Magnesium in PDB 4iem: Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
Enzymatic activity of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
All present enzymatic activity of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+:
4.2.99.18;
Protein crystallography data
The structure of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+, PDB code: 4iem
was solved by
S.E.Tsutakawa,
C.D.Mol,
A.S.Arvai,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.64 /
2.39
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.639,
74.090,
112.138,
90.00,
111.98,
90.00
|
|
R / Rfree (%)
|
20.8 /
24.6
|
Other elements in 4iem:
The structure of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
(pdb code 4iem). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+, PDB code: 4iem:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 1 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:55.1
occ:1.00
|
H22
|
G:DG518
|
2.0
|
52.6
|
1.0
|
|
O2
|
E:DC505
|
2.0
|
39.0
|
1.0
|
|
O
|
G:HOH606
|
2.0
|
53.0
|
1.0
|
|
O
|
A:HOH641
|
2.1
|
34.0
|
1.0
|
|
N2
|
G:DG518
|
2.4
|
43.8
|
1.0
|
|
H21
|
G:DG518
|
2.4
|
52.6
|
1.0
|
|
O2
|
G:DT519
|
2.7
|
42.0
|
1.0
|
|
H1'
|
E:DC505
|
3.0
|
45.4
|
1.0
|
|
C2
|
E:DC505
|
3.2
|
37.5
|
1.0
|
|
O
|
A:HOH602
|
3.2
|
44.9
|
1.0
|
|
H2
|
E:DA504
|
3.4
|
44.5
|
1.0
|
|
C2
|
G:DG518
|
3.6
|
42.6
|
1.0
|
|
O
|
A:HOH603
|
3.6
|
40.0
|
1.0
|
|
O
|
A:HOH651
|
3.8
|
39.7
|
1.0
|
|
H1
|
G:DG518
|
3.8
|
45.1
|
1.0
|
|
C1'
|
E:DC505
|
3.9
|
37.8
|
1.0
|
|
C2
|
G:DT519
|
3.9
|
45.1
|
1.0
|
|
H1'
|
G:DT519
|
4.0
|
44.7
|
1.0
|
|
N1
|
E:DC505
|
4.0
|
38.2
|
1.0
|
|
O
|
E:HOH702
|
4.0
|
38.7
|
1.0
|
|
HZ1
|
A:LYS98
|
4.1
|
55.7
|
1.0
|
|
C2
|
E:DA504
|
4.1
|
37.1
|
1.0
|
|
N1
|
G:DG518
|
4.1
|
37.6
|
1.0
|
|
N3
|
E:DC505
|
4.1
|
36.1
|
1.0
|
|
OD1
|
A:ASP70
|
4.2
|
42.3
|
1.0
|
|
OD2
|
A:ASP308
|
4.3
|
25.3
|
1.0
|
|
H3
|
G:DT519
|
4.4
|
53.7
|
1.0
|
|
OD2
|
A:ASP70
|
4.4
|
43.0
|
1.0
|
|
N3
|
G:DG518
|
4.5
|
46.3
|
1.0
|
|
HD2
|
A:TYR269
|
4.5
|
32.6
|
1.0
|
|
N3
|
E:DA504
|
4.6
|
39.6
|
1.0
|
|
CG
|
A:ASP70
|
4.6
|
44.2
|
1.0
|
|
N3
|
G:DT519
|
4.7
|
44.8
|
1.0
|
|
O4'
|
E:DC505
|
4.7
|
37.9
|
1.0
|
|
H2''
|
E:DC505
|
4.7
|
46.0
|
1.0
|
|
N1
|
E:DA504
|
4.8
|
40.8
|
1.0
|
|
NZ
|
A:LYS98
|
4.8
|
46.4
|
1.0
|
|
O
|
A:HOH635
|
4.8
|
25.5
|
1.0
|
|
HZ2
|
A:LYS98
|
4.8
|
55.7
|
1.0
|
|
C1'
|
G:DT519
|
4.8
|
37.2
|
1.0
|
|
N1
|
G:DT519
|
4.9
|
43.9
|
1.0
|
|
HE2
|
A:TYR269
|
4.9
|
39.0
|
1.0
|
|
O3'
|
E:DC505
|
4.9
|
35.1
|
1.0
|
|
C2'
|
E:DC505
|
4.9
|
38.4
|
1.0
|
|
HZ3
|
A:LYS98
|
5.0
|
55.7
|
1.0
|
|
MG
|
A:MG502
|
5.0
|
42.5
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 4iem
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Magnesium Binding Sites List in 4iem
Magnesium binding site 2 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:42.5
occ:1.00
|
O
|
A:HOH603
|
1.9
|
40.0
|
1.0
|
|
OP1
|
F:3DR506
|
2.0
|
28.8
|
1.0
|
|
O
|
A:HOH601
|
2.2
|
26.8
|
1.0
|
|
O3'
|
E:DC505
|
2.2
|
35.1
|
1.0
|
|
OE1
|
A:GLU96
|
2.4
|
36.1
|
1.0
|
|
O
|
A:HOH602
|
2.9
|
44.9
|
1.0
|
|
P
|
F:3DR506
|
3.1
|
33.1
|
1.0
|
|
H2''
|
E:DC505
|
3.2
|
46.0
|
1.0
|
|
HE2
|
A:HIS309
|
3.2
|
32.1
|
1.0
|
|
C3'
|
E:DC505
|
3.3
|
37.4
|
1.0
|
|
OP3
|
F:3DR506
|
3.3
|
23.1
|
1.0
|
|
H3'
|
E:DC505
|
3.5
|
44.9
|
1.0
|
|
CD
|
A:GLU96
|
3.6
|
40.6
|
1.0
|
|
HD22
|
A:ASN68
|
3.6
|
33.6
|
1.0
|
|
C2'
|
E:DC505
|
3.7
|
38.4
|
1.0
|
|
O5'
|
F:3DR506
|
3.7
|
32.2
|
1.0
|
|
H1'
|
E:DC505
|
3.8
|
45.4
|
1.0
|
|
NE2
|
A:HIS309
|
3.9
|
26.8
|
1.0
|
|
HH
|
A:TYR171
|
4.0
|
66.2
|
1.0
|
|
OE2
|
A:GLU96
|
4.0
|
45.1
|
1.0
|
|
O
|
A:HOH641
|
4.1
|
34.0
|
1.0
|
|
HD2
|
A:HIS309
|
4.1
|
29.9
|
1.0
|
|
OD2
|
A:ASP308
|
4.2
|
25.3
|
1.0
|
|
ND2
|
A:ASN68
|
4.2
|
28.0
|
1.0
|
|
O
|
E:HOH702
|
4.3
|
38.7
|
1.0
|
|
C1'
|
E:DC505
|
4.3
|
37.8
|
1.0
|
|
H5''
|
F:3DR506
|
4.4
|
31.4
|
1.0
|
|
CD2
|
A:HIS309
|
4.4
|
24.9
|
1.0
|
|
OP2
|
F:3DR506
|
4.4
|
21.6
|
1.0
|
|
OD1
|
A:ASP308
|
4.4
|
31.2
|
1.0
|
|
HE1
|
A:PHE266
|
4.4
|
38.5
|
1.0
|
|
H2'
|
E:DC505
|
4.5
|
46.0
|
1.0
|
|
HE2
|
A:TYR171
|
4.6
|
35.3
|
1.0
|
|
C4'
|
E:DC505
|
4.6
|
39.8
|
1.0
|
|
C5'
|
F:3DR506
|
4.6
|
26.1
|
1.0
|
|
CG
|
A:ASP308
|
4.7
|
32.9
|
1.0
|
|
OH
|
A:TYR171
|
4.7
|
55.2
|
1.0
|
|
OD1
|
A:ASN68
|
4.7
|
29.1
|
1.0
|
|
HD21
|
A:ASN68
|
4.7
|
33.6
|
1.0
|
|
H4'
|
E:DC505
|
4.7
|
47.7
|
1.0
|
|
HG3
|
A:GLU96
|
4.8
|
42.3
|
1.0
|
|
CG
|
A:ASN68
|
4.8
|
26.6
|
1.0
|
|
CG
|
A:GLU96
|
4.8
|
35.2
|
1.0
|
|
HB2
|
A:ASP70
|
4.9
|
45.1
|
1.0
|
|
O4'
|
E:DC505
|
4.9
|
37.9
|
1.0
|
|
MG
|
A:MG501
|
5.0
|
55.1
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 3 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:38.1
occ:1.00
|
O2
|
L:DT509
|
2.1
|
32.6
|
1.0
|
|
O2
|
M:DT515
|
2.3
|
42.1
|
1.0
|
|
H2
|
M:DA514
|
3.1
|
55.0
|
1.0
|
|
H1'
|
L:DT509
|
3.3
|
47.1
|
1.0
|
|
C2
|
L:DT509
|
3.3
|
34.6
|
1.0
|
|
H2
|
L:DA508
|
3.4
|
42.9
|
1.0
|
|
C2
|
M:DT515
|
3.4
|
38.5
|
1.0
|
|
H1'
|
M:DT515
|
3.8
|
53.8
|
1.0
|
|
H3
|
M:DT515
|
3.9
|
42.1
|
1.0
|
|
C2
|
M:DA514
|
3.9
|
45.8
|
1.0
|
|
C2
|
L:DA508
|
4.0
|
35.8
|
1.0
|
|
H3
|
L:DT509
|
4.1
|
42.0
|
1.0
|
|
N3
|
M:DT515
|
4.1
|
35.1
|
1.0
|
|
C1'
|
L:DT509
|
4.2
|
39.3
|
1.0
|
|
N1
|
L:DT509
|
4.2
|
34.1
|
1.0
|
|
N3
|
L:DT509
|
4.3
|
35.0
|
1.0
|
|
N1
|
M:DT515
|
4.5
|
43.1
|
1.0
|
|
N1
|
M:DA514
|
4.5
|
41.7
|
1.0
|
|
N1
|
L:DA508
|
4.5
|
34.5
|
1.0
|
|
N3
|
L:DA508
|
4.6
|
33.9
|
1.0
|
|
C1'
|
M:DT515
|
4.6
|
44.8
|
1.0
|
|
O2
|
M:DC516
|
4.7
|
31.0
|
1.0
|
|
N3
|
M:DA514
|
4.7
|
44.4
|
1.0
|
|
O4'
|
L:DC510
|
4.7
|
47.9
|
1.0
|
|
O2
|
L:DC510
|
4.7
|
41.7
|
1.0
|
|
O4'
|
L:DT509
|
4.8
|
44.7
|
1.0
|
|
O4'
|
M:DC516
|
5.0
|
43.7
|
1.0
|
|
H5'
|
L:DC510
|
5.0
|
46.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 4 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:61.7
occ:1.00
|
O
|
I:HOH601
|
2.1
|
53.2
|
1.0
|
|
O
|
B:HOH503
|
2.1
|
51.4
|
1.0
|
|
OE1
|
B:GLU96
|
2.1
|
54.5
|
1.0
|
|
O3'
|
H:DC505
|
2.1
|
53.8
|
1.0
|
|
OP1
|
I:3DR506
|
2.4
|
52.7
|
1.0
|
|
O
|
B:HOH502
|
2.9
|
58.1
|
1.0
|
|
CD
|
B:GLU96
|
3.2
|
51.0
|
1.0
|
|
C3'
|
H:DC505
|
3.4
|
46.8
|
1.0
|
|
H2''
|
H:DC505
|
3.5
|
55.9
|
1.0
|
|
H1'
|
H:DC505
|
3.6
|
57.7
|
1.0
|
|
OE2
|
B:GLU96
|
3.6
|
52.0
|
1.0
|
|
HD22
|
B:ASN68
|
3.6
|
60.5
|
1.0
|
|
P
|
I:3DR506
|
3.6
|
43.0
|
1.0
|
|
HE2
|
B:HIS309
|
3.7
|
60.0
|
1.0
|
|
OP3
|
I:3DR506
|
3.8
|
44.0
|
1.0
|
|
HH
|
B:TYR171
|
3.8
|
58.8
|
1.0
|
|
H3'
|
H:DC505
|
3.8
|
56.2
|
1.0
|
|
C2'
|
H:DC505
|
3.9
|
46.6
|
1.0
|
|
OD1
|
B:ASP308
|
4.1
|
51.7
|
1.0
|
|
OD2
|
B:ASP308
|
4.2
|
54.9
|
1.0
|
|
C1'
|
H:DC505
|
4.2
|
48.1
|
1.0
|
|
HD2
|
B:HIS309
|
4.3
|
58.6
|
1.0
|
|
ND2
|
B:ASN68
|
4.3
|
50.4
|
1.0
|
|
NE2
|
B:HIS309
|
4.3
|
50.0
|
1.0
|
|
OD1
|
B:ASP70
|
4.4
|
68.4
|
1.0
|
|
OD1
|
B:ASN68
|
4.4
|
41.3
|
1.0
|
|
HG3
|
B:GLU96
|
4.5
|
60.0
|
1.0
|
|
CG
|
B:GLU96
|
4.5
|
50.0
|
1.0
|
|
C4'
|
H:DC505
|
4.5
|
49.2
|
1.0
|
|
HB2
|
B:ASP70
|
4.5
|
66.2
|
1.0
|
|
H4'
|
H:DC505
|
4.5
|
59.1
|
1.0
|
|
O5'
|
I:3DR506
|
4.5
|
54.7
|
1.0
|
|
CG
|
B:ASP308
|
4.6
|
58.8
|
1.0
|
|
OH
|
B:TYR171
|
4.6
|
49.0
|
1.0
|
|
CD2
|
B:HIS309
|
4.6
|
48.8
|
1.0
|
|
HA
|
B:ASP70
|
4.6
|
56.7
|
1.0
|
|
OP2
|
I:3DR506
|
4.7
|
52.3
|
1.0
|
|
CG
|
B:ASN68
|
4.7
|
49.1
|
1.0
|
|
O4'
|
H:DC505
|
4.7
|
42.3
|
1.0
|
|
O
|
J:HOH602
|
4.8
|
58.9
|
1.0
|
|
H2'
|
H:DC505
|
4.8
|
55.9
|
1.0
|
|
CG
|
B:ASP70
|
4.9
|
65.8
|
1.0
|
|
HD21
|
B:ASN68
|
4.9
|
60.5
|
1.0
|
|
H5'
|
I:3DR506
|
5.0
|
73.9
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 5 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:49.3
occ:1.00
|
O3'
|
K:DC505
|
1.9
|
40.3
|
1.0
|
|
O
|
C:HOH602
|
1.9
|
35.2
|
1.0
|
|
OP1
|
L:3DR506
|
2.1
|
34.2
|
1.0
|
|
O
|
C:HOH601
|
2.4
|
34.7
|
1.0
|
|
O
|
K:HOH701
|
2.4
|
46.2
|
1.0
|
|
OE1
|
C:GLU96
|
2.5
|
34.2
|
1.0
|
|
H2''
|
K:DC505
|
2.9
|
46.9
|
1.0
|
|
C3'
|
K:DC505
|
3.0
|
38.5
|
1.0
|
|
H1'
|
K:DC505
|
3.3
|
49.8
|
1.0
|
|
P
|
L:3DR506
|
3.3
|
35.0
|
1.0
|
|
HE2
|
C:HIS309
|
3.4
|
36.1
|
1.0
|
|
C2'
|
K:DC505
|
3.4
|
39.1
|
1.0
|
|
H3'
|
K:DC505
|
3.4
|
46.3
|
1.0
|
|
OP3
|
L:3DR506
|
3.5
|
25.4
|
1.0
|
|
CD
|
C:GLU96
|
3.6
|
41.5
|
1.0
|
|
C1'
|
K:DC505
|
3.8
|
41.5
|
1.0
|
|
HD22
|
C:ASN68
|
3.9
|
35.9
|
1.0
|
|
OE2
|
C:GLU96
|
3.9
|
44.2
|
1.0
|
|
O5'
|
L:3DR506
|
4.0
|
37.4
|
1.0
|
|
HH
|
C:TYR171
|
4.0
|
55.6
|
1.0
|
|
O
|
C:HOH668
|
4.0
|
38.1
|
1.0
|
|
NE2
|
C:HIS309
|
4.2
|
30.1
|
1.0
|
|
OD1
|
C:ASP308
|
4.2
|
34.0
|
1.0
|
|
C4'
|
K:DC505
|
4.2
|
46.3
|
1.0
|
|
H2'
|
K:DC505
|
4.3
|
46.9
|
1.0
|
|
O
|
K:HOH706
|
4.3
|
40.4
|
1.0
|
|
H4'
|
K:DC505
|
4.3
|
55.5
|
1.0
|
|
MG
|
C:MG402
|
4.4
|
48.8
|
1.0
|
|
HD2
|
C:HIS309
|
4.4
|
37.0
|
1.0
|
|
H5''
|
L:3DR506
|
4.5
|
38.8
|
1.0
|
|
O4'
|
K:DC505
|
4.5
|
40.4
|
1.0
|
|
OD2
|
C:ASP308
|
4.5
|
30.7
|
1.0
|
|
HE1
|
C:PHE266
|
4.5
|
34.3
|
1.0
|
|
OP2
|
L:3DR506
|
4.5
|
29.4
|
1.0
|
|
ND2
|
C:ASN68
|
4.5
|
29.9
|
1.0
|
|
CD2
|
C:HIS309
|
4.7
|
30.9
|
1.0
|
|
OH
|
C:TYR171
|
4.7
|
46.3
|
1.0
|
|
OD1
|
C:ASP70
|
4.7
|
42.1
|
1.0
|
|
CG
|
C:ASP308
|
4.7
|
34.5
|
1.0
|
|
O2
|
K:DC505
|
4.8
|
38.8
|
1.0
|
|
OD1
|
C:ASN68
|
4.8
|
30.2
|
1.0
|
|
HE2
|
C:TYR171
|
4.8
|
46.5
|
1.0
|
|
C5'
|
L:3DR506
|
4.8
|
32.3
|
1.0
|
|
HG3
|
C:GLU96
|
4.9
|
48.8
|
1.0
|
|
CG
|
C:GLU96
|
4.9
|
40.6
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 6 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:48.8
occ:1.00
|
O
|
C:HOH614
|
2.2
|
33.5
|
1.0
|
|
O
|
C:HOH668
|
2.2
|
38.1
|
1.0
|
|
O2
|
K:DC505
|
2.2
|
38.8
|
1.0
|
|
O
|
K:HOH701
|
2.3
|
46.2
|
1.0
|
|
H1'
|
K:DC505
|
2.9
|
49.8
|
1.0
|
|
O2
|
M:DT519
|
3.1
|
45.2
|
1.0
|
|
H22
|
M:DG518
|
3.1
|
46.6
|
1.0
|
|
C2
|
K:DC505
|
3.4
|
45.6
|
1.0
|
|
H2
|
K:DA504
|
3.4
|
50.2
|
1.0
|
|
H21
|
M:DG518
|
3.4
|
46.6
|
1.0
|
|
N2
|
M:DG518
|
3.5
|
38.8
|
1.0
|
|
OD1
|
C:ASP70
|
3.6
|
42.1
|
1.0
|
|
O
|
C:HOH602
|
3.6
|
35.2
|
1.0
|
|
C1'
|
K:DC505
|
3.8
|
41.5
|
1.0
|
|
N1
|
K:DC505
|
4.0
|
47.5
|
1.0
|
|
C2
|
K:DA504
|
4.1
|
41.9
|
1.0
|
|
H1'
|
M:DT519
|
4.2
|
45.1
|
1.0
|
|
HZ3
|
C:LYS98
|
4.3
|
54.8
|
1.0
|
|
C2
|
M:DT519
|
4.3
|
43.8
|
1.0
|
|
N3
|
K:DC505
|
4.4
|
48.9
|
1.0
|
|
MG
|
C:MG401
|
4.4
|
49.3
|
1.0
|
|
O4'
|
K:DC505
|
4.4
|
40.4
|
1.0
|
|
O
|
K:HOH706
|
4.4
|
40.4
|
1.0
|
|
HZ2
|
C:LYS98
|
4.5
|
54.8
|
1.0
|
|
OD1
|
C:ASP308
|
4.5
|
34.0
|
1.0
|
|
N3
|
K:DA504
|
4.5
|
36.1
|
1.0
|
|
CG
|
C:ASP70
|
4.5
|
51.5
|
1.0
|
|
C2
|
M:DG518
|
4.5
|
47.0
|
1.0
|
|
O3'
|
K:DC505
|
4.7
|
40.3
|
1.0
|
|
NZ
|
C:LYS98
|
4.7
|
45.7
|
1.0
|
|
H2''
|
K:DC505
|
4.8
|
46.9
|
1.0
|
|
H1
|
M:DG518
|
4.8
|
63.3
|
1.0
|
|
OD2
|
C:ASP70
|
4.8
|
47.8
|
1.0
|
|
H3
|
M:DT519
|
4.8
|
54.4
|
1.0
|
|
HZ1
|
C:LYS98
|
4.9
|
54.8
|
1.0
|
|
C2'
|
K:DC505
|
4.9
|
39.1
|
1.0
|
|
O
|
M:HOH601
|
4.9
|
43.6
|
1.0
|
|
HE2
|
C:TYR269
|
4.9
|
38.8
|
1.0
|
|
N1
|
K:DA504
|
5.0
|
46.4
|
1.0
|
|
O
|
C:HOH601
|
5.0
|
34.7
|
1.0
|
|
HD2
|
C:TYR269
|
5.0
|
36.1
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 4iem
Go back to
Magnesium Binding Sites List in 4iem
Magnesium binding site 7 out
of 7 in the Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Human Apurinic/Apyrimidinic Endonuclease (APE1) with Product Dna and MG2+ within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:61.6
occ:1.00
|
O3'
|
N:DC505
|
1.8
|
52.0
|
1.0
|
|
O
|
D:HOH502
|
1.9
|
47.5
|
1.0
|
|
O
|
N:HOH701
|
2.3
|
49.3
|
1.0
|
|
O
|
D:HOH501
|
2.4
|
39.6
|
1.0
|
|
OE1
|
D:GLU96
|
2.4
|
46.0
|
1.0
|
|
OP1
|
O:3DR506
|
2.4
|
40.0
|
1.0
|
|
C3'
|
N:DC505
|
3.1
|
53.4
|
1.0
|
|
H2''
|
N:DC505
|
3.2
|
59.6
|
1.0
|
|
H1'
|
N:DC505
|
3.2
|
64.3
|
1.0
|
|
CD
|
D:GLU96
|
3.4
|
50.7
|
1.0
|
|
HE2
|
D:HIS309
|
3.5
|
46.5
|
1.0
|
|
P
|
O:3DR506
|
3.5
|
42.9
|
1.0
|
|
C2'
|
N:DC505
|
3.5
|
49.6
|
1.0
|
|
OP3
|
O:3DR506
|
3.5
|
40.5
|
1.0
|
|
H3'
|
N:DC505
|
3.6
|
64.1
|
1.0
|
|
OE2
|
D:GLU96
|
3.7
|
56.8
|
1.0
|
|
HH
|
D:TYR171
|
3.8
|
60.7
|
1.0
|
|
C1'
|
N:DC505
|
3.8
|
53.6
|
1.0
|
|
HD22
|
D:ASN68
|
3.8
|
46.1
|
1.0
|
|
OD1
|
D:ASP308
|
4.1
|
46.2
|
1.0
|
|
O
|
D:HOH539
|
4.1
|
48.8
|
1.0
|
|
C4'
|
N:DC505
|
4.1
|
49.2
|
1.0
|
|
H4'
|
N:DC505
|
4.2
|
59.1
|
1.0
|
|
NE2
|
D:HIS309
|
4.2
|
38.8
|
1.0
|
|
O5'
|
O:3DR506
|
4.3
|
51.8
|
1.0
|
|
O4'
|
N:DC505
|
4.4
|
46.1
|
1.0
|
|
HD2
|
D:HIS309
|
4.4
|
40.3
|
1.0
|
|
H2'
|
N:DC505
|
4.5
|
59.6
|
1.0
|
|
ND2
|
D:ASN68
|
4.5
|
38.4
|
1.0
|
|
HE1
|
D:PHE266
|
4.6
|
53.8
|
1.0
|
|
OH
|
D:TYR171
|
4.6
|
50.6
|
1.0
|
|
OD2
|
D:ASP308
|
4.6
|
44.3
|
1.0
|
|
OD1
|
D:ASP70
|
4.7
|
58.3
|
1.0
|
|
CD2
|
D:HIS309
|
4.7
|
33.6
|
1.0
|
|
OP2
|
O:3DR506
|
4.7
|
40.7
|
1.0
|
|
CG
|
D:ASP308
|
4.8
|
46.6
|
1.0
|
|
H5'
|
O:3DR506
|
4.8
|
56.8
|
1.0
|
|
CG
|
D:GLU96
|
4.8
|
49.9
|
1.0
|
|
HG3
|
D:GLU96
|
4.8
|
59.9
|
1.0
|
|
O2
|
N:DC505
|
4.8
|
52.6
|
1.0
|
|
OD1
|
D:ASN68
|
5.0
|
35.4
|
1.0
|
|
HE2
|
D:TYR171
|
5.0
|
48.7
|
1.0
|
|
Reference:
S.E.Tsutakawa,
D.S.Shin,
C.D.Mol,
T.Izumi,
A.S.Arvai,
A.K.Mantha,
B.Szczesny,
I.N.Ivanov,
D.J.Hosfield,
B.Maiti,
M.E.Pique,
K.A.Frankel,
K.Hitomi,
R.P.Cunningham,
S.Mitra,
J.A.Tainer.
Conserved Structural Chemistry For Incision Activity in Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV Dna Repair Enzymes. J.Biol.Chem. V. 288 8445 2013.
ISSN: ISSN 0021-9258
PubMed: 23355472
DOI: 10.1074/JBC.M112.422774
Page generated: Fri Aug 16 16:40:23 2024
|
