Magnesium in PDB 6hh5: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm
Protein crystallography data
The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm, PDB code: 6hh5
was solved by
A.Ariza,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.46 /
1.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.869,
98.178,
105.554,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
21.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm
(pdb code 6hh5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm, PDB code: 6hh5:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6hh5
Go back to
Magnesium Binding Sites List in 6hh5
Magnesium binding site 1 out
of 2 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm
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 Adp-Hpm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:62.2
occ:1.00
|
O
|
A:HOH518
|
2.2
|
49.7
|
1.0
|
OG1
|
A:THR62
|
2.2
|
53.0
|
1.0
|
O
|
A:HOH540
|
2.2
|
50.7
|
1.0
|
OD1
|
A:ASP64
|
2.2
|
55.3
|
1.0
|
OD2
|
A:ASP305
|
2.2
|
66.1
|
0.6
|
OD2
|
A:ASP305
|
2.2
|
61.6
|
0.4
|
OD1
|
A:ASP63
|
2.3
|
58.1
|
1.0
|
CG
|
A:ASP305
|
3.0
|
65.0
|
0.6
|
CG
|
A:ASP305
|
3.2
|
60.0
|
0.4
|
CB
|
A:THR62
|
3.2
|
52.5
|
1.0
|
CB
|
A:ASP305
|
3.4
|
57.6
|
0.4
|
CG
|
A:ASP64
|
3.5
|
52.8
|
1.0
|
CG
|
A:ASP63
|
3.5
|
57.4
|
1.0
|
CB
|
A:ASP305
|
3.8
|
60.2
|
0.6
|
OD1
|
A:ASP305
|
3.8
|
70.6
|
0.6
|
CG2
|
A:THR62
|
3.9
|
53.5
|
1.0
|
OD1
|
A:ASP26
|
3.9
|
51.0
|
1.0
|
C1N
|
A:A3R402
|
3.9
|
70.6
|
1.0
|
N
|
A:ASP63
|
4.1
|
52.9
|
1.0
|
N
|
A:ASP64
|
4.1
|
51.3
|
1.0
|
OD2
|
A:ASP63
|
4.1
|
57.6
|
1.0
|
CB
|
A:ASP64
|
4.3
|
50.0
|
1.0
|
C2N
|
A:A3R402
|
4.3
|
72.3
|
1.0
|
OD2
|
A:ASP64
|
4.3
|
53.6
|
1.0
|
OD1
|
A:ASP305
|
4.4
|
60.2
|
0.4
|
CA
|
A:THR62
|
4.4
|
50.9
|
1.0
|
OG1
|
A:THR306
|
4.5
|
56.9
|
1.0
|
C
|
A:THR62
|
4.6
|
51.0
|
1.0
|
O
|
A:GLY101
|
4.6
|
59.2
|
1.0
|
CB
|
A:ASP63
|
4.7
|
56.3
|
1.0
|
N4N
|
A:A3R402
|
4.8
|
68.8
|
1.0
|
CA
|
A:ASP63
|
4.8
|
53.7
|
1.0
|
CA
|
A:ASP64
|
4.8
|
49.4
|
1.0
|
OE1
|
A:GLU33
|
4.8
|
75.9
|
1.0
|
CA
|
A:ASP305
|
4.9
|
57.6
|
0.4
|
C
|
A:ASP63
|
4.9
|
51.6
|
1.0
|
CG
|
A:ASP26
|
4.9
|
48.4
|
1.0
|
C3N
|
A:A3R402
|
5.0
|
69.4
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6hh5
Go back to
Magnesium Binding Sites List in 6hh5
Magnesium binding site 2 out
of 2 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Hpm
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 Adp-Hpm within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:44.5
occ:1.00
|
O
|
B:HOH535
|
2.2
|
45.7
|
1.0
|
OG1
|
B:THR62
|
2.2
|
41.5
|
1.0
|
O
|
B:HOH604
|
2.2
|
39.3
|
1.0
|
OD1
|
B:ASP64
|
2.2
|
40.8
|
1.0
|
OD2
|
B:ASP305
|
2.2
|
46.0
|
0.4
|
OD2
|
B:ASP305
|
2.3
|
50.5
|
0.6
|
OD1
|
B:ASP63
|
2.3
|
43.6
|
1.0
|
CG
|
B:ASP305
|
2.8
|
44.5
|
0.4
|
CB
|
B:THR62
|
3.2
|
41.1
|
1.0
|
CG
|
B:ASP305
|
3.2
|
50.1
|
0.6
|
CG
|
B:ASP64
|
3.4
|
41.0
|
1.0
|
OD1
|
B:ASP305
|
3.5
|
43.8
|
0.4
|
CG
|
B:ASP63
|
3.5
|
43.5
|
1.0
|
CB
|
B:ASP305
|
3.6
|
44.0
|
0.4
|
C1N
|
B:A3R402
|
3.7
|
49.3
|
1.0
|
CG2
|
B:THR62
|
3.9
|
42.4
|
1.0
|
CB
|
B:ASP305
|
4.0
|
46.8
|
0.6
|
N4N
|
B:A3R402
|
4.0
|
47.4
|
1.0
|
OD1
|
B:ASP305
|
4.0
|
55.5
|
0.6
|
N
|
B:ASP63
|
4.1
|
41.7
|
1.0
|
OD1
|
B:ASP26
|
4.1
|
39.6
|
1.0
|
N
|
B:ASP64
|
4.1
|
39.3
|
1.0
|
OE1
|
B:GLU33
|
4.1
|
53.0
|
0.5
|
OD2
|
B:ASP63
|
4.2
|
43.3
|
1.0
|
CB
|
B:ASP64
|
4.3
|
40.0
|
1.0
|
OD2
|
B:ASP64
|
4.3
|
40.8
|
1.0
|
OG1
|
B:THR306
|
4.4
|
42.2
|
1.0
|
CA
|
B:THR62
|
4.4
|
40.8
|
1.0
|
C
|
B:THR62
|
4.6
|
40.8
|
1.0
|
O
|
B:HOH612
|
4.6
|
56.0
|
1.0
|
O
|
B:GLY101
|
4.6
|
44.2
|
1.0
|
CB
|
B:ASP63
|
4.7
|
42.9
|
1.0
|
CA
|
B:ASP63
|
4.8
|
41.7
|
1.0
|
CA
|
B:ASP64
|
4.8
|
40.3
|
1.0
|
C
|
B:ASP63
|
4.9
|
40.8
|
1.0
|
O
|
B:HOH503
|
5.0
|
45.7
|
1.0
|
CA
|
B:ASP305
|
5.0
|
43.2
|
0.4
|
|
Reference:
J.G.M.Rack,
A.Ariza,
B.S.Drown,
C.Henfrey,
E.Bartlett,
T.Shirai,
P.J.Hergenrother,
I.Ahel.
(Adp-Ribosyl)Hydrolases: Structural Basis For Differential Substrate Recognition and Inhibition. Cell Chem Biol V. 25 1533 2018.
ISSN: ESSN 2451-9448
PubMed: 30472116
DOI: 10.1016/J.CHEMBIOL.2018.11.001
Page generated: Mon Dec 14 22:49:49 2020
|