Magnesium in PDB 7zeh: Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
Enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
All present enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE:
3.1.3.5;
3.1.3.91;
Protein crystallography data
The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE, PDB code: 7zeh
was solved by
D.Kubacka,
M.Kozarski,
M.R.Baranowski,
R.Wojcik,
J.Jemielity,
J.Kowalska,
J.Basquin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.08 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.59,
80.89,
83.17,
82.22,
72.46,
68.2
|
R / Rfree (%)
|
18.8 /
22
|
Other elements in 7zeh:
The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
(pdb code 7zeh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE, PDB code: 7zeh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7zeh
Go back to
Magnesium Binding Sites List in 7zeh
Magnesium binding site 1 out
of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:17.0
occ:1.00
|
OD2
|
A:ASP41
|
2.0
|
19.7
|
1.0
|
O
|
A:HOH541
|
2.0
|
17.2
|
1.0
|
OD1
|
A:ASP230
|
2.0
|
18.9
|
1.0
|
O
|
A:ASP43
|
2.1
|
20.1
|
1.0
|
O
|
A:HOH522
|
2.1
|
19.6
|
1.0
|
O
|
A:HOH582
|
2.1
|
21.2
|
1.0
|
CG
|
A:ASP41
|
3.0
|
18.3
|
1.0
|
CG
|
A:ASP230
|
3.0
|
19.4
|
1.0
|
C
|
A:ASP43
|
3.3
|
19.9
|
1.0
|
OD2
|
A:ASP230
|
3.3
|
21.2
|
1.0
|
OD1
|
A:ASP41
|
3.4
|
20.3
|
1.0
|
CA
|
A:ASP43
|
4.0
|
19.5
|
1.0
|
OD2
|
A:ASP234
|
4.0
|
21.0
|
1.0
|
N
|
A:ASP43
|
4.1
|
18.4
|
1.0
|
OG1
|
A:THR45
|
4.1
|
16.9
|
1.0
|
CB
|
A:ASP43
|
4.1
|
21.5
|
1.0
|
OG
|
A:SER231
|
4.2
|
21.9
|
0.6
|
O
|
A:HOH645
|
4.3
|
23.4
|
1.0
|
CB
|
A:ASP41
|
4.3
|
17.8
|
1.0
|
N
|
A:MET44
|
4.3
|
18.7
|
1.0
|
O1
|
A:PO4410
|
4.4
|
22.7
|
1.0
|
CB
|
A:ASP230
|
4.4
|
16.9
|
1.0
|
CB
|
A:MET44
|
4.4
|
18.4
|
1.0
|
O
|
A:HOH742
|
4.4
|
32.7
|
1.0
|
N
|
A:THR45
|
4.5
|
16.7
|
1.0
|
C
|
A:MET44
|
4.6
|
18.1
|
1.0
|
CA
|
A:MET44
|
4.6
|
18.4
|
1.0
|
C
|
A:PHE42
|
4.7
|
18.1
|
1.0
|
N
|
A:ASP230
|
4.7
|
16.6
|
1.0
|
CB
|
A:THR45
|
4.9
|
15.9
|
1.0
|
CG
|
A:MET44
|
4.9
|
20.1
|
1.0
|
CG
|
A:ASP234
|
4.9
|
20.3
|
1.0
|
O
|
A:PHE42
|
5.0
|
18.0
|
1.0
|
OD1
|
A:ASP234
|
5.0
|
20.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7zeh
Go back to
Magnesium Binding Sites List in 7zeh
Magnesium binding site 2 out
of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg408
b:17.3
occ:1.00
|
OD2
|
B:ASP41
|
2.0
|
18.8
|
1.0
|
O
|
B:HOH544
|
2.0
|
15.8
|
1.0
|
O
|
B:ASP43
|
2.1
|
19.5
|
1.0
|
OD1
|
B:ASP230
|
2.1
|
18.3
|
1.0
|
O
|
B:HOH582
|
2.1
|
19.7
|
1.0
|
O
|
B:HOH526
|
2.1
|
18.4
|
1.0
|
CG
|
B:ASP41
|
3.0
|
18.2
|
1.0
|
CG
|
B:ASP230
|
3.0
|
18.7
|
1.0
|
C
|
B:ASP43
|
3.2
|
18.5
|
1.0
|
OD1
|
B:ASP41
|
3.4
|
18.5
|
1.0
|
OD2
|
B:ASP230
|
3.4
|
20.6
|
1.0
|
CA
|
B:ASP43
|
3.9
|
19.4
|
1.0
|
N
|
B:ASP43
|
4.0
|
19.1
|
1.0
|
CB
|
B:ASP43
|
4.1
|
20.1
|
1.0
|
OD2
|
B:ASP234
|
4.1
|
18.8
|
1.0
|
OG1
|
B:THR45
|
4.1
|
16.5
|
1.0
|
O
|
B:HOH643
|
4.3
|
25.2
|
1.0
|
CB
|
B:ASP41
|
4.3
|
17.7
|
1.0
|
N
|
B:MET44
|
4.3
|
17.4
|
1.0
|
O4
|
B:PO4409
|
4.3
|
22.4
|
1.0
|
CB
|
B:MET44
|
4.4
|
17.6
|
1.0
|
CB
|
B:ASP230
|
4.4
|
17.5
|
1.0
|
O
|
B:HOH734
|
4.4
|
32.4
|
1.0
|
OG
|
B:SER231
|
4.4
|
19.2
|
0.5
|
N
|
B:THR45
|
4.5
|
18.2
|
1.0
|
CA
|
B:MET44
|
4.6
|
16.8
|
1.0
|
C
|
B:MET44
|
4.6
|
16.7
|
1.0
|
C
|
B:PHE42
|
4.6
|
18.2
|
1.0
|
N
|
B:ASP230
|
4.8
|
16.3
|
1.0
|
CG
|
B:MET44
|
4.9
|
20.5
|
1.0
|
CB
|
B:THR45
|
4.9
|
16.8
|
1.0
|
CG
|
B:ASP234
|
5.0
|
17.9
|
1.0
|
NZ
|
B:LYS205
|
5.0
|
20.5
|
1.0
|
O
|
B:PHE42
|
5.0
|
18.9
|
1.0
|
OD1
|
B:ASP234
|
5.0
|
18.8
|
1.0
|
CA
|
B:ASP230
|
5.0
|
16.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7zeh
Go back to
Magnesium Binding Sites List in 7zeh
Magnesium binding site 3 out
of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg413
b:14.0
occ:1.00
|
O
|
C:HOH576
|
2.0
|
17.2
|
1.0
|
O
|
C:HOH542
|
2.0
|
15.9
|
1.0
|
OD2
|
C:ASP41
|
2.0
|
17.1
|
1.0
|
O
|
C:ASP43
|
2.1
|
16.7
|
1.0
|
OD1
|
C:ASP230
|
2.1
|
17.4
|
1.0
|
O
|
C:HOH527
|
2.1
|
18.5
|
1.0
|
CG
|
C:ASP41
|
3.0
|
16.7
|
1.0
|
CG
|
C:ASP230
|
3.1
|
15.9
|
1.0
|
C
|
C:ASP43
|
3.2
|
15.9
|
1.0
|
OD2
|
C:ASP230
|
3.4
|
17.1
|
1.0
|
OD1
|
C:ASP41
|
3.4
|
17.8
|
1.0
|
CA
|
C:ASP43
|
4.0
|
17.0
|
1.0
|
OD2
|
C:ASP234
|
4.0
|
17.4
|
1.0
|
N
|
C:ASP43
|
4.1
|
16.5
|
1.0
|
CB
|
C:ASP43
|
4.1
|
18.0
|
1.0
|
OG1
|
C:THR45
|
4.1
|
17.3
|
1.0
|
O
|
C:HOH671
|
4.1
|
39.8
|
1.0
|
O
|
C:HOH732
|
4.3
|
24.8
|
1.0
|
O
|
C:HOH612
|
4.3
|
25.2
|
1.0
|
CB
|
C:ASP41
|
4.3
|
17.2
|
1.0
|
O2
|
C:PO4414
|
4.3
|
28.1
|
1.0
|
N
|
C:MET44
|
4.3
|
16.5
|
1.0
|
OG
|
C:SER231
|
4.3
|
16.2
|
0.5
|
CB
|
C:MET44
|
4.4
|
19.1
|
1.0
|
CB
|
C:ASP230
|
4.4
|
16.0
|
1.0
|
N
|
C:THR45
|
4.6
|
16.9
|
1.0
|
CA
|
C:MET44
|
4.6
|
16.9
|
1.0
|
C
|
C:MET44
|
4.6
|
17.2
|
1.0
|
C
|
C:PHE42
|
4.7
|
18.1
|
1.0
|
N
|
C:ASP230
|
4.7
|
14.8
|
1.0
|
CG
|
C:MET44
|
4.9
|
21.8
|
1.0
|
CB
|
C:THR45
|
4.9
|
16.8
|
1.0
|
CG
|
C:ASP234
|
4.9
|
17.5
|
1.0
|
O
|
C:HOH645
|
4.9
|
20.3
|
1.0
|
OD1
|
C:ASP234
|
4.9
|
19.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7zeh
Go back to
Magnesium Binding Sites List in 7zeh
Magnesium binding site 4 out
of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg411
b:14.1
occ:1.00
|
O
|
D:HOH2642
|
1.9
|
17.8
|
1.0
|
OD2
|
D:ASP41
|
2.0
|
17.9
|
1.0
|
O
|
D:HOH2628
|
2.0
|
15.2
|
1.0
|
OD1
|
D:ASP230
|
2.0
|
18.6
|
1.0
|
O
|
D:HOH2634
|
2.1
|
18.3
|
1.0
|
O
|
D:ASP43
|
2.1
|
18.3
|
1.0
|
CG
|
D:ASP41
|
3.0
|
16.4
|
1.0
|
CG
|
D:ASP230
|
3.0
|
18.3
|
1.0
|
C
|
D:ASP43
|
3.3
|
18.7
|
1.0
|
OD2
|
D:ASP230
|
3.3
|
18.3
|
1.0
|
OD1
|
D:ASP41
|
3.4
|
18.1
|
1.0
|
OD2
|
D:ASP234
|
4.0
|
18.2
|
1.0
|
CA
|
D:ASP43
|
4.0
|
19.1
|
1.0
|
CB
|
D:ASP43
|
4.1
|
20.6
|
1.0
|
OG1
|
D:THR45
|
4.1
|
16.8
|
1.0
|
N
|
D:ASP43
|
4.1
|
18.4
|
1.0
|
OG
|
D:SER231
|
4.2
|
17.8
|
0.5
|
O
|
D:HOH2832
|
4.3
|
27.4
|
1.0
|
O
|
D:HOH2750
|
4.3
|
24.4
|
1.0
|
CB
|
D:ASP41
|
4.3
|
17.7
|
1.0
|
O4
|
D:PO4412
|
4.3
|
26.3
|
1.0
|
N
|
D:MET44
|
4.3
|
17.6
|
1.0
|
CB
|
D:MET44
|
4.3
|
19.5
|
1.0
|
CB
|
D:ASP230
|
4.4
|
17.1
|
1.0
|
N
|
D:THR45
|
4.5
|
17.5
|
1.0
|
CA
|
D:MET44
|
4.6
|
17.9
|
1.0
|
C
|
D:MET44
|
4.6
|
17.7
|
1.0
|
C
|
D:PHE42
|
4.7
|
18.1
|
1.0
|
N
|
D:ASP230
|
4.7
|
16.9
|
1.0
|
CG
|
D:MET44
|
4.9
|
21.1
|
1.0
|
CG
|
D:ASP234
|
4.9
|
17.9
|
1.0
|
OD1
|
D:ASP234
|
4.9
|
19.2
|
1.0
|
CB
|
D:THR45
|
4.9
|
16.7
|
1.0
|
O
|
D:PHE42
|
5.0
|
18.1
|
1.0
|
NZ
|
D:LYS205
|
5.0
|
20.7
|
1.0
|
O
|
D:HOH2720
|
5.0
|
21.7
|
1.0
|
|
Reference:
D.Kubacka,
M.Kozarski,
M.R.Baranowski,
R.Wojcik,
J.Panecka-Hofman,
D.Strzelecka,
J.Basquin,
J.Jemielity,
J.Kowalska.
Substrate-Based Design of Cytosolic Nucleotidase Iiib Inhibitors and Structural Insights Into Inhibition Mechanism. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 35631380
DOI: 10.3390/PH15050554
Page generated: Thu Oct 3 16:44:39 2024
|