Magnesium in PDB 7ltt: SAMHD1(113-626) H206R D207N R366C
Protein crystallography data
The structure of SAMHD1(113-626) H206R D207N R366C, PDB code: 7ltt
was solved by
J.T.Temple,
N.E.Bowen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.38 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.926,
140.105,
97.193,
90,
114.18,
90
|
R / Rfree (%)
|
17.8 /
21.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the SAMHD1(113-626) H206R D207N R366C
(pdb code 7ltt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
SAMHD1(113-626) H206R D207N R366C, PDB code: 7ltt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7ltt
Go back to
Magnesium Binding Sites List in 7ltt
Magnesium binding site 1 out
of 4 in the SAMHD1(113-626) H206R D207N R366C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg703
b:28.2
occ:1.00
|
O3G
|
A:DGT704
|
1.9
|
27.2
|
1.0
|
O3G
|
B:DGT703
|
2.0
|
27.1
|
1.0
|
O2B
|
A:DGT704
|
2.0
|
28.9
|
1.0
|
O1B
|
B:DGT703
|
2.1
|
26.7
|
1.0
|
O
|
A:HOH858
|
2.1
|
27.1
|
1.0
|
O2A
|
A:DGT704
|
2.1
|
26.5
|
1.0
|
PB
|
A:DGT704
|
3.1
|
30.6
|
1.0
|
PG
|
A:DGT704
|
3.1
|
30.8
|
1.0
|
O3B
|
A:DGT704
|
3.3
|
29.6
|
1.0
|
PB
|
B:DGT703
|
3.3
|
26.7
|
1.0
|
PG
|
B:DGT703
|
3.3
|
30.6
|
1.0
|
PA
|
A:DGT704
|
3.4
|
27.0
|
1.0
|
O3A
|
A:DGT704
|
3.6
|
29.0
|
1.0
|
O3B
|
B:DGT703
|
3.7
|
28.2
|
1.0
|
NZ
|
A:LYS116
|
3.8
|
40.6
|
1.0
|
O1G
|
A:DGT704
|
4.0
|
34.8
|
1.0
|
O3'
|
A:DGT704
|
4.0
|
25.9
|
1.0
|
NZ
|
B:LYS523
|
4.0
|
49.6
|
1.0
|
O2G
|
A:DGT704
|
4.1
|
32.8
|
1.0
|
O1G
|
B:DGT703
|
4.1
|
29.6
|
1.0
|
O2B
|
B:DGT703
|
4.2
|
26.4
|
1.0
|
O
|
B:HOH862
|
4.2
|
46.8
|
1.0
|
O
|
A:HOH890
|
4.3
|
55.1
|
1.0
|
C5'
|
A:DGT704
|
4.3
|
26.0
|
1.0
|
O5'
|
A:DGT704
|
4.3
|
25.0
|
1.0
|
O2G
|
B:DGT703
|
4.4
|
31.3
|
1.0
|
O1B
|
A:DGT704
|
4.5
|
31.9
|
1.0
|
O3A
|
B:DGT703
|
4.5
|
26.4
|
1.0
|
C3'
|
A:DGT704
|
4.6
|
26.1
|
1.0
|
O1A
|
A:DGT704
|
4.6
|
28.6
|
1.0
|
O
|
A:HOH840
|
4.7
|
29.3
|
1.0
|
O
|
B:HOH802
|
4.8
|
68.8
|
1.0
|
C4'
|
A:DGT704
|
5.0
|
26.4
|
1.0
|
CE
|
A:LYS116
|
5.0
|
40.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7ltt
Go back to
Magnesium Binding Sites List in 7ltt
Magnesium binding site 2 out
of 4 in the SAMHD1(113-626) H206R D207N R366C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg701
b:33.8
occ:1.00
|
O3G
|
A:DGT702
|
1.9
|
33.1
|
1.0
|
O1B
|
B:DGT702
|
2.0
|
34.5
|
1.0
|
O
|
B:HOH853
|
2.0
|
32.7
|
1.0
|
O1B
|
A:DGT702
|
2.0
|
30.5
|
1.0
|
O2G
|
B:DGT702
|
2.1
|
36.6
|
1.0
|
O2A
|
B:DGT702
|
2.1
|
32.9
|
1.0
|
PB
|
B:DGT702
|
3.2
|
39.4
|
1.0
|
PG
|
B:DGT702
|
3.2
|
38.8
|
1.0
|
PB
|
A:DGT702
|
3.3
|
31.0
|
1.0
|
PG
|
A:DGT702
|
3.3
|
34.8
|
1.0
|
PA
|
B:DGT702
|
3.4
|
35.4
|
1.0
|
O3B
|
B:DGT702
|
3.4
|
36.4
|
1.0
|
O3B
|
A:DGT702
|
3.6
|
35.5
|
1.0
|
O3A
|
B:DGT702
|
3.6
|
36.0
|
1.0
|
NZ
|
B:LYS116
|
3.7
|
45.3
|
1.0
|
O3'
|
B:DGT702
|
3.9
|
33.4
|
1.0
|
O1G
|
A:DGT702
|
4.0
|
33.3
|
1.0
|
O3G
|
B:DGT702
|
4.1
|
38.8
|
1.0
|
C5'
|
B:DGT702
|
4.2
|
34.2
|
1.0
|
O2B
|
A:DGT702
|
4.2
|
30.6
|
1.0
|
NZ
|
A:LYS523
|
4.2
|
54.4
|
1.0
|
O
|
B:HOH842
|
4.2
|
48.7
|
1.0
|
O5'
|
B:DGT702
|
4.2
|
35.7
|
1.0
|
O1G
|
B:DGT702
|
4.3
|
43.2
|
1.0
|
O3A
|
A:DGT702
|
4.4
|
32.6
|
1.0
|
O
|
B:HOH814
|
4.4
|
26.9
|
1.0
|
O2G
|
A:DGT702
|
4.5
|
36.0
|
1.0
|
C3'
|
B:DGT702
|
4.5
|
31.9
|
1.0
|
O2B
|
B:DGT702
|
4.5
|
36.7
|
1.0
|
O1A
|
B:DGT702
|
4.6
|
35.3
|
1.0
|
C4'
|
B:DGT702
|
4.8
|
33.1
|
1.0
|
CE
|
B:LYS116
|
4.9
|
44.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7ltt
Go back to
Magnesium Binding Sites List in 7ltt
Magnesium binding site 3 out
of 4 in the SAMHD1(113-626) H206R D207N R366C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:25.8
occ:1.00
|
O3G
|
A:DGT701
|
2.0
|
30.1
|
1.0
|
O2B
|
A:DGT701
|
2.0
|
26.3
|
1.0
|
O
|
A:HOH862
|
2.1
|
23.7
|
1.0
|
O2B
|
C:DGT701
|
2.1
|
24.6
|
1.0
|
O2A
|
A:DGT701
|
2.1
|
25.3
|
1.0
|
O2G
|
C:DGT701
|
2.3
|
25.9
|
1.0
|
PB
|
A:DGT701
|
3.2
|
30.3
|
1.0
|
PG
|
A:DGT701
|
3.3
|
31.0
|
1.0
|
PB
|
C:DGT701
|
3.3
|
25.4
|
1.0
|
PA
|
A:DGT701
|
3.4
|
25.9
|
1.0
|
O3B
|
A:DGT701
|
3.4
|
29.1
|
1.0
|
PG
|
C:DGT701
|
3.5
|
27.7
|
1.0
|
O3A
|
A:DGT701
|
3.6
|
28.4
|
1.0
|
O3B
|
C:DGT701
|
3.7
|
24.5
|
1.0
|
NZ
|
D:LYS116
|
3.8
|
31.8
|
1.0
|
O3'
|
A:DGT701
|
3.8
|
24.1
|
1.0
|
O
|
C:HOH884
|
3.9
|
54.2
|
1.0
|
NZ
|
C:LYS523
|
4.0
|
56.8
|
1.0
|
O1B
|
C:DGT701
|
4.1
|
24.1
|
1.0
|
O3G
|
C:DGT701
|
4.2
|
26.4
|
1.0
|
O1G
|
A:DGT701
|
4.2
|
31.8
|
1.0
|
C5'
|
A:DGT701
|
4.2
|
24.5
|
1.0
|
O5'
|
A:DGT701
|
4.2
|
24.4
|
1.0
|
O2G
|
A:DGT701
|
4.3
|
33.0
|
1.0
|
C3'
|
A:DGT701
|
4.5
|
23.4
|
1.0
|
O
|
A:HOH864
|
4.5
|
23.9
|
1.0
|
O1B
|
A:DGT701
|
4.5
|
30.7
|
1.0
|
O3A
|
C:DGT701
|
4.5
|
24.7
|
1.0
|
O
|
A:HOH914
|
4.5
|
62.8
|
1.0
|
O1A
|
A:DGT701
|
4.6
|
27.4
|
1.0
|
O1G
|
C:DGT701
|
4.7
|
27.4
|
1.0
|
C4'
|
A:DGT701
|
4.8
|
23.1
|
1.0
|
CE
|
C:LYS523
|
4.9
|
56.1
|
1.0
|
CE
|
D:LYS116
|
4.9
|
32.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7ltt
Go back to
Magnesium Binding Sites List in 7ltt
Magnesium binding site 4 out
of 4 in the SAMHD1(113-626) H206R D207N R366C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of SAMHD1(113-626) H206R D207N R366C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg703
b:41.5
occ:1.00
|
O1G
|
C:DGT704
|
1.9
|
44.7
|
1.0
|
O2B
|
D:DGT800
|
2.0
|
37.3
|
1.0
|
O2G
|
D:DGT800
|
2.0
|
41.0
|
1.0
|
O
|
C:HOH866
|
2.1
|
35.4
|
1.0
|
O1B
|
C:DGT704
|
2.1
|
42.0
|
1.0
|
O1A
|
C:DGT704
|
2.1
|
39.1
|
1.0
|
PB
|
C:DGT704
|
3.2
|
49.3
|
1.0
|
PG
|
C:DGT704
|
3.2
|
47.1
|
1.0
|
PB
|
D:DGT800
|
3.3
|
36.0
|
1.0
|
PG
|
D:DGT800
|
3.3
|
42.3
|
1.0
|
O3B
|
C:DGT704
|
3.4
|
43.8
|
1.0
|
PA
|
C:DGT704
|
3.5
|
42.2
|
1.0
|
NZ
|
C:LYS116
|
3.5
|
53.3
|
1.0
|
O3B
|
D:DGT800
|
3.5
|
41.7
|
1.0
|
O3A
|
C:DGT704
|
3.6
|
43.5
|
1.0
|
NZ
|
D:LYS523
|
3.8
|
56.6
|
1.0
|
O3'
|
C:DGT704
|
4.0
|
37.7
|
1.0
|
O3G
|
D:DGT800
|
4.1
|
45.8
|
1.0
|
O2G
|
C:DGT704
|
4.2
|
50.0
|
1.0
|
O3G
|
C:DGT704
|
4.2
|
43.4
|
1.0
|
O1B
|
D:DGT800
|
4.2
|
35.0
|
1.0
|
C5'
|
C:DGT704
|
4.3
|
40.3
|
1.0
|
O5'
|
C:DGT704
|
4.4
|
41.3
|
1.0
|
O1G
|
D:DGT800
|
4.4
|
44.9
|
1.0
|
O3A
|
D:DGT800
|
4.4
|
37.6
|
1.0
|
O
|
C:HOH904
|
4.5
|
54.8
|
1.0
|
O2B
|
C:DGT704
|
4.5
|
46.8
|
1.0
|
O
|
C:HOH844
|
4.6
|
36.7
|
1.0
|
C3'
|
C:DGT704
|
4.6
|
35.9
|
1.0
|
O2A
|
C:DGT704
|
4.6
|
40.3
|
1.0
|
CE
|
C:LYS116
|
4.9
|
51.1
|
1.0
|
C4'
|
C:DGT704
|
4.9
|
37.4
|
1.0
|
NZ
|
B:LYS377
|
5.0
|
78.1
|
1.0
|
CE
|
D:LYS523
|
5.0
|
57.8
|
1.0
|
|
Reference:
N.E.Bowen,
J.Temple,
C.Shepard,
A.Oo,
F.Arizaga,
P.Kapoor-Vazirani,
M.Persaud,
C.H.Yu,
D.H.Kim,
R.F.Schinazi,
D.N.Ivanov,
F.Diaz-Griffero,
D.S.Yu,
Y.Xiong,
B.Kim.
Structural and Functional Characterization Explains Loss of Dntpase Activity of the Cancer-Specific R366C/H Mutant SAMHD1 Proteins. J.Biol.Chem. V. 297 01170 2021.
ISSN: ESSN 1083-351X
PubMed: 34492268
DOI: 10.1016/J.JBC.2021.101170
Page generated: Wed Oct 2 23:33:55 2024
|