Calcium in PDB 8d9j: SAMHD1-Dna Complex
Protein crystallography data
The structure of SAMHD1-Dna Complex, PDB code: 8d9j
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)
|
39.05 /
2.82
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.43,
179.678,
79.891,
90,
109,
90
|
R / Rfree (%)
|
18.2 /
24.2
|
Other elements in 8d9j:
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 8d9j). 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: 8d9j:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8d9j
Go back to
Calcium Binding Sites List in 8d9j
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:110.8
occ:1.00
|
O
|
A:HOH827
|
2.6
|
46.6
|
1.0
|
NE2
|
A:HIS233
|
3.2
|
54.1
|
1.0
|
OD1
|
A:ASP207
|
3.7
|
56.6
|
1.0
|
OD2
|
A:ASP311
|
3.9
|
53.3
|
1.0
|
CD2
|
A:HIS206
|
4.0
|
45.3
|
1.0
|
CE1
|
A:HIS233
|
4.0
|
57.9
|
1.0
|
FE
|
A:FE701
|
4.2
|
44.8
|
1.0
|
CD2
|
A:HIS233
|
4.2
|
48.8
|
1.0
|
OE2
|
A:GLU234
|
4.4
|
75.7
|
1.0
|
CG
|
A:GLU234
|
4.5
|
61.3
|
1.0
|
CG
|
A:ASP311
|
4.6
|
55.3
|
1.0
|
NE2
|
A:HIS206
|
4.6
|
57.4
|
1.0
|
O
|
A:HOH845
|
4.6
|
50.7
|
1.0
|
CG
|
A:ASP207
|
4.6
|
54.8
|
1.0
|
OD1
|
A:ASP311
|
4.7
|
51.5
|
1.0
|
CD
|
A:GLU234
|
4.8
|
71.9
|
1.0
|
OD2
|
A:ASP207
|
4.8
|
57.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8d9j
Go back to
Calcium Binding Sites List in 8d9j
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:84.8
occ:1.00
|
O
|
B:HOH826
|
2.7
|
43.2
|
1.0
|
O
|
B:HOH809
|
2.8
|
63.3
|
1.0
|
NE2
|
B:HIS233
|
2.8
|
55.7
|
1.0
|
OD1
|
B:ASP207
|
3.1
|
50.4
|
1.0
|
CE1
|
B:HIS233
|
3.6
|
57.1
|
1.0
|
OD2
|
B:ASP311
|
3.7
|
61.0
|
1.0
|
CD2
|
B:HIS233
|
3.9
|
54.8
|
1.0
|
OE2
|
B:GLU234
|
4.0
|
59.3
|
1.0
|
FE
|
B:FE701
|
4.0
|
44.2
|
1.0
|
CG
|
B:ASP207
|
4.1
|
49.2
|
1.0
|
OD2
|
B:ASP207
|
4.3
|
44.6
|
1.0
|
CD2
|
B:HIS206
|
4.5
|
40.3
|
1.0
|
O
|
B:HOH824
|
4.5
|
50.2
|
1.0
|
NE2
|
B:HIS210
|
4.6
|
52.0
|
1.0
|
CG
|
B:GLU234
|
4.6
|
53.5
|
1.0
|
CD
|
B:GLU234
|
4.6
|
63.0
|
1.0
|
CG
|
B:ASP311
|
4.8
|
52.3
|
1.0
|
ND1
|
B:HIS233
|
4.8
|
52.6
|
1.0
|
CE1
|
B:HIS215
|
5.0
|
57.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8d9j
Go back to
Calcium Binding Sites List in 8d9j
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:68.1
occ:1.00
|
O
|
C:HOH830
|
2.4
|
57.6
|
1.0
|
OD1
|
C:ASP207
|
2.5
|
41.3
|
1.0
|
O
|
C:HOH853
|
2.6
|
64.8
|
1.0
|
NE2
|
C:HIS233
|
2.9
|
54.1
|
1.0
|
CG
|
C:ASP207
|
3.5
|
48.9
|
1.0
|
FE
|
C:FE701
|
3.6
|
32.9
|
1.0
|
CD2
|
C:HIS206
|
3.6
|
35.0
|
1.0
|
CD2
|
C:HIS233
|
3.8
|
50.0
|
1.0
|
CE1
|
C:HIS233
|
3.8
|
52.3
|
1.0
|
OD2
|
C:ASP207
|
3.9
|
44.6
|
1.0
|
OD2
|
C:ASP311
|
4.1
|
59.2
|
1.0
|
O
|
C:HIS206
|
4.2
|
45.6
|
1.0
|
NE2
|
C:HIS206
|
4.2
|
41.0
|
1.0
|
NE2
|
C:HIS210
|
4.4
|
40.5
|
1.0
|
CG
|
C:HIS206
|
4.6
|
41.5
|
1.0
|
CG
|
C:ASP311
|
4.6
|
41.2
|
1.0
|
OD1
|
C:ASP311
|
4.7
|
43.6
|
1.0
|
CB
|
C:ASP207
|
4.8
|
39.7
|
1.0
|
C
|
C:HIS206
|
4.8
|
37.0
|
1.0
|
CA
|
C:ASP207
|
4.9
|
45.1
|
1.0
|
CG
|
C:HIS233
|
5.0
|
51.3
|
1.0
|
O
|
C:HOH822
|
5.0
|
67.4
|
1.0
|
ND1
|
C:HIS233
|
5.0
|
54.5
|
1.0
|
CG
|
C:GLU234
|
5.0
|
51.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8d9j
Go back to
Calcium Binding Sites List in 8d9j
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:Ca701
b:86.7
occ:1.00
|
OD1
|
D:ASP207
|
2.3
|
61.6
|
1.0
|
O
|
D:HOH851
|
2.4
|
68.4
|
1.0
|
NE2
|
D:HIS233
|
2.4
|
50.1
|
1.0
|
O
|
D:HOH828
|
2.5
|
50.5
|
1.0
|
O
|
D:HOH836
|
2.5
|
63.0
|
1.0
|
CD2
|
D:HIS233
|
3.0
|
40.4
|
1.0
|
CG
|
D:ASP207
|
3.4
|
56.3
|
1.0
|
CE1
|
D:HIS233
|
3.6
|
45.2
|
1.0
|
NE2
|
D:HIS210
|
3.8
|
41.7
|
1.0
|
FE
|
D:FE702
|
3.8
|
45.5
|
1.0
|
OD2
|
D:ASP207
|
3.8
|
51.4
|
1.0
|
CD2
|
D:HIS206
|
4.1
|
32.2
|
1.0
|
O
|
D:HIS206
|
4.1
|
38.0
|
1.0
|
CG
|
D:HIS233
|
4.3
|
47.2
|
1.0
|
CD2
|
D:HIS210
|
4.4
|
49.1
|
1.0
|
ND1
|
D:HIS233
|
4.5
|
47.8
|
1.0
|
NE2
|
D:HIS206
|
4.6
|
44.2
|
1.0
|
O
|
D:HOH835
|
4.6
|
59.7
|
1.0
|
CB
|
D:ASP207
|
4.6
|
47.4
|
1.0
|
CE1
|
D:HIS210
|
4.6
|
45.3
|
1.0
|
CA
|
D:ASP207
|
4.7
|
43.4
|
1.0
|
OE2
|
D:GLU234
|
4.8
|
68.5
|
1.0
|
CG
|
D:GLU234
|
4.8
|
56.5
|
1.0
|
C
|
D:HIS206
|
4.9
|
40.1
|
1.0
|
CD
|
D:GLU234
|
5.0
|
63.7
|
1.0
|
|
Reference:
T.J.Hollis,
S.M.Batalis.
SAMHD1-Dna Complex To Be Published.
Page generated: Fri Jul 19 07:52:51 2024
|