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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Go back to Magnesium Binding Sites List in 8xoo
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy