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

Go back to Magnesium Binding Sites List in 9c87
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

Go back to Magnesium Binding Sites List in 9c87
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: Thu Oct 31 22:23:15 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