Iron 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:
Iron Binding Sites:
The binding sites of Iron atom in the SAMHD1-Dna Complex
(pdb code 8d9j). 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: 8d9j:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8d9j
Go back to
Iron Binding Sites List in 8d9j
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:44.8
occ:1.00
|
OD1
|
A:ASP311
|
2.1
|
51.5
|
1.0
|
OD2
|
A:ASP207
|
2.2
|
57.0
|
1.0
|
NE2
|
A:HIS206
|
2.2
|
57.4
|
1.0
|
NE2
|
A:HIS167
|
2.2
|
51.0
|
1.0
|
O
|
A:HOH845
|
2.5
|
50.7
|
1.0
|
CE1
|
A:HIS167
|
2.9
|
40.4
|
1.0
|
CG
|
A:ASP311
|
3.0
|
55.3
|
1.0
|
O
|
A:HOH827
|
3.0
|
46.6
|
1.0
|
CG
|
A:ASP207
|
3.2
|
54.8
|
1.0
|
CE1
|
A:HIS206
|
3.2
|
55.8
|
1.0
|
CD2
|
A:HIS206
|
3.2
|
45.3
|
1.0
|
OD2
|
A:ASP311
|
3.2
|
53.3
|
1.0
|
CD2
|
A:HIS167
|
3.3
|
52.0
|
1.0
|
OD1
|
A:ASP207
|
3.6
|
56.6
|
1.0
|
NH1
|
A:ARG164
|
3.9
|
50.7
|
1.0
|
ND1
|
A:HIS167
|
4.1
|
32.8
|
1.0
|
CA
|
A:CA702
|
4.2
|
110.8
|
1.0
|
CG
|
A:HIS167
|
4.3
|
35.0
|
1.0
|
ND1
|
A:HIS206
|
4.3
|
44.6
|
1.0
|
CG
|
A:HIS206
|
4.4
|
45.9
|
1.0
|
CB
|
A:ASP311
|
4.4
|
49.5
|
1.0
|
CB
|
A:ASP207
|
4.4
|
47.9
|
1.0
|
O
|
A:HOH817
|
4.5
|
59.4
|
1.0
|
CD2
|
A:TYR315
|
4.7
|
54.6
|
1.0
|
O
|
A:ASP311
|
4.9
|
44.0
|
1.0
|
CG2
|
A:VAL171
|
4.9
|
41.8
|
1.0
|
CE2
|
A:TYR315
|
5.0
|
54.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 8d9j
Go back to
Iron Binding Sites List in 8d9j
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:44.2
occ:1.00
|
OD2
|
B:ASP207
|
2.0
|
44.6
|
1.0
|
NE2
|
B:HIS167
|
2.1
|
27.0
|
1.0
|
OD1
|
B:ASP311
|
2.4
|
59.7
|
1.0
|
NE2
|
B:HIS206
|
2.5
|
44.6
|
1.0
|
OD2
|
B:ASP311
|
2.6
|
61.0
|
1.0
|
CE1
|
B:HIS167
|
2.8
|
25.9
|
1.0
|
CG
|
B:ASP311
|
2.8
|
52.3
|
1.0
|
CG
|
B:ASP207
|
3.1
|
49.2
|
1.0
|
CD2
|
B:HIS167
|
3.3
|
38.8
|
1.0
|
CD2
|
B:HIS206
|
3.3
|
40.3
|
1.0
|
O
|
B:HOH826
|
3.5
|
43.2
|
1.0
|
CE1
|
B:HIS206
|
3.5
|
40.0
|
1.0
|
OD1
|
B:ASP207
|
3.5
|
50.4
|
1.0
|
NH1
|
B:ARG164
|
3.7
|
42.5
|
1.0
|
ND1
|
B:HIS167
|
4.0
|
17.5
|
1.0
|
O
|
B:HOH829
|
4.0
|
57.2
|
1.0
|
CA
|
B:CA702
|
4.0
|
84.8
|
1.0
|
CG
|
B:HIS167
|
4.2
|
31.0
|
1.0
|
CB
|
B:ASP311
|
4.3
|
48.2
|
1.0
|
CB
|
B:ASP207
|
4.4
|
44.0
|
1.0
|
CD2
|
B:TYR315
|
4.4
|
45.2
|
1.0
|
CG
|
B:HIS206
|
4.4
|
38.9
|
1.0
|
ND1
|
B:HIS206
|
4.5
|
49.8
|
1.0
|
CE2
|
B:TYR315
|
4.8
|
60.4
|
1.0
|
O
|
B:HOH809
|
4.9
|
63.3
|
1.0
|
CG2
|
B:VAL171
|
4.9
|
36.1
|
1.0
|
CA
|
B:ASP311
|
4.9
|
49.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 8d9j
Go back to
Iron Binding Sites List in 8d9j
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:32.9
occ:1.00
|
OD1
|
C:ASP311
|
2.1
|
43.6
|
1.0
|
NE2
|
C:HIS167
|
2.2
|
23.5
|
1.0
|
OD2
|
C:ASP207
|
2.3
|
44.6
|
1.0
|
NE2
|
C:HIS206
|
2.3
|
41.0
|
1.0
|
CG
|
C:ASP311
|
3.0
|
41.2
|
1.0
|
CD2
|
C:HIS206
|
3.1
|
35.0
|
1.0
|
CD2
|
C:HIS167
|
3.1
|
30.2
|
1.0
|
CG
|
C:ASP207
|
3.2
|
48.9
|
1.0
|
CE1
|
C:HIS167
|
3.2
|
29.4
|
1.0
|
OD2
|
C:ASP311
|
3.3
|
59.2
|
1.0
|
CE1
|
C:HIS206
|
3.3
|
35.4
|
1.0
|
NH1
|
C:ARG164
|
3.4
|
35.8
|
1.0
|
OD1
|
C:ASP207
|
3.5
|
41.3
|
1.0
|
O
|
C:HOH840
|
3.6
|
49.5
|
1.0
|
CA
|
C:CA702
|
3.6
|
68.1
|
1.0
|
O
|
C:HOH830
|
4.1
|
57.6
|
1.0
|
CB
|
C:ASP311
|
4.2
|
49.3
|
1.0
|
CG
|
C:HIS206
|
4.3
|
41.5
|
1.0
|
ND1
|
C:HIS167
|
4.3
|
30.3
|
1.0
|
CG
|
C:HIS167
|
4.3
|
28.8
|
1.0
|
ND1
|
C:HIS206
|
4.3
|
45.5
|
1.0
|
CB
|
C:ASP207
|
4.4
|
39.7
|
1.0
|
CZ
|
C:ARG164
|
4.7
|
42.7
|
1.0
|
CD2
|
C:TYR315
|
4.9
|
45.3
|
1.0
|
CG2
|
C:VAL171
|
4.9
|
34.8
|
1.0
|
CA
|
C:ASP311
|
4.9
|
48.0
|
1.0
|
O
|
C:ASP311
|
5.0
|
43.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 8d9j
Go back to
Iron Binding Sites List in 8d9j
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:Fe702
b:45.5
occ:1.00
|
O
|
D:HOH835
|
2.1
|
59.7
|
1.0
|
OD2
|
D:ASP207
|
2.1
|
51.4
|
1.0
|
OD1
|
D:ASP311
|
2.2
|
51.1
|
1.0
|
NE2
|
D:HIS167
|
2.2
|
37.0
|
1.0
|
NE2
|
D:HIS206
|
2.3
|
44.2
|
1.0
|
O
|
D:HOH828
|
2.5
|
50.5
|
1.0
|
CD2
|
D:HIS206
|
3.1
|
32.2
|
1.0
|
CE1
|
D:HIS167
|
3.1
|
37.5
|
1.0
|
CG
|
D:ASP207
|
3.1
|
56.3
|
1.0
|
CG
|
D:ASP311
|
3.1
|
49.6
|
1.0
|
CD2
|
D:HIS167
|
3.2
|
43.4
|
1.0
|
CE1
|
D:HIS206
|
3.4
|
41.1
|
1.0
|
OD1
|
D:ASP207
|
3.4
|
61.6
|
1.0
|
OD2
|
D:ASP311
|
3.5
|
48.1
|
1.0
|
CA
|
D:CA701
|
3.8
|
86.7
|
1.0
|
NH1
|
D:ARG164
|
3.9
|
45.1
|
1.0
|
O
|
D:HOH836
|
3.9
|
63.0
|
1.0
|
ND1
|
D:HIS167
|
4.2
|
39.8
|
1.0
|
CG
|
D:HIS206
|
4.3
|
38.1
|
1.0
|
CG
|
D:HIS167
|
4.3
|
32.2
|
1.0
|
ND1
|
D:HIS206
|
4.4
|
31.0
|
1.0
|
CB
|
D:ASP207
|
4.4
|
47.4
|
1.0
|
CB
|
D:ASP311
|
4.5
|
49.3
|
1.0
|
CD2
|
D:TYR315
|
4.7
|
63.2
|
1.0
|
O
|
D:HOH851
|
4.7
|
68.4
|
1.0
|
O
|
D:ASP311
|
4.9
|
44.7
|
1.0
|
CE2
|
D:TYR315
|
4.9
|
65.3
|
1.0
|
CG2
|
D:VAL171
|
5.0
|
35.1
|
1.0
|
|
Reference:
T.J.Hollis,
S.M.Batalis.
SAMHD1-Dna Complex To Be Published.
Page generated: Fri Aug 9 23:25:42 2024
|