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

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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

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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

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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

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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: Sun Jul 11 15:42:18 2021

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