Magnesium in PDB 4fs2: Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
Enzymatic activity of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
All present enzymatic activity of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota:
2.7.7.7;
Protein crystallography data
The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota, PDB code: 4fs2
was solved by
L.Zhao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
84.26 /
2.05
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
97.298,
97.298,
202.906,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.4 /
26.1
|
Other elements in 4fs2:
The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
(pdb code 4fs2). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota, PDB code: 4fs2:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 4fs2
Go back to
Magnesium Binding Sites List in 4fs2
Magnesium binding site 1 out
of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:15.1
occ:0.50
|
OD2
|
A:ASP126
|
2.0
|
42.2
|
1.0
|
O1G
|
A:DCP503
|
2.1
|
38.8
|
1.0
|
O1A
|
A:DCP503
|
2.1
|
39.0
|
1.0
|
OD1
|
A:ASP34
|
2.2
|
35.3
|
1.0
|
O2B
|
A:DCP503
|
2.3
|
29.8
|
1.0
|
O
|
A:LEU35
|
2.3
|
39.0
|
1.0
|
CG
|
A:ASP126
|
3.1
|
38.8
|
1.0
|
MG
|
A:MG505
|
3.2
|
30.0
|
1.0
|
PB
|
A:DCP503
|
3.3
|
41.8
|
1.0
|
PG
|
A:DCP503
|
3.4
|
40.2
|
1.0
|
PA
|
A:DCP503
|
3.4
|
38.7
|
1.0
|
C
|
A:LEU35
|
3.5
|
32.4
|
1.0
|
CG
|
A:ASP34
|
3.5
|
33.6
|
1.0
|
OD1
|
A:ASP126
|
3.5
|
36.7
|
1.0
|
O3A
|
A:DCP503
|
3.7
|
42.5
|
1.0
|
O3B
|
A:DCP503
|
3.8
|
44.4
|
1.0
|
O
|
A:HOH664
|
3.8
|
39.8
|
1.0
|
N
|
A:LEU35
|
3.9
|
32.8
|
1.0
|
O2G
|
A:DCP503
|
4.0
|
37.5
|
1.0
|
OD2
|
A:ASP34
|
4.1
|
39.4
|
1.0
|
C
|
A:ASP34
|
4.1
|
33.7
|
1.0
|
C5'
|
A:DCP503
|
4.2
|
41.4
|
1.0
|
CA
|
A:LEU35
|
4.2
|
32.8
|
1.0
|
O5'
|
A:DCP503
|
4.3
|
41.7
|
1.0
|
CB
|
A:ASP126
|
4.4
|
33.7
|
1.0
|
O
|
A:ASP34
|
4.5
|
31.4
|
1.0
|
N
|
A:CYS37
|
4.5
|
31.1
|
1.0
|
N
|
A:ASP36
|
4.5
|
33.5
|
1.0
|
O2A
|
A:DCP503
|
4.6
|
42.4
|
1.0
|
O3G
|
A:DCP503
|
4.6
|
41.8
|
1.0
|
CB
|
A:ASP34
|
4.6
|
32.8
|
1.0
|
CA
|
A:ASP34
|
4.7
|
29.5
|
1.0
|
O1B
|
A:DCP503
|
4.7
|
37.7
|
1.0
|
CA
|
A:ASP36
|
4.7
|
34.5
|
1.0
|
CB
|
A:LEU35
|
4.8
|
33.5
|
1.0
|
C
|
A:ASP36
|
4.8
|
34.3
|
1.0
|
N
|
A:PHE38
|
4.8
|
35.5
|
1.0
|
O
|
A:ASP126
|
4.8
|
31.5
|
1.0
|
CB
|
A:PHE38
|
5.0
|
30.3
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 4fs2
Go back to
Magnesium Binding Sites List in 4fs2
Magnesium binding site 2 out
of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg504
b:41.1
occ:1.00
|
O
|
A:HOH601
|
2.7
|
33.1
|
1.0
|
O
|
A:GLY124
|
2.7
|
33.0
|
1.0
|
O
|
A:GLU127
|
2.9
|
30.0
|
1.0
|
NH2
|
A:ARG122
|
3.2
|
31.0
|
1.0
|
C
|
A:PHE125
|
3.5
|
34.0
|
1.0
|
CZ
|
A:ARG122
|
3.5
|
31.2
|
1.0
|
O
|
A:PHE125
|
3.5
|
31.7
|
1.0
|
CG
|
A:ARG122
|
3.6
|
30.9
|
1.0
|
ND2
|
A:ASN128
|
3.6
|
26.4
|
1.0
|
CB
|
A:ARG122
|
3.6
|
30.0
|
1.0
|
OG
|
A:SER106
|
3.7
|
31.5
|
1.0
|
N
|
A:ASP126
|
3.7
|
32.2
|
1.0
|
N
|
A:GLU127
|
3.7
|
27.4
|
1.0
|
C
|
A:GLY124
|
3.8
|
30.6
|
1.0
|
C
|
A:GLU127
|
3.8
|
29.1
|
1.0
|
OD1
|
A:ASN128
|
3.9
|
32.1
|
1.0
|
CA
|
A:PHE125
|
3.9
|
31.4
|
1.0
|
NH1
|
A:ARG122
|
4.0
|
28.7
|
1.0
|
OG1
|
A:THR110
|
4.0
|
29.2
|
1.0
|
CA
|
A:ARG122
|
4.0
|
29.1
|
1.0
|
CG
|
A:ASN128
|
4.0
|
29.6
|
1.0
|
NE
|
A:ARG122
|
4.1
|
30.5
|
1.0
|
N
|
A:LEU123
|
4.1
|
27.9
|
1.0
|
CA
|
A:ASP126
|
4.2
|
31.1
|
1.0
|
C
|
A:ASP126
|
4.3
|
30.9
|
1.0
|
N
|
A:PHE125
|
4.3
|
29.8
|
1.0
|
CD
|
A:ARG122
|
4.4
|
29.0
|
1.0
|
O
|
A:LEU123
|
4.4
|
31.2
|
1.0
|
CA
|
A:GLU127
|
4.5
|
27.2
|
1.0
|
C
|
A:ARG122
|
4.5
|
29.4
|
1.0
|
C
|
A:LEU123
|
4.7
|
33.0
|
1.0
|
N
|
A:ASN128
|
4.8
|
29.0
|
1.0
|
O
|
A:SER106
|
4.8
|
32.6
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 4fs2
Go back to
Magnesium Binding Sites List in 4fs2
Magnesium binding site 3 out
of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dctp By Human Polymerase Iota within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg505
b:30.0
occ:1.00
|
O1A
|
A:DCP503
|
2.1
|
39.0
|
1.0
|
OE2
|
A:GLU127
|
2.2
|
38.0
|
1.0
|
OD1
|
A:ASP34
|
2.9
|
35.3
|
1.0
|
OD1
|
A:ASP126
|
2.9
|
36.7
|
1.0
|
OD2
|
A:ASP34
|
3.0
|
39.4
|
1.0
|
CD
|
A:GLU127
|
3.1
|
32.4
|
1.0
|
PA
|
A:DCP503
|
3.2
|
38.7
|
1.0
|
CG
|
A:ASP34
|
3.2
|
33.6
|
1.0
|
MG
|
A:MG501
|
3.2
|
15.1
|
0.5
|
CG
|
A:GLU127
|
3.3
|
28.1
|
1.0
|
O2A
|
A:DCP503
|
3.6
|
42.4
|
1.0
|
C3'
|
B:DOC13
|
3.6
|
47.4
|
1.0
|
CG
|
A:ASP126
|
3.7
|
38.8
|
1.0
|
OD2
|
A:ASP126
|
3.7
|
42.2
|
1.0
|
O5'
|
A:DCP503
|
4.0
|
41.7
|
1.0
|
O1G
|
A:DCP503
|
4.0
|
38.8
|
1.0
|
O
|
A:HOH635
|
4.1
|
31.3
|
1.0
|
C4'
|
B:DOC13
|
4.3
|
48.0
|
1.0
|
OE1
|
A:GLU127
|
4.3
|
33.8
|
1.0
|
CB
|
A:ASP34
|
4.5
|
32.8
|
1.0
|
O3A
|
A:DCP503
|
4.5
|
42.5
|
1.0
|
C5'
|
A:DCP503
|
4.5
|
41.4
|
1.0
|
C5'
|
B:DOC13
|
4.7
|
48.5
|
1.0
|
C2'
|
B:DOC13
|
4.7
|
46.9
|
1.0
|
O2B
|
A:DCP503
|
4.7
|
29.8
|
1.0
|
CB
|
A:GLU127
|
4.8
|
27.4
|
1.0
|
O
|
A:ASP126
|
5.0
|
31.5
|
1.0
|
|
Reference:
L.Zhao,
M.G.Pence,
P.P.Christov,
Z.Wawrzak,
J.Y.Choi,
C.J.Rizzo,
M.Egli,
F.P.Guengerich.
Basis of Miscoding of the Dna Adduct N2,3-Ethenoguanine By Human Y-Family Dna Polymerases. J.Biol.Chem. V. 287 35516 2012.
ISSN: ISSN 0021-9258
PubMed: 22910910
DOI: 10.1074/JBC.M112.403253
Page generated: Fri Aug 16 15:17:09 2024
|