Calcium in PDB 8d94: SAMHD1-Dna Complex
Protein crystallography data
The structure of SAMHD1-Dna Complex, PDB code: 8d94
was solved by
T.J.Hollis,
S.M.Batalis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.98 /
2.44
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.116,
179.936,
79.792,
90,
108.95,
90
|
R / Rfree (%)
|
19 /
24.3
|
Other elements in 8d94:
The structure of SAMHD1-Dna Complex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the SAMHD1-Dna Complex
(pdb code 8d94). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
SAMHD1-Dna Complex, PDB code: 8d94:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8d94
Go back to
Calcium Binding Sites List in 8d94
Calcium binding site 1 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:63.4
occ:1.00
|
O
|
A:HOH824
|
2.4
|
33.2
|
1.0
|
O
|
A:HOH835
|
2.5
|
35.1
|
1.0
|
NE2
|
A:HIS233
|
2.6
|
40.4
|
1.0
|
OD1
|
A:ASP207
|
2.7
|
31.5
|
1.0
|
CE1
|
A:HIS233
|
3.5
|
31.8
|
1.0
|
CD2
|
A:HIS233
|
3.7
|
26.6
|
1.0
|
CG
|
A:ASP207
|
3.7
|
34.1
|
1.0
|
FE
|
A:FE701
|
3.8
|
33.0
|
1.0
|
OD2
|
A:ASP311
|
3.8
|
51.3
|
1.0
|
CD2
|
A:HIS206
|
3.9
|
27.8
|
1.0
|
OD2
|
A:ASP207
|
4.1
|
27.8
|
1.0
|
NE2
|
A:HIS210
|
4.3
|
37.0
|
1.0
|
OE2
|
A:GLU234
|
4.4
|
52.7
|
1.0
|
O
|
A:HOH864
|
4.4
|
34.4
|
1.0
|
NE2
|
A:HIS206
|
4.4
|
25.3
|
1.0
|
O
|
A:HOH833
|
4.5
|
35.1
|
1.0
|
CG
|
A:GLU234
|
4.7
|
37.4
|
1.0
|
ND1
|
A:HIS233
|
4.7
|
48.0
|
1.0
|
CD
|
A:GLU234
|
4.7
|
44.1
|
1.0
|
O
|
A:HIS206
|
4.8
|
31.3
|
1.0
|
CG
|
A:HIS233
|
4.8
|
37.2
|
1.0
|
CG
|
A:ASP311
|
5.0
|
19.9
|
1.0
|
CD2
|
A:HIS210
|
5.0
|
34.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8d94
Go back to
Calcium Binding Sites List in 8d94
Calcium binding site 2 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:69.7
occ:1.00
|
O
|
B:HOH846
|
2.5
|
34.5
|
1.0
|
NE2
|
B:HIS233
|
2.8
|
39.5
|
1.0
|
OD1
|
B:ASP207
|
3.2
|
34.6
|
1.0
|
CE1
|
B:HIS233
|
3.6
|
26.5
|
1.0
|
FE
|
B:FE701
|
3.7
|
42.6
|
1.0
|
CD2
|
B:HIS233
|
3.8
|
35.5
|
1.0
|
CG
|
B:ASP207
|
4.3
|
26.8
|
1.0
|
CD2
|
B:HIS206
|
4.3
|
27.3
|
1.0
|
OE2
|
B:GLU234
|
4.4
|
54.8
|
1.0
|
CG
|
B:GLU234
|
4.5
|
28.4
|
1.0
|
O
|
B:HOH861
|
4.5
|
36.2
|
1.0
|
OD2
|
B:ASP311
|
4.5
|
38.8
|
1.0
|
CD
|
B:GLU234
|
4.6
|
49.2
|
1.0
|
OD2
|
B:ASP207
|
4.6
|
38.7
|
1.0
|
NE2
|
B:HIS210
|
4.7
|
28.5
|
1.0
|
NE2
|
B:HIS206
|
4.8
|
45.2
|
1.0
|
ND1
|
B:HIS233
|
4.8
|
39.3
|
1.0
|
CG
|
B:HIS233
|
4.9
|
37.7
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8d94
Go back to
Calcium Binding Sites List in 8d94
Calcium binding site 3 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca702
b:56.0
occ:1.00
|
O
|
C:HOH868
|
2.4
|
45.1
|
1.0
|
O
|
C:HOH808
|
2.5
|
40.2
|
1.0
|
OD1
|
C:ASP207
|
2.6
|
29.2
|
1.0
|
NE2
|
C:HIS233
|
2.9
|
41.3
|
1.0
|
FE
|
C:FE701
|
3.2
|
42.4
|
1.0
|
CD2
|
C:HIS233
|
3.6
|
27.9
|
1.0
|
CD2
|
C:HIS206
|
3.6
|
34.1
|
1.0
|
CG
|
C:ASP207
|
3.7
|
35.2
|
1.0
|
CE1
|
C:HIS233
|
4.0
|
34.8
|
1.0
|
NE2
|
C:HIS206
|
4.1
|
46.3
|
1.0
|
OD2
|
C:ASP311
|
4.1
|
37.0
|
1.0
|
OD2
|
C:ASP207
|
4.1
|
47.5
|
1.0
|
NE2
|
C:HIS210
|
4.1
|
30.3
|
1.0
|
O
|
C:HOH901
|
4.3
|
46.1
|
1.0
|
O
|
C:HIS206
|
4.5
|
24.5
|
1.0
|
OE2
|
C:GLU234
|
4.7
|
56.9
|
1.0
|
CG
|
C:HIS206
|
4.8
|
33.4
|
1.0
|
CG
|
C:ASP311
|
4.8
|
42.3
|
1.0
|
CG
|
C:HIS233
|
4.9
|
30.6
|
1.0
|
CD2
|
C:HIS210
|
4.9
|
29.9
|
1.0
|
OD1
|
C:ASP311
|
4.9
|
43.9
|
1.0
|
CB
|
C:ASP207
|
4.9
|
39.6
|
1.0
|
CG
|
C:GLU234
|
4.9
|
35.4
|
1.0
|
CA
|
C:ASP207
|
5.0
|
37.5
|
1.0
|
ND1
|
C:HIS233
|
5.0
|
28.9
|
1.0
|
CD
|
C:GLU234
|
5.0
|
41.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8d94
Go back to
Calcium Binding Sites List in 8d94
Calcium binding site 4 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca702
b:80.2
occ:1.00
|
O
|
D:HOH826
|
2.3
|
43.5
|
1.0
|
O
|
D:HOH841
|
2.5
|
50.2
|
1.0
|
NE2
|
D:HIS233
|
2.9
|
51.9
|
1.0
|
OD1
|
D:ASP207
|
3.2
|
35.4
|
1.0
|
CE1
|
D:HIS233
|
3.7
|
45.1
|
1.0
|
OD2
|
D:ASP311
|
3.9
|
44.6
|
1.0
|
FE
|
D:FE701
|
4.0
|
35.7
|
1.0
|
CD2
|
D:HIS233
|
4.0
|
45.3
|
1.0
|
CG
|
D:ASP207
|
4.2
|
33.7
|
1.0
|
CD2
|
D:HIS206
|
4.2
|
31.3
|
1.0
|
OE2
|
D:GLU234
|
4.3
|
38.6
|
1.0
|
OD2
|
D:ASP207
|
4.5
|
34.2
|
1.0
|
NE2
|
D:HIS210
|
4.5
|
38.1
|
1.0
|
NE2
|
D:HIS206
|
4.7
|
28.0
|
1.0
|
O
|
D:HOH811
|
4.7
|
41.1
|
1.0
|
CG
|
D:ASP311
|
4.8
|
44.9
|
1.0
|
CD
|
D:GLU234
|
4.9
|
45.5
|
1.0
|
ND1
|
D:HIS233
|
4.9
|
49.3
|
1.0
|
CG
|
D:GLU234
|
4.9
|
45.3
|
1.0
|
OD1
|
D:ASP311
|
5.0
|
43.1
|
1.0
|
CE1
|
D:HIS215
|
5.0
|
42.8
|
1.0
|
|
Reference:
T.J.Hollis,
S.M.Batalis.
SAMHD1-Dna Complex To Be Published.
Page generated: Fri Jul 19 07:52:25 2024
|