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Magnesium in PDB 9c87: Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx

Enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx

All present enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx:
1.5.1.3; 3.4.21.92;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx (pdb code 9c87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx, PDB code: 9c87:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9c87

Go back to Magnesium Binding Sites List in 9c87
Magnesium binding site 1 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx


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 A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:128.4
occ:1.00
 O1A A:ATP500 2.0 135.8 1.0
O2B A:ATP500 2.0 135.8 1.0
O3A A:ATP500 2.1 135.8 1.0
OG1 A:THR126 2.3 137.0 1.0
HB A:THR126 2.4 137.0 1.0
PB A:ATP500 2.5 135.8 1.0
PA A:ATP500 2.5 135.8 1.0
H A:THR126 2.9 137.0 1.0
HH21 A:ARG370 2.9 132.4 1.0
CB A:THR126 2.9 137.0 1.0
O3B A:ATP500 3.2 135.8 1.0
O5' A:ATP500 3.3 135.8 1.0
HH22 A:ARG370 3.3 132.4 1.0
NH2 A:ARG370 3.4 132.4 1.0
OE1 B:GLU216 3.5 139.3 1.0
N A:THR126 3.6 137.0 1.0
H5'1 A:ATP500 3.7 135.8 1.0
CA A:THR126 3.8 137.0 1.0
O2A A:ATP500 3.8 135.8 1.0
HH22 B:ARG307 3.8 132.0 1.0
HH21 B:ARG307 3.9 132.0 1.0
O1B A:ATP500 3.9 135.8 1.0
HG21 A:THR126 3.9 137.0 1.0
C5' A:ATP500 4.0 135.8 1.0
NH2 B:ARG307 4.0 132.0 1.0
CG2 A:THR126 4.0 137.0 1.0
HB2 A:LYS125 4.0 137.0 1.0
H5'2 A:ATP500 4.2 135.8 1.0
CD B:GLU216 4.3 139.3 1.0
H A:LEU127 4.4 136.3 1.0
O2G A:ATP500 4.4 135.8 1.0
OE2 B:GLU216 4.5 139.3 1.0
HA A:THR126 4.5 137.0 1.0
HG22 A:THR126 4.5 137.0 1.0
OD2 A:ASP184 4.5 149.6 1.0
PG A:ATP500 4.5 135.8 1.0
HE2 A:LYS125 4.6 137.0 1.0
CZ A:ARG370 4.7 132.4 1.0
HG23 A:THR126 4.7 137.0 1.0
C A:LYS125 4.8 137.0 1.0
CZ B:ARG307 4.8 132.0 1.0
C A:THR126 4.8 137.0 1.0
H A:LYS125 4.8 137.0 1.0
HE A:ARG370 4.8 132.4 1.0
N A:LEU127 4.9 136.3 1.0
CB A:LYS125 4.9 137.0 1.0
HH A:TYR182 4.9 145.4 1.0
HZ3 A:LYS125 5.0 137.0 1.0

Magnesium binding site 2 out of 4 in 9c87

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Magnesium binding site 2 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx


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 A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:117.6
occ:1.00
 O1A B:ATP500 2.0 122.5 1.0
O2B B:ATP500 2.1 122.5 1.0
HB B:THR126 2.1 123.3 1.0
O3A B:ATP500 2.2 122.5 1.0
OG1 B:THR126 2.4 123.3 1.0
PB B:ATP500 2.5 122.5 1.0
PA B:ATP500 2.6 122.5 1.0
CB B:THR126 2.7 123.3 1.0
H B:THR126 2.8 123.3 1.0
O3B B:ATP500 2.9 122.5 1.0
HH22 B:ARG370 3.1 120.8 1.0
HH21 B:ARG370 3.1 120.8 1.0
HG1 B:THR126 3.3 123.3 1.0
O5' B:ATP500 3.4 122.5 1.0
NH2 B:ARG370 3.4 120.8 1.0
N B:THR126 3.5 123.3 1.0
H5'1 B:ATP500 3.5 122.5 1.0
CA B:THR126 3.7 123.3 1.0
OE2 C:GLU216 3.7 126.6 1.0
HG21 B:THR126 3.7 123.3 1.0
OE1 C:GLU216 3.8 126.6 1.0
CG2 B:THR126 3.8 123.3 1.0
HH12 C:ARG307 3.8 120.4 1.0
O1B B:ATP500 3.9 122.5 1.0
C5' B:ATP500 3.9 122.5 1.0
O2A B:ATP500 3.9 122.5 1.0
O2G B:ATP500 3.9 122.5 1.0
PG B:ATP500 4.0 122.5 1.0
H B:LEU127 4.0 123.9 1.0
HH22 C:ARG307 4.1 120.4 1.0
CD C:GLU216 4.2 126.6 1.0
H5'2 B:ATP500 4.2 122.5 1.0
HG22 B:THR126 4.2 123.3 1.0
HB2 B:LYS125 4.3 119.0 1.0
HA B:THR126 4.4 123.3 1.0
C B:THR126 4.4 123.3 1.0
N B:LEU127 4.4 123.9 1.0
O3G B:ATP500 4.5 122.5 1.0
HG23 B:THR126 4.5 123.3 1.0
NH1 C:ARG307 4.6 120.4 1.0
H B:LYS125 4.7 119.0 1.0
CZ B:ARG370 4.7 120.8 1.0
OD2 B:ASP184 4.7 124.3 1.0
C B:LYS125 4.8 119.0 1.0
NH2 C:ARG307 4.8 120.4 1.0
N B:LYS125 4.9 119.0 1.0
HE2 B:LYS125 5.0 119.0 1.0

Magnesium binding site 3 out of 4 in 9c87

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Magnesium binding site 3 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx


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 A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:123.0
occ:1.00
 O2G C:ATP500 2.1 121.5 1.0
O3B C:ATP500 2.1 121.5 1.0
O2B C:ATP500 2.1 121.5 1.0
HG1 C:THR126 2.3 119.4 1.0
PB C:ATP500 2.5 121.5 1.0
PG C:ATP500 2.6 121.5 1.0
OG1 C:THR126 2.7 119.4 1.0
HH22 D:ARG307 2.9 125.6 1.0
HH21 C:ARG370 3.0 119.3 1.0
O3A C:ATP500 3.0 121.5 1.0
NH2 D:ARG307 3.3 125.6 1.0
HH21 D:ARG307 3.3 125.6 1.0
O3G C:ATP500 3.3 121.5 1.0
HH22 C:ARG370 3.4 119.3 1.0
NH2 C:ARG370 3.5 119.3 1.0
OE1 D:GLU216 3.6 129.6 1.0
OE2 C:GLU185 3.7 127.5 1.0
O1G C:ATP500 3.8 121.5 1.0
O1A C:ATP500 3.8 121.5 1.0
O1B C:ATP500 3.9 121.5 1.0
CB C:THR126 3.9 119.4 1.0
HB C:THR126 4.0 119.4 1.0
H C:THR126 4.0 119.4 1.0
PA C:ATP500 4.1 121.5 1.0
OD2 C:ASP184 4.1 121.1 1.0
CZ D:ARG307 4.3 125.6 1.0
OE2 D:GLU216 4.4 129.6 1.0
HE2 C:LYS125 4.4 121.0 1.0
CD D:GLU216 4.4 129.6 1.0
HG21 C:THR126 4.5 119.4 1.0
OD1 C:ASP184 4.5 121.1 1.0
HH12 D:ARG307 4.5 125.6 1.0
HB2 C:LYS125 4.5 121.0 1.0
CG C:ASP184 4.7 121.1 1.0
N C:THR126 4.7 119.4 1.0
CZ C:ARG370 4.7 119.3 1.0
NH1 D:ARG307 4.8 125.6 1.0
CG2 C:THR126 4.8 119.4 1.0
HZ1 C:LYS125 4.8 121.0 1.0
CD C:GLU185 4.9 127.5 1.0
O5' C:ATP500 4.9 121.5 1.0
HZ1 D:LYS213 4.9 130.0 1.0
HZ3 C:LYS125 4.9 121.0 1.0
CA C:THR126 5.0 119.4 1.0
HE C:ARG370 5.0 119.3 1.0

Magnesium binding site 4 out of 4 in 9c87

Go back to Magnesium Binding Sites List in 9c87
Magnesium binding site 4 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx


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 A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:138.2
occ:1.00
 HG1 D:THR126 1.8 134.8 1.0
O2B D:ADP500 2.0 136.8 1.0
O2A D:ADP500 2.1 136.8 1.0
O1B D:ADP500 2.4 136.8 1.0
OG1 D:THR126 2.5 134.8 1.0
PB D:ADP500 2.5 136.8 1.0
H D:THR126 2.6 134.8 1.0
PA D:ADP500 2.6 136.8 1.0
HB D:THR126 2.8 134.8 1.0
O3A D:ADP500 2.9 136.8 1.0
O1A D:ADP500 2.9 136.8 1.0
CB D:THR126 3.1 134.8 1.0
N D:THR126 3.4 134.8 1.0
HB2 D:LYS125 3.6 131.3 1.0
HE2 D:LYS125 3.8 131.3 1.0
HH21 D:ARG370 3.8 146.3 1.0
CA D:THR126 3.9 134.8 1.0
H D:LYS125 4.0 131.3 1.0
O3B D:ADP500 4.0 136.8 1.0
O5' D:ADP500 4.2 136.8 1.0
N D:LYS125 4.4 131.3 1.0
CG2 D:THR126 4.4 134.8 1.0
HG21 D:THR126 4.4 134.8 1.0
CB D:LYS125 4.5 131.3 1.0
C D:LYS125 4.5 131.3 1.0
NH2 D:ARG370 4.5 146.3 1.0
HH22 D:ARG370 4.5 146.3 1.0
HA D:THR126 4.6 134.8 1.0
OD2 D:ASP184 4.6 140.2 1.0
H D:LEU127 4.6 131.7 1.0
CA D:LYS125 4.7 131.3 1.0
H D:GLY124 4.7 132.9 1.0
HH22 E:ARG307 4.7 155.1 1.0
CE D:LYS125 4.7 131.3 1.0
C D:THR126 4.8 134.8 1.0
H5'1 D:ADP500 4.9 136.8 1.0
HZ3 D:LYS125 4.9 131.3 1.0
HG22 D:THR126 5.0 134.8 1.0
C5' D:ADP500 5.0 136.8 1.0

Reference:

A.Ghanbarpour, R.T.Sauer, J.H.Davis. Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Linear-Degron Dhfr-Ssra Substrate Bound with Mtx To Be Published.
Page generated: Fri Aug 15 23:44:21 2025

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