.0
PB R:ATP902 3.3 86.2 1.0
PG R:ATP902 3.4 86.2 1.0
O3B R:ATP902 3.6 86.2 1.0
OD1 R:ASP621 3.6 83.8 1.0
O3A R:ATP902 4.1 86.2 1.0
N R:THR556 4.1 84.9 1.0
OD2 R:ASP621 4.1 83.8 1.0
O1A R:ATP902 4.2 86.2 1.0
CG2 R:THR556 4.2 84.9 1.0
CG R:ASP621 4.3 83.8 1.0
NH2 Q:ARG709 4.3 113.5 1.0
O3G R:ATP902 4.3 86.2 1.0
CA R:THR556 4.3 84.9 1.0
O1G R:ATP902 4.4 86.2 1.0
O2B R:ATP902 4.6 86.2 1.0
PA R:ATP902 4.7 86.2 1.0
NH2 R:ARG768 4.8 87.2 1.0

Magnesium binding site 5 out of 7 in 8xon

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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
Q:Mg903

b:83.3
occ:1.00
 O2G Q:ATP902 2.1 88.1 1.0
OG1 Q:THR556 2.1 81.2 1.0
O1B Q:ATP902 2.3 88.1 1.0
CB Q:THR556 3.3 81.2 1.0
PG Q:ATP902 3.3 88.1 1.0
PB Q:ATP902 3.4 88.1 1.0
O3B Q:ATP902 3.6 88.1 1.0
O1A Q:ATP902 3.7 88.1 1.0
OD1 Q:ASP621 3.8 85.3 1.0
OD2 Q:ASP621 4.0 85.3 1.0
O1G Q:ATP902 4.0 88.1 1.0
O3A Q:ATP902 4.0 88.1 1.0
N Q:THR556 4.0 81.2 1.0
CA Q:THR556 4.3 81.2 1.0
CG2 Q:THR556 4.3 81.2 1.0
NH2 P:ARG709 4.3 96.1 1.0
CG Q:ASP621 4.3 85.3 1.0
PA Q:ATP902 4.4 88.1 1.0
O3G Q:ATP902 4.5 88.1 1.0
O2B Q:ATP902 4.7 88.1 1.0
NH2 Q:ARG768 4.9 92.9 1.0
O2A Q:ATP902 5.0 88.1 1.0
CB Q:LYS555 5.0 81.3 1.0

Magnesium binding site 6 out of 7 in 8xon

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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
P:Mg903

b:134.9
occ:1.00
 O1B P:ATP902 2.0 139.7 1.0
O2G P:ATP902 2.1 139.7 1.0
PB P:ATP902 2.5 139.7 1.0
OG1 P:THR556 2.6 128.7 1.0
PG P:ATP902 2.6 139.7 1.0
O3B P:ATP902 2.6 139.7 1.0
O3A P:ATP902 2.8 139.7 1.0
O1A P:ATP902 2.8 139.7 1.0
O1G P:ATP902 2.9 139.7 1.0
PA P:ATP902 3.3 139.7 1.0
CB P:THR556 3.4 128.7 1.0
NH2 P:ARG768 3.9 160.0 1.0
O2A P:ATP902 3.9 139.7 1.0
O2B P:ATP902 4.0 139.7 1.0
O3G P:ATP902 4.1 139.7 1.0
N P:THR556 4.1 128.7 1.0
CA P:THR556 4.4 128.7 1.0
CG2 P:THR556 4.4 128.7 1.0
O5' P:ATP902 4.7 139.7 1.0
CZ P:ARG768 4.8 160.0 1.0

Magnesium binding site 7 out of 7 in 8xon

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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
T:Mg903

b:166.5
occ:1.00
 O1B T:ATP902 2.1 172.8 1.0
O3B T:ATP902 2.1 172.8 1.0
OG1 T:THR556 2.4 182.8 1.0
PB T:ATP902 2.5 172.8 1.0
O1G T:ATP902 2.9 172.8 1.0
PG T:ATP902 3.0 172.8 1.0
O3A T:ATP902 3.4 172.8 1.0
CB T:THR556 3.6 182.8 1.0
O1A T:ATP902 3.7 172.8 1.0
O2G T:ATP902 3.7 172.8 1.0
O2B T:ATP902 3.8 172.8 1.0
NH2 S:ARG709 4.0 136.3 1.0
PA T:ATP902 4.1 172.8 1.0
CG2 T:THR556 4.2 182.8 1.0
O3G T:ATP902 4.3 172.8 1.0
O2A T:ATP902 4.6 172.8 1.0
CA T:THR556 4.8 182.8 1.0
N T:THR556 4.9 182.8 1.0
O T:GLY554 4.9 180.0 1.0
NH2 T:ARG768 4.9 154.3 1.0
CB T:LYS555 5.0 181.8 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 07:48:20 2024

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