Atomistry » Magnesium » PDB 7aom-7b19 » 7aqm
Atomistry »
  Magnesium »
    PDB 7aom-7b19 »
      7aqm »

Magnesium in PDB 7aqm: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)

Enzymatic activity of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)

All present enzymatic activity of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr):
3.2.1.143;

Protein crystallography data

The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr), PDB code: 7aqm was solved by J.G.M.Rack, V.Zorzini, I.Ahel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.70 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.825, 97.613, 107.396, 90, 90, 90
R / Rfree (%) 22.3 / 28.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr) (pdb code 7aqm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr), PDB code: 7aqm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7aqm

Go back to Magnesium Binding Sites List in 7aqm
Magnesium binding site 1 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:58.8
occ:1.00
OD2 A:ASP305 2.0 88.1 1.0
OG1 A:THR62 2.5 55.8 1.0
OD1 A:ASP64 2.5 52.4 1.0
OD1 A:ASP63 2.5 73.7 1.0
O2D A:RVK403 2.9 75.4 1.0
MG A:MG402 3.1 68.9 1.0
CG A:ASP305 3.2 74.0 1.0
CB A:THR62 3.3 60.4 1.0
CG A:ASP64 3.6 48.9 1.0
CG A:ASP63 3.6 65.1 1.0
OD2 A:ASP26 3.9 58.9 1.0
OD1 A:ASP305 3.9 74.2 1.0
OE2 A:GLU33 4.0 127.1 1.0
CG2 A:THR62 4.1 60.4 1.0
CB A:ASP305 4.1 61.6 1.0
OD2 A:ASP63 4.1 71.4 1.0
N A:ASP63 4.1 62.0 1.0
C2D A:RVK403 4.1 76.0 1.0
OD2 A:ASP64 4.2 55.4 1.0
N A:ASP64 4.3 44.9 1.0
O A:GLY101 4.4 73.0 1.0
O3D A:RVK403 4.5 62.4 1.0
CB A:ASP64 4.5 43.1 1.0
OG1 A:THR306 4.5 54.1 1.0
O1D A:RVK403 4.5 95.3 1.0
CA A:THR62 4.6 60.4 1.0
C1 A:RVK403 4.6 91.2 1.0
C A:THR62 4.7 63.2 1.0
C3D A:RVK403 4.8 69.5 1.0
CD A:GLU33 4.8 118.2 1.0
CB A:ASP63 4.8 59.7 1.0
C1D A:RVK403 4.9 85.7 1.0
CA A:ASP63 4.9 60.0 1.0
CG A:ASP26 5.0 51.0 1.0

Magnesium binding site 2 out of 4 in 7aqm

Go back to Magnesium Binding Sites List in 7aqm
Magnesium binding site 2 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:68.9
occ:1.00
OE2 A:GLU33 2.1 127.1 1.0
O3D A:RVK403 2.4 62.4 1.0
OD1 A:ASP305 2.4 74.2 1.0
OD2 A:ASP305 2.6 88.1 1.0
OD1 A:ASP303 2.6 99.7 1.0
O1D A:RVK403 2.8 95.3 1.0
CG A:ASP305 2.8 74.0 1.0
MG A:MG401 3.1 58.8 1.0
C3D A:RVK403 3.2 69.5 1.0
O2D A:RVK403 3.2 75.4 1.0
OG1 A:THR306 3.3 54.1 1.0
CD A:GLU33 3.3 118.2 1.0
C2D A:RVK403 3.4 76.0 1.0
CG A:ASP303 3.6 99.0 1.0
C1 A:RVK403 3.6 91.2 1.0
C1D A:RVK403 3.6 85.7 1.0
OD2 A:ASP303 3.9 98.9 1.0
CG A:GLU33 4.0 106.4 1.0
C4D A:RVK403 4.1 74.5 1.0
OE1 A:GLU33 4.2 118.8 1.0
CB A:ASP305 4.3 61.6 1.0
OD1 A:ASP64 4.4 52.4 1.0
CB A:THR306 4.5 67.6 1.0
O4D A:RVK403 4.5 79.3 1.0
N A:THR306 4.5 60.2 1.0
OD1 A:ASP63 4.9 73.7 1.0
CB A:ASP303 4.9 96.5 1.0
N A:ASP305 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in 7aqm

Go back to Magnesium Binding Sites List in 7aqm
Magnesium binding site 3 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:51.5
occ:1.00
OD1 B:ASP64 2.0 72.0 1.0
OD1 B:ASP63 2.2 83.2 1.0
OG1 B:THR62 2.5 43.5 1.0
OD2 B:ASP305 2.5 56.6 1.0
O2D B:RVK403 2.9 65.8 1.0
CG B:ASP63 3.2 77.0 1.0
CG B:ASP64 3.2 58.3 1.0
CB B:THR62 3.2 53.4 1.0
CG B:ASP305 3.5 54.0 1.0
N B:ASP64 3.6 56.1 1.0
OD2 B:ASP63 3.6 81.9 1.0
N B:ASP63 3.7 62.5 1.0
OD2 B:ASP26 3.9 58.9 1.0
MG B:MG402 4.0 71.1 1.0
OE1 B:GLU33 4.0 91.1 1.0
CB B:ASP64 4.0 53.5 1.0
OD2 B:ASP64 4.1 49.0 1.0
CG2 B:THR62 4.1 56.2 1.0
OD1 B:ASP305 4.2 57.5 1.0
C2D B:RVK403 4.3 61.4 1.0
C B:THR62 4.3 66.6 1.0
CB B:ASP63 4.3 64.2 1.0
CA B:ASP63 4.4 62.5 1.0
O B:GLY101 4.4 62.1 1.0
CA B:THR62 4.4 55.7 1.0
CA B:ASP64 4.4 56.3 1.0
CB B:ASP305 4.4 52.7 1.0
C B:ASP63 4.4 62.6 1.0
OG1 B:THR306 4.7 51.4 1.0
O3D B:RVK403 4.8 68.9 1.0
O B:ARG100 4.9 56.9 1.0
CG B:ASP26 4.9 53.4 1.0

Magnesium binding site 4 out of 4 in 7aqm

Go back to Magnesium Binding Sites List in 7aqm
Magnesium binding site 4 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Alpha-1''-O-Methyl-Adp-Ribose (Meadpr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:71.1
occ:1.00
OD1 B:ASP303 2.4 83.6 1.0
OE1 B:GLU33 2.4 91.1 1.0
O1D B:RVK403 2.5 72.0 1.0
OD1 B:ASP305 2.5 57.5 1.0
O3D B:RVK403 2.6 68.9 1.0
OD2 B:ASP305 3.1 56.6 1.0
CG B:ASP305 3.2 54.0 1.0
O2D B:RVK403 3.3 65.8 1.0
C1 B:RVK403 3.4 69.0 1.0
CG B:ASP303 3.4 81.5 1.0
C3D B:RVK403 3.4 64.9 1.0
OG1 B:THR306 3.4 51.4 1.0
CD B:GLU33 3.5 87.6 1.0
C2D B:RVK403 3.5 61.4 1.0
C1D B:RVK403 3.5 64.0 1.0
OD2 B:ASP303 3.7 79.2 1.0
CG B:GLU33 3.8 83.6 1.0
MG B:MG401 4.0 51.5 1.0
C4D B:RVK403 4.1 66.3 1.0
O4D B:RVK403 4.4 65.4 1.0
CB B:THR306 4.6 59.6 1.0
OE2 B:GLU33 4.6 91.6 1.0
N B:THR306 4.6 59.9 1.0
OD1 B:ASP64 4.6 72.0 1.0
CB B:ASP305 4.7 52.7 1.0
CB B:ASP303 4.7 75.5 1.0
CA B:ASP303 4.9 73.1 1.0

Reference:

J.G.M.Rack, Q.Liu, V.Zorzini, J.Voorneveld, A.Ariza, K.H.Ebrahimi, J.Mccullagh, D.V.Filippov, I.Ahel. Mechanistic Insights Into the Three Steps of Poly(Adp-Ribosylation) Reversal Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Wed Oct 2 10:12:02 2024

Last articles

Mg in 7WIW
Mg in 7WJH
Mg in 7WIX
Mg in 7WIK
Mg in 7WDC
Mg in 7WHW
Mg in 7WGR
Mg in 7WHV
Mg in 7WH5
Mg in 7WCF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy