Magnesium in PDB 6pwy: Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
Protein crystallography data
The structure of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog, PDB code: 6pwy
was solved by
C.S.Lim,
T.Maehigashi,
L.R.Wade,
N.Bowen,
K.Knecht,
Y.Xiong,
B.Kim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.03 /
1.81
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.681,
90.557,
93.357,
65.58,
65.49,
86.22
|
R / Rfree (%)
|
18.2 /
20.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
(pdb code 6pwy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of C. Elegans ZK177.8, SAMHD1 Ortholog, PDB code: 6pwy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6pwy
Go back to
Magnesium Binding Sites List in 6pwy
Magnesium binding site 1 out
of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:12.4
occ:1.00
|
O
|
C:HOH915
|
2.0
|
12.1
|
1.0
|
O3G
|
B:DTP603
|
2.1
|
12.7
|
1.0
|
O2A
|
B:GTP602
|
2.1
|
11.4
|
1.0
|
O1G
|
B:GTP602
|
2.1
|
16.0
|
1.0
|
O2B
|
B:DTP603
|
2.1
|
10.6
|
1.0
|
O1B
|
B:GTP602
|
2.2
|
13.4
|
1.0
|
PB
|
B:GTP602
|
3.2
|
13.5
|
1.0
|
PG
|
B:GTP602
|
3.3
|
17.9
|
1.0
|
PB
|
B:DTP603
|
3.3
|
11.6
|
1.0
|
PG
|
B:DTP603
|
3.3
|
12.7
|
1.0
|
PA
|
B:GTP602
|
3.4
|
11.8
|
1.0
|
O3B
|
B:GTP602
|
3.4
|
13.8
|
1.0
|
O3B
|
B:DTP603
|
3.5
|
12.0
|
1.0
|
O3A
|
B:GTP602
|
3.7
|
12.6
|
1.0
|
O
|
B:HOH787
|
3.9
|
20.4
|
1.0
|
O3'
|
B:GTP602
|
3.9
|
11.0
|
1.0
|
NZ
|
A:LYS493
|
3.9
|
21.2
|
1.0
|
O
|
B:HOH813
|
4.0
|
13.9
|
1.0
|
O2G
|
B:DTP603
|
4.0
|
12.5
|
1.0
|
O3G
|
B:GTP602
|
4.1
|
18.0
|
1.0
|
O
|
B:HOH864
|
4.1
|
29.5
|
1.0
|
O1B
|
B:DTP603
|
4.1
|
11.0
|
1.0
|
ND1
|
C:HIS44
|
4.2
|
14.3
|
1.0
|
NZ
|
B:LYS409
|
4.3
|
43.6
|
1.0
|
C5'
|
B:GTP602
|
4.3
|
11.0
|
1.0
|
O2G
|
B:GTP602
|
4.3
|
18.0
|
1.0
|
O5'
|
B:GTP602
|
4.3
|
11.1
|
1.0
|
CE1
|
C:HIS44
|
4.3
|
16.3
|
1.0
|
O1G
|
B:DTP603
|
4.4
|
12.3
|
1.0
|
O3A
|
B:DTP603
|
4.4
|
9.8
|
1.0
|
C3'
|
B:GTP602
|
4.4
|
11.4
|
1.0
|
O1A
|
B:GTP602
|
4.6
|
11.8
|
1.0
|
O2B
|
B:GTP602
|
4.6
|
14.5
|
1.0
|
C4'
|
B:GTP602
|
4.9
|
11.0
|
1.0
|
CE
|
A:LYS493
|
4.9
|
22.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6pwy
Go back to
Magnesium Binding Sites List in 6pwy
Magnesium binding site 2 out
of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg605
b:18.6
occ:1.00
|
O2A
|
D:GTP603
|
2.0
|
15.3
|
1.0
|
O
|
D:HOH922
|
2.1
|
15.7
|
1.0
|
O2G
|
D:GTP603
|
2.1
|
21.8
|
1.0
|
O1B
|
D:GTP603
|
2.1
|
15.9
|
1.0
|
O1B
|
D:DTP604
|
2.1
|
14.4
|
1.0
|
O1G
|
D:DTP604
|
2.2
|
14.6
|
1.0
|
PB
|
D:GTP603
|
3.1
|
18.0
|
1.0
|
PG
|
D:GTP603
|
3.2
|
22.7
|
1.0
|
PA
|
D:GTP603
|
3.3
|
16.6
|
1.0
|
PB
|
D:DTP604
|
3.3
|
13.2
|
1.0
|
O3B
|
D:GTP603
|
3.4
|
20.8
|
1.0
|
PG
|
D:DTP604
|
3.4
|
14.8
|
1.0
|
O3A
|
D:GTP603
|
3.5
|
17.8
|
1.0
|
O3B
|
D:DTP604
|
3.6
|
13.7
|
1.0
|
O3'
|
D:GTP603
|
3.8
|
14.2
|
1.0
|
O
|
D:HOH821
|
4.0
|
21.9
|
1.0
|
NZ
|
C:LYS493
|
4.0
|
25.2
|
1.0
|
O1G
|
D:GTP603
|
4.0
|
22.0
|
1.0
|
O
|
D:HOH887
|
4.1
|
33.9
|
1.0
|
O2B
|
D:DTP604
|
4.1
|
14.0
|
1.0
|
O3G
|
D:DTP604
|
4.1
|
13.8
|
1.0
|
C5'
|
D:GTP603
|
4.2
|
14.5
|
1.0
|
O
|
D:HOH772
|
4.2
|
16.1
|
1.0
|
O5'
|
D:GTP603
|
4.2
|
15.2
|
1.0
|
O3G
|
D:GTP603
|
4.3
|
22.6
|
1.0
|
ND1
|
A:HIS44
|
4.3
|
16.0
|
1.0
|
C3'
|
D:GTP603
|
4.3
|
14.9
|
1.0
|
CE1
|
A:HIS44
|
4.4
|
17.6
|
1.0
|
O1A
|
D:GTP603
|
4.4
|
16.8
|
1.0
|
O3A
|
D:DTP604
|
4.5
|
13.2
|
1.0
|
O2G
|
D:DTP604
|
4.5
|
16.0
|
1.0
|
O2B
|
D:GTP603
|
4.5
|
18.1
|
1.0
|
NZ
|
D:LYS409
|
4.6
|
37.9
|
1.0
|
C4'
|
D:GTP603
|
4.8
|
14.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6pwy
Go back to
Magnesium Binding Sites List in 6pwy
Magnesium binding site 3 out
of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:13.4
occ:1.00
|
O
|
B:HOH888
|
2.0
|
12.8
|
1.0
|
O1G
|
C:GTP602
|
2.1
|
14.6
|
1.0
|
O3G
|
C:DTP603
|
2.1
|
12.9
|
1.0
|
O2A
|
C:GTP602
|
2.1
|
10.5
|
1.0
|
O2B
|
C:DTP603
|
2.1
|
11.2
|
1.0
|
O1B
|
C:GTP602
|
2.1
|
12.9
|
1.0
|
PB
|
C:GTP602
|
3.2
|
13.7
|
1.0
|
PG
|
C:GTP602
|
3.3
|
16.4
|
1.0
|
PB
|
C:DTP603
|
3.3
|
11.9
|
1.0
|
PG
|
C:DTP603
|
3.3
|
13.0
|
1.0
|
PA
|
C:GTP602
|
3.4
|
11.9
|
1.0
|
O3B
|
C:GTP602
|
3.4
|
13.6
|
1.0
|
O3B
|
C:DTP603
|
3.5
|
12.3
|
1.0
|
O3A
|
C:GTP602
|
3.6
|
12.7
|
1.0
|
O
|
C:HOH756
|
3.8
|
19.3
|
1.0
|
O3'
|
C:GTP602
|
3.9
|
11.9
|
1.0
|
NZ
|
D:LYS493
|
3.9
|
22.6
|
1.0
|
O
|
C:HOH828
|
4.0
|
13.3
|
1.0
|
O3G
|
C:GTP602
|
4.0
|
17.3
|
1.0
|
O2G
|
C:DTP603
|
4.0
|
13.6
|
1.0
|
O
|
C:HOH836
|
4.1
|
28.3
|
1.0
|
O1B
|
C:DTP603
|
4.2
|
11.3
|
1.0
|
NZ
|
C:LYS409
|
4.2
|
44.9
|
1.0
|
ND1
|
B:HIS44
|
4.2
|
16.2
|
1.0
|
C5'
|
C:GTP602
|
4.2
|
10.9
|
1.0
|
O5'
|
C:GTP602
|
4.3
|
10.8
|
1.0
|
CE1
|
B:HIS44
|
4.3
|
17.7
|
1.0
|
O2G
|
C:GTP602
|
4.4
|
17.6
|
1.0
|
C3'
|
C:GTP602
|
4.4
|
11.9
|
1.0
|
O1G
|
C:DTP603
|
4.4
|
12.8
|
1.0
|
O3A
|
C:DTP603
|
4.4
|
11.0
|
1.0
|
O1A
|
C:GTP602
|
4.5
|
11.3
|
1.0
|
O2B
|
C:GTP602
|
4.6
|
14.5
|
1.0
|
C4'
|
C:GTP602
|
4.8
|
11.4
|
1.0
|
CE
|
D:LYS493
|
5.0
|
22.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6pwy
Go back to
Magnesium Binding Sites List in 6pwy
Magnesium binding site 4 out
of 4 in the Structure of C. Elegans ZK177.8, SAMHD1 Ortholog
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of C. Elegans ZK177.8, SAMHD1 Ortholog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:15.0
occ:1.00
|
O2A
|
A:GTP602
|
2.0
|
14.1
|
1.0
|
O1G
|
A:DTP603
|
2.1
|
14.5
|
1.0
|
O1B
|
A:DTP603
|
2.1
|
12.5
|
1.0
|
O
|
D:HOH901
|
2.1
|
16.8
|
1.0
|
O2G
|
A:GTP602
|
2.1
|
20.2
|
1.0
|
O1B
|
A:GTP602
|
2.2
|
14.8
|
1.0
|
PB
|
A:GTP602
|
3.2
|
17.8
|
1.0
|
PB
|
A:DTP603
|
3.2
|
13.7
|
1.0
|
PG
|
A:GTP602
|
3.3
|
23.6
|
1.0
|
PG
|
A:DTP603
|
3.3
|
15.8
|
1.0
|
PA
|
A:GTP602
|
3.3
|
14.8
|
1.0
|
O3B
|
A:GTP602
|
3.4
|
18.7
|
1.0
|
O3B
|
A:DTP603
|
3.5
|
14.8
|
1.0
|
O3A
|
A:GTP602
|
3.6
|
16.3
|
1.0
|
O3'
|
A:GTP602
|
3.8
|
14.7
|
1.0
|
O
|
A:HOH805
|
3.9
|
24.2
|
1.0
|
NZ
|
B:LYS493
|
4.0
|
25.6
|
1.0
|
O
|
A:HOH929
|
4.0
|
32.8
|
1.0
|
O2B
|
A:DTP603
|
4.1
|
12.7
|
1.0
|
O1G
|
A:GTP602
|
4.1
|
21.9
|
1.0
|
O3G
|
A:DTP603
|
4.1
|
14.0
|
1.0
|
O
|
A:HOH802
|
4.2
|
19.8
|
1.0
|
C5'
|
A:GTP602
|
4.2
|
14.4
|
1.0
|
O5'
|
A:GTP602
|
4.3
|
14.5
|
1.0
|
ND1
|
D:HIS44
|
4.3
|
15.9
|
1.0
|
O3G
|
A:GTP602
|
4.4
|
22.9
|
1.0
|
C3'
|
A:GTP602
|
4.4
|
15.0
|
1.0
|
CE1
|
D:HIS44
|
4.4
|
18.4
|
1.0
|
O3A
|
A:DTP603
|
4.4
|
13.1
|
1.0
|
O2G
|
A:DTP603
|
4.4
|
16.8
|
1.0
|
O1A
|
A:GTP602
|
4.5
|
15.4
|
1.0
|
O2B
|
A:GTP602
|
4.6
|
18.0
|
1.0
|
NZ
|
A:LYS409
|
4.6
|
34.3
|
1.0
|
C4'
|
A:GTP602
|
4.8
|
14.4
|
1.0
|
|
Reference:
T.Maehigashi,
C.Lim,
L.R.Wade,
N.Bowen,
K.Knecht,
R.F.Schinazi,
Y.Xiong,
B.Kim.
ZK177.8 of Caenorhabditis Elegans: Aicardi-Goutieres Syndrome SAMHD1 Ortholog To Be Published.
Page generated: Tue Oct 1 15:20:49 2024
|