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
|