Iron 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:
Iron Binding Sites:
The binding sites of Iron atom in the SAMHD1-Dna Complex
(pdb code 8d94). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
SAMHD1-Dna Complex, PDB code: 8d94:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8d94
Go back to
Iron Binding Sites List in 8d94
Iron binding site 1 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:33.0
occ:1.00
|
NE2
|
A:HIS167
|
2.1
|
24.2
|
1.0
|
NE2
|
A:HIS206
|
2.3
|
25.3
|
1.0
|
OD2
|
A:ASP207
|
2.4
|
27.8
|
1.0
|
O
|
A:HOH833
|
2.6
|
35.1
|
1.0
|
OD1
|
A:ASP311
|
2.6
|
45.2
|
1.0
|
OD2
|
A:ASP311
|
2.7
|
51.3
|
1.0
|
CE1
|
A:HIS167
|
2.8
|
32.2
|
1.0
|
CG
|
A:ASP311
|
3.0
|
19.9
|
1.0
|
CG
|
A:ASP207
|
3.1
|
34.1
|
1.0
|
CD2
|
A:HIS206
|
3.1
|
27.8
|
1.0
|
CD2
|
A:HIS167
|
3.3
|
46.4
|
1.0
|
CE1
|
A:HIS206
|
3.3
|
30.0
|
1.0
|
OD1
|
A:ASP207
|
3.4
|
31.5
|
1.0
|
NH1
|
A:ARG164
|
3.7
|
29.5
|
1.0
|
O
|
A:HOH824
|
3.8
|
33.2
|
1.0
|
CA
|
A:CA702
|
3.8
|
63.4
|
1.0
|
ND1
|
A:HIS167
|
4.0
|
27.4
|
1.0
|
CG
|
A:HIS167
|
4.2
|
27.1
|
1.0
|
CB
|
A:ASP207
|
4.3
|
22.2
|
1.0
|
CD2
|
A:TYR315
|
4.3
|
44.7
|
1.0
|
CG
|
A:HIS206
|
4.3
|
33.6
|
1.0
|
ND1
|
A:HIS206
|
4.4
|
38.3
|
1.0
|
CB
|
A:ASP311
|
4.4
|
35.8
|
1.0
|
CE2
|
A:TYR315
|
4.5
|
48.3
|
1.0
|
CG2
|
A:VAL171
|
4.8
|
22.4
|
1.0
|
O
|
A:HOH835
|
5.0
|
35.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 8d94
Go back to
Iron Binding Sites List in 8d94
Iron binding site 2 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe701
b:42.6
occ:1.00
|
OD1
|
B:ASP311
|
2.6
|
49.1
|
1.0
|
OD2
|
B:ASP207
|
2.6
|
38.7
|
1.0
|
O
|
B:HOH861
|
2.7
|
36.2
|
1.0
|
NE2
|
B:HIS206
|
2.7
|
45.2
|
1.0
|
NE2
|
B:HIS167
|
2.7
|
32.1
|
1.0
|
OD2
|
B:ASP311
|
3.2
|
38.8
|
1.0
|
CG
|
B:ASP311
|
3.2
|
32.1
|
1.0
|
CG
|
B:ASP207
|
3.3
|
26.8
|
1.0
|
O
|
B:HOH846
|
3.3
|
34.5
|
1.0
|
OD1
|
B:ASP207
|
3.3
|
34.6
|
1.0
|
CD2
|
B:HIS206
|
3.5
|
27.3
|
1.0
|
CE1
|
B:HIS167
|
3.5
|
47.5
|
1.0
|
CD2
|
B:HIS167
|
3.6
|
37.0
|
1.0
|
NH1
|
B:ARG164
|
3.7
|
28.4
|
1.0
|
CE1
|
B:HIS206
|
3.7
|
39.2
|
1.0
|
CA
|
B:CA702
|
3.7
|
69.7
|
1.0
|
ND1
|
B:HIS167
|
4.6
|
34.9
|
1.0
|
CB
|
B:ASP207
|
4.6
|
31.0
|
1.0
|
CB
|
B:ASP311
|
4.7
|
40.4
|
1.0
|
CD2
|
B:TYR315
|
4.7
|
43.6
|
1.0
|
CG
|
B:HIS206
|
4.7
|
37.2
|
1.0
|
CG
|
B:HIS167
|
4.7
|
32.1
|
1.0
|
ND1
|
B:HIS206
|
4.7
|
36.1
|
1.0
|
O
|
B:HOH865
|
4.7
|
53.8
|
1.0
|
CZ
|
B:ARG164
|
4.9
|
31.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 8d94
Go back to
Iron Binding Sites List in 8d94
Iron binding site 3 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe701
b:42.4
occ:1.00
|
OD1
|
C:ASP311
|
2.6
|
43.9
|
1.0
|
OD2
|
C:ASP207
|
2.6
|
47.5
|
1.0
|
O
|
C:HOH901
|
2.7
|
46.1
|
1.0
|
NE2
|
C:HIS206
|
2.7
|
46.3
|
1.0
|
NE2
|
C:HIS167
|
2.8
|
31.5
|
1.0
|
O
|
C:HOH868
|
3.1
|
45.1
|
1.0
|
CA
|
C:CA702
|
3.2
|
56.0
|
1.0
|
OD2
|
C:ASP311
|
3.2
|
37.0
|
1.0
|
CG
|
C:ASP311
|
3.2
|
42.3
|
1.0
|
OD1
|
C:ASP207
|
3.2
|
29.2
|
1.0
|
CG
|
C:ASP207
|
3.2
|
35.2
|
1.0
|
CD2
|
C:HIS206
|
3.4
|
34.1
|
1.0
|
CE1
|
C:HIS167
|
3.6
|
29.6
|
1.0
|
NH1
|
C:ARG164
|
3.6
|
30.5
|
1.0
|
CE1
|
C:HIS206
|
3.8
|
37.8
|
1.0
|
CD2
|
C:HIS167
|
3.8
|
26.6
|
1.0
|
CD2
|
C:TYR315
|
4.4
|
46.6
|
1.0
|
CE2
|
C:TYR315
|
4.4
|
47.6
|
1.0
|
CB
|
C:ASP207
|
4.7
|
39.6
|
1.0
|
CB
|
C:ASP311
|
4.7
|
47.1
|
1.0
|
CG
|
C:HIS206
|
4.7
|
33.4
|
1.0
|
ND1
|
C:HIS167
|
4.8
|
23.0
|
1.0
|
ND1
|
C:HIS206
|
4.8
|
39.9
|
1.0
|
O
|
C:HOH808
|
4.9
|
40.2
|
1.0
|
CG
|
C:HIS167
|
4.9
|
23.1
|
1.0
|
CZ
|
C:ARG164
|
4.9
|
39.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 8d94
Go back to
Iron Binding Sites List in 8d94
Iron binding site 4 out
of 4 in the SAMHD1-Dna Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of SAMHD1-Dna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe701
b:35.7
occ:1.00
|
OD1
|
D:ASP311
|
2.2
|
43.1
|
1.0
|
NE2
|
D:HIS167
|
2.3
|
27.9
|
1.0
|
OD2
|
D:ASP207
|
2.4
|
34.2
|
1.0
|
NE2
|
D:HIS206
|
2.4
|
28.0
|
1.0
|
O
|
D:HOH811
|
2.9
|
41.1
|
1.0
|
CG
|
D:ASP311
|
3.1
|
44.9
|
1.0
|
CG
|
D:ASP207
|
3.1
|
33.7
|
1.0
|
CD2
|
D:HIS167
|
3.2
|
27.4
|
1.0
|
CE1
|
D:HIS167
|
3.3
|
33.2
|
1.0
|
CD2
|
D:HIS206
|
3.3
|
31.3
|
1.0
|
CE1
|
D:HIS206
|
3.3
|
34.4
|
1.0
|
OD2
|
D:ASP311
|
3.4
|
44.6
|
1.0
|
OD1
|
D:ASP207
|
3.4
|
35.4
|
1.0
|
NH1
|
D:ARG164
|
3.6
|
35.9
|
1.0
|
CA
|
D:CA702
|
4.0
|
80.2
|
1.0
|
O
|
D:HOH826
|
4.1
|
43.5
|
1.0
|
CG
|
D:HIS167
|
4.3
|
30.1
|
1.0
|
ND1
|
D:HIS167
|
4.4
|
19.9
|
1.0
|
CB
|
D:ASP207
|
4.4
|
28.5
|
1.0
|
ND1
|
D:HIS206
|
4.4
|
46.7
|
1.0
|
CG
|
D:HIS206
|
4.4
|
33.8
|
1.0
|
CD2
|
D:TYR315
|
4.4
|
39.8
|
1.0
|
CB
|
D:ASP311
|
4.4
|
30.4
|
1.0
|
CG2
|
D:VAL171
|
4.7
|
26.1
|
1.0
|
CE2
|
D:TYR315
|
4.8
|
35.2
|
1.0
|
O
|
D:ASP311
|
4.9
|
30.5
|
1.0
|
CZ
|
D:ARG164
|
4.9
|
37.0
|
1.0
|
O
|
D:HOH841
|
5.0
|
50.2
|
1.0
|
|
Reference:
T.J.Hollis,
S.M.Batalis.
SAMHD1-Dna Complex To Be Published.
Page generated: Fri Aug 9 23:23:31 2024
|