Magnesium in PDB 1e0j: GP4D Helicase From Phage T7 Adpnp Complex
Protein crystallography data
The structure of GP4D Helicase From Phage T7 Adpnp Complex, PDB code: 1e0j
was solved by
M.R.Singleton,
M.R.Sawaya,
T.Ellenberger,
D.B.Wigley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.0 /
3.0
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.180,
119.180,
283.420,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.3 /
30.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the GP4D Helicase From Phage T7 Adpnp Complex
(pdb code 1e0j). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
GP4D Helicase From Phage T7 Adpnp Complex, PDB code: 1e0j:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1e0j
Go back to
Magnesium Binding Sites List in 1e0j
Magnesium binding site 1 out
of 4 in the GP4D Helicase From Phage T7 Adpnp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of GP4D Helicase From Phage T7 Adpnp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg701
b:38.5
occ:1.00
|
O1B
|
A:ANP700
|
2.1
|
49.6
|
1.0
|
O2G
|
A:ANP700
|
2.4
|
45.5
|
1.0
|
OG
|
A:SER319
|
2.7
|
55.7
|
1.0
|
PB
|
A:ANP700
|
3.1
|
51.6
|
1.0
|
N3B
|
A:ANP700
|
3.1
|
50.0
|
1.0
|
PG
|
A:ANP700
|
3.3
|
49.2
|
1.0
|
OE1
|
A:GLU343
|
3.7
|
84.0
|
1.0
|
OD2
|
A:ASP424
|
3.8
|
63.0
|
1.0
|
CB
|
A:SER319
|
3.9
|
57.8
|
1.0
|
O3A
|
A:ANP700
|
4.1
|
46.8
|
1.0
|
OD1
|
A:ASP424
|
4.2
|
60.7
|
1.0
|
O1G
|
A:ANP700
|
4.2
|
55.4
|
1.0
|
O2B
|
A:ANP700
|
4.2
|
44.5
|
1.0
|
CG
|
A:ASP424
|
4.4
|
60.8
|
1.0
|
O3G
|
A:ANP700
|
4.5
|
47.9
|
1.0
|
O2A
|
A:ANP700
|
4.7
|
50.4
|
1.0
|
PA
|
A:ANP700
|
4.9
|
46.9
|
1.0
|
CD
|
A:GLU343
|
4.9
|
81.2
|
1.0
|
N
|
A:SER319
|
5.0
|
62.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1e0j
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Magnesium Binding Sites List in 1e0j
Magnesium binding site 2 out
of 4 in the GP4D Helicase From Phage T7 Adpnp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of GP4D Helicase From Phage T7 Adpnp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg701
b:39.0
occ:1.00
|
OG
|
B:SER319
|
2.1
|
46.6
|
1.0
|
O1B
|
B:ANP700
|
2.3
|
48.4
|
1.0
|
O2G
|
B:ANP700
|
2.5
|
45.9
|
1.0
|
PB
|
B:ANP700
|
3.3
|
53.7
|
1.0
|
N3B
|
B:ANP700
|
3.3
|
49.7
|
1.0
|
CB
|
B:SER319
|
3.3
|
48.0
|
1.0
|
PG
|
B:ANP700
|
3.5
|
46.8
|
1.0
|
OD2
|
B:ASP424
|
3.6
|
55.0
|
1.0
|
OD1
|
B:ASP424
|
4.0
|
50.7
|
1.0
|
OE1
|
B:GLU343
|
4.0
|
65.3
|
1.0
|
CG
|
B:ASP424
|
4.2
|
52.9
|
1.0
|
O3A
|
B:ANP700
|
4.3
|
45.0
|
1.0
|
O1G
|
B:ANP700
|
4.3
|
57.9
|
1.0
|
O2B
|
B:ANP700
|
4.4
|
46.6
|
1.0
|
NH2
|
C:ARG522
|
4.5
|
87.2
|
1.0
|
CA
|
B:SER319
|
4.5
|
47.7
|
1.0
|
N
|
B:SER319
|
4.5
|
49.7
|
1.0
|
O3G
|
B:ANP700
|
4.6
|
46.5
|
1.0
|
O2A
|
B:ANP700
|
4.9
|
43.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1e0j
Go back to
Magnesium Binding Sites List in 1e0j
Magnesium binding site 3 out
of 4 in the GP4D Helicase From Phage T7 Adpnp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of GP4D Helicase From Phage T7 Adpnp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg701
b:43.3
occ:1.00
|
O1B
|
D:ANP700
|
2.0
|
52.3
|
1.0
|
O2G
|
D:ANP700
|
2.2
|
48.8
|
1.0
|
OG
|
D:SER319
|
2.6
|
50.3
|
1.0
|
PB
|
D:ANP700
|
2.9
|
56.5
|
1.0
|
N3B
|
D:ANP700
|
3.0
|
52.7
|
1.0
|
PG
|
D:ANP700
|
3.1
|
52.8
|
1.0
|
CB
|
D:SER319
|
3.7
|
54.3
|
1.0
|
O1G
|
D:ANP700
|
3.9
|
59.5
|
1.0
|
O2B
|
D:ANP700
|
4.0
|
46.7
|
1.0
|
O3A
|
D:ANP700
|
4.1
|
46.2
|
1.0
|
OD2
|
D:ASP424
|
4.1
|
58.7
|
1.0
|
OD1
|
D:ASP424
|
4.2
|
54.3
|
1.0
|
OE1
|
D:GLU343
|
4.3
|
77.8
|
1.0
|
O3G
|
D:ANP700
|
4.4
|
48.9
|
1.0
|
N
|
D:SER319
|
4.4
|
59.4
|
1.0
|
CG
|
D:ASP424
|
4.6
|
56.0
|
1.0
|
CA
|
D:SER319
|
4.7
|
57.1
|
1.0
|
CE
|
D:LYS318
|
4.7
|
63.2
|
1.0
|
O2A
|
D:ANP700
|
4.8
|
50.7
|
1.0
|
NZ
|
D:LYS318
|
4.9
|
62.8
|
1.0
|
PA
|
D:ANP700
|
4.9
|
45.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1e0j
Go back to
Magnesium Binding Sites List in 1e0j
Magnesium binding site 4 out
of 4 in the GP4D Helicase From Phage T7 Adpnp Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of GP4D Helicase From Phage T7 Adpnp Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg701
b:43.8
occ:1.00
|
OG
|
E:SER319
|
2.4
|
51.3
|
1.0
|
O2G
|
E:ANP700
|
2.6
|
50.9
|
1.0
|
O1B
|
E:ANP700
|
2.7
|
50.3
|
1.0
|
OD2
|
E:ASP424
|
3.6
|
54.8
|
1.0
|
N3B
|
E:ANP700
|
3.6
|
52.1
|
1.0
|
CB
|
E:SER319
|
3.6
|
49.4
|
1.0
|
PB
|
E:ANP700
|
3.7
|
53.4
|
1.0
|
OE1
|
E:GLU343
|
3.7
|
70.8
|
1.0
|
PG
|
E:ANP700
|
3.7
|
55.4
|
1.0
|
OD1
|
E:ASP424
|
4.0
|
53.1
|
1.0
|
CG
|
E:ASP424
|
4.2
|
54.7
|
1.0
|
NH2
|
F:ARG522
|
4.5
|
93.3
|
1.0
|
O3A
|
E:ANP700
|
4.6
|
43.3
|
1.0
|
O1G
|
E:ANP700
|
4.7
|
55.8
|
1.0
|
CA
|
E:SER319
|
4.7
|
50.0
|
1.0
|
O3G
|
E:ANP700
|
4.7
|
51.8
|
1.0
|
N
|
E:SER319
|
4.8
|
51.1
|
1.0
|
O2B
|
E:ANP700
|
4.9
|
45.6
|
1.0
|
CD
|
E:GLU343
|
4.9
|
68.7
|
1.0
|
O2A
|
E:ANP700
|
5.0
|
47.4
|
1.0
|
|
Reference:
M.R.Singleton,
M.R.Sawaya,
T.Ellenberger,
D.B.Wigley.
Crystal Structure of T7 Gene 4 Ring Helicase Indicates A Mechanism For Sequential Hydrolysis of Nucleotides Cell(Cambridge,Mass.) V. 101 589 2000.
ISSN: ISSN 0092-8674
PubMed: 10892646
DOI: 10.1016/S0092-8674(00)80871-5
Page generated: Tue Aug 13 02:48:19 2024
|