Atomistry » Magnesium » PDB 8v4k-8vbg » 8v9r
Atomistry »
  Magnesium »
    PDB 8v4k-8vbg »
      8v9r »

Magnesium in PDB 8v9r: Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx

Enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx:
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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx (pdb code 8v9r). 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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx, PDB code: 8v9r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8v9r

Go back to Magnesium Binding Sites List in 8v9r
Magnesium binding site 1 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:87.2
occ:1.00
 HG1 A:THR126 1.9 90.8 1.0
O2B A:ATP500 2.0 84.9 1.0
O2G A:ATP500 2.1 84.9 1.0
OG1 A:THR126 2.3 90.8 1.0
OD2 A:ASP184 3.1 97.4 1.0
PB A:ATP500 3.3 84.9 1.0
PG A:ATP500 3.4 84.9 1.0
HB A:THR126 3.4 90.8 1.0
CB A:THR126 3.5 90.8 1.0
O1A A:ATP500 3.5 84.9 1.0
O3B A:ATP500 3.6 84.9 1.0
H A:THR126 3.8 90.8 1.0
CG A:ASP184 4.0 97.4 1.0
HG21 A:THR126 4.0 90.8 1.0
OD1 A:ASP184 4.1 97.4 1.0
HH22 B:ARG307 4.1 79.0 1.0
HE2 A:LYS125 4.2 88.7 1.0
HH A:TYR182 4.2 98.0 1.0
O3A A:ATP500 4.3 84.9 1.0
OE2 A:GLU185 4.3 96.5 1.0
HB2 A:LYS125 4.3 88.7 1.0
HH21 B:ARG307 4.3 79.0 1.0
O1G A:ATP500 4.3 84.9 1.0
CG2 A:THR126 4.4 90.8 1.0
OE2 B:GLU216 4.4 85.3 1.0
N A:THR126 4.4 90.8 1.0
O1B A:ATP500 4.4 84.9 1.0
PA A:ATP500 4.4 84.9 1.0
NH2 B:ARG307 4.4 79.0 1.0
O3G A:ATP500 4.5 84.9 1.0
HH21 A:ARG370 4.5 80.7 1.0
CA A:THR126 4.5 90.8 1.0
OE1 B:GLU216 4.6 85.3 1.0
HH22 A:ARG370 4.7 80.7 1.0
HA A:THR126 4.8 90.8 1.0
HG23 A:THR126 4.9 90.8 1.0
CD B:GLU216 4.9 85.3 1.0
NH2 A:ARG370 5.0 80.7 1.0
OH A:TYR182 5.0 98.0 1.0
HG22 A:THR126 5.0 90.8 1.0

Magnesium binding site 2 out of 4 in 8v9r

Go back to Magnesium Binding Sites List in 8v9r
Magnesium binding site 2 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:70.8
occ:1.00
 OG1 B:THR126 2.0 71.2 1.0
O3B B:ATP500 2.1 72.2 1.0
O3A B:ATP500 2.5 72.2 1.0
PB B:ATP500 2.9 72.2 1.0
CB B:THR126 3.3 71.2 1.0
HB B:THR126 3.4 71.2 1.0
H B:THR126 3.5 71.2 1.0
PG B:ATP500 3.5 72.2 1.0
O3G B:ATP500 3.6 72.2 1.0
O2B B:ATP500 3.7 72.2 1.0
OD2 B:ASP184 3.7 72.9 1.0
PA B:ATP500 3.8 72.2 1.0
HG21 B:THR126 4.0 71.2 1.0
O1A B:ATP500 4.0 72.2 1.0
O1G B:ATP500 4.0 72.2 1.0
HB2 B:LYS125 4.0 70.3 1.0
HH22 B:ARG370 4.1 70.8 1.0
O1B B:ATP500 4.1 72.2 1.0
N B:THR126 4.1 71.2 1.0
HH21 B:ARG370 4.1 70.8 1.0
HE2 B:LYS125 4.1 70.3 1.0
HH22 C:ARG307 4.1 68.5 1.0
CG2 B:THR126 4.2 71.2 1.0
HH21 C:ARG307 4.2 68.5 1.0
CA B:THR126 4.3 71.2 1.0
OD1 B:ASP184 4.3 72.9 1.0
NH2 C:ARG307 4.4 68.5 1.0
OE1 C:GLU216 4.4 72.8 1.0
CG B:ASP184 4.4 72.9 1.0
NH2 B:ARG370 4.4 70.8 1.0
OE2 B:GLU185 4.5 72.8 1.0
HG23 B:THR126 4.5 71.2 1.0
O2G B:ATP500 4.5 72.2 1.0
O5' B:ATP500 4.7 72.2 1.0
HA B:THR126 4.7 71.2 1.0
HH B:TYR182 4.7 72.5 1.0
HZ3 C:LYS213 4.8 72.0 1.0
O2A B:ATP500 4.8 72.2 1.0
CB B:LYS125 4.9 70.3 1.0
HB3 B:LYS125 5.0 70.3 1.0

Magnesium binding site 3 out of 4 in 8v9r

Go back to Magnesium Binding Sites List in 8v9r
Magnesium binding site 3 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:71.9
occ:1.00
 O2B C:ATP500 2.0 70.7 1.0
OG1 C:THR126 2.0 68.1 1.0
O2G C:ATP500 2.2 70.7 1.0
OD2 C:ASP184 3.0 70.5 1.0
PB C:ATP500 3.4 70.7 1.0
CB C:THR126 3.4 68.1 1.0
OD1 C:ASP184 3.5 70.5 1.0
PG C:ATP500 3.5 70.7 1.0
CG C:ASP184 3.6 70.5 1.0
O3B C:ATP500 3.7 70.7 1.0
HG21 C:THR126 3.7 68.1 1.0
HB C:THR126 3.7 68.1 1.0
H C:THR126 3.9 68.1 1.0
OE2 C:GLU185 4.0 70.8 1.0
CG2 C:THR126 4.0 68.1 1.0
O1A C:ATP500 4.1 70.7 1.0
HG23 C:THR126 4.2 68.1 1.0
O1G C:ATP500 4.2 70.7 1.0
HH21 D:ARG307 4.2 72.5 1.0
HE2 C:LYS125 4.3 69.0 1.0
O3A C:ATP500 4.4 70.7 1.0
HH22 D:ARG307 4.4 72.5 1.0
N C:THR126 4.4 68.1 1.0
HH C:TYR182 4.4 68.1 1.0
O1B C:ATP500 4.4 70.7 1.0
HZ3 D:LYS213 4.4 74.0 1.0
CA C:THR126 4.4 68.1 1.0
HB2 C:LYS125 4.4 69.0 1.0
HZ2 D:LYS213 4.5 74.0 1.0
NH2 D:ARG307 4.6 72.5 1.0
HH21 C:ARG370 4.6 72.2 1.0
HH22 C:ARG370 4.6 72.2 1.0
HA C:THR126 4.6 68.1 1.0
OE1 D:GLU216 4.6 74.9 1.0
O3G C:ATP500 4.7 70.7 1.0
PA C:ATP500 4.9 70.7 1.0
NZ D:LYS213 4.9 74.0 1.0
HG22 C:THR126 4.9 68.1 1.0
CD C:GLU185 4.9 70.8 1.0
NH2 C:ARG370 4.9 72.2 1.0
HG2 C:GLU185 5.0 70.8 1.0
HG2 D:LYS213 5.0 74.0 1.0

Magnesium binding site 4 out of 4 in 8v9r

Go back to Magnesium Binding Sites List in 8v9r
Magnesium binding site 4 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-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 Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:72.7
occ:1.00
 O2B D:ADP500 2.0 80.0 1.0
HG22 D:THR126 2.1 76.3 1.0
HG21 D:THR126 2.6 76.3 1.0
HB D:THR126 2.7 76.3 1.0
CG2 D:THR126 2.7 76.3 1.0
CB D:THR126 3.2 76.3 1.0
PB D:ADP500 3.4 80.0 1.0
O2A D:ADP500 3.5 80.0 1.0
H D:THR126 3.5 76.3 1.0
HG23 D:THR126 3.6 76.3 1.0
OD2 D:ASP184 3.7 80.4 1.0
O1B D:ADP500 3.8 80.0 1.0
N D:THR126 4.1 76.3 1.0
OG1 D:THR126 4.2 76.3 1.0
HB2 D:LYS125 4.2 75.3 1.0
OD1 D:ASP184 4.2 80.4 1.0
PA D:ADP500 4.2 80.0 1.0
O3A D:ADP500 4.2 80.0 1.0
CA D:THR126 4.3 76.3 1.0
HE2 D:LYS125 4.3 75.3 1.0
CG D:ASP184 4.3 80.4 1.0
O3B D:ADP500 4.5 80.0 1.0
HH22 E:ARG307 4.5 111.1 1.0
O1A D:ADP500 4.5 80.0 1.0
HH21 D:ARG370 4.6 97.9 1.0
OE2 D:GLU185 4.7 85.2 1.0
HG1 D:THR126 4.7 76.3 1.0
HZ3 E:LYS213 4.7 113.9 1.0
HA D:THR126 4.8 76.3 1.0
HH D:TYR182 4.9 72.6 1.0
HZ3 D:LYS125 5.0 75.3 1.0

Reference:

A.Ghanbarpour, R.T.Sauer, J.H.Davis. Cryo-Em Structure of A Fully-Engaged Dhfr-Ssra Substrate and the Aaa+ Clpxp Protease To Be Published.
Page generated: Fri Aug 15 17:31:41 2025

Last articles

Mg in 8XLP
Mg in 8XTS
Mg in 8XW6
Mg in 8XVS
Mg in 8XTU
Mg in 8XTR
Mg in 8XTQ
Mg in 8XLS
Mg in 8XTP
Mg in 8XST
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy