Sodium in PDB 3jpp: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate:
2.7.7.7;
Protein crystallography data
The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate, PDB code: 3jpp
was solved by
V.K.Batra,
J.Upton,
B.Kashmerov,
W.A.Beard,
S.H.Wilson,
M.F.Goodman,
C.E.Mckenna,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
26.42 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.700,
80.110,
55.550,
90.00,
107.95,
90.00
|
R / Rfree (%)
|
19.8 /
25
|
Other elements in 3jpp:
The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
(pdb code 3jpp). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate, PDB code: 3jpp:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 3jpp
Go back to
Sodium Binding Sites List in 3jpp
Sodium binding site 1 out
of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na340
b:24.1
occ:1.00
|
OD1
|
A:ASP192
|
2.0
|
18.5
|
1.0
|
O
|
P:HOH273
|
2.1
|
35.2
|
1.0
|
OD2
|
A:ASP190
|
2.1
|
19.5
|
1.0
|
OD2
|
A:ASP256
|
2.2
|
25.8
|
1.0
|
O1A
|
A:G1M338
|
2.6
|
20.6
|
0.5
|
O1A
|
A:G1M338
|
2.6
|
15.2
|
0.5
|
CG
|
A:ASP190
|
3.0
|
20.1
|
1.0
|
CG
|
A:ASP192
|
3.1
|
17.0
|
1.0
|
OD1
|
A:ASP190
|
3.3
|
19.1
|
1.0
|
CG
|
A:ASP256
|
3.4
|
21.9
|
1.0
|
OD2
|
A:ASP192
|
3.4
|
17.7
|
1.0
|
PA
|
A:G1M338
|
3.5
|
21.5
|
0.5
|
PA
|
A:G1M338
|
3.5
|
15.8
|
0.5
|
MG
|
A:MG339
|
3.6
|
18.6
|
1.0
|
O5'
|
A:G1M338
|
3.6
|
20.0
|
0.5
|
O5'
|
A:G1M338
|
3.7
|
15.4
|
0.5
|
C3'
|
P:DOC10
|
3.7
|
41.1
|
1.0
|
O2A
|
A:G1M338
|
4.0
|
15.2
|
0.5
|
O2A
|
A:G1M338
|
4.0
|
20.9
|
0.5
|
C5'
|
A:G1M338
|
4.0
|
19.9
|
0.5
|
CB
|
A:ASP256
|
4.1
|
20.8
|
1.0
|
C5'
|
A:G1M338
|
4.1
|
16.8
|
0.5
|
O
|
P:HOH196
|
4.2
|
36.0
|
1.0
|
C5'
|
P:DOC10
|
4.3
|
38.0
|
1.0
|
OD1
|
A:ASP256
|
4.4
|
20.4
|
1.0
|
O
|
A:HOH578
|
4.4
|
27.9
|
1.0
|
CB
|
A:ASP192
|
4.4
|
18.1
|
1.0
|
CB
|
A:ASP190
|
4.4
|
16.8
|
1.0
|
O5'
|
P:DOC10
|
4.5
|
36.3
|
1.0
|
C4'
|
P:DOC10
|
4.5
|
39.7
|
1.0
|
O1G
|
A:G1M338
|
4.6
|
24.7
|
0.5
|
O1G
|
A:G1M338
|
4.6
|
16.1
|
0.5
|
O
|
A:MET191
|
4.7
|
19.8
|
1.0
|
OP1
|
P:DOC10
|
4.7
|
29.9
|
1.0
|
C2'
|
P:DOC10
|
4.7
|
39.8
|
1.0
|
O3A
|
A:G1M338
|
4.9
|
21.0
|
0.5
|
O3A
|
A:G1M338
|
4.9
|
14.5
|
0.5
|
O2B
|
A:G1M338
|
4.9
|
11.0
|
0.5
|
O2B
|
A:G1M338
|
4.9
|
18.4
|
0.5
|
NH2
|
A:ARG254
|
4.9
|
18.0
|
1.0
|
CA
|
A:ASP192
|
5.0
|
17.8
|
1.0
|
|
Sodium binding site 2 out
of 4 in 3jpp
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Sodium Binding Sites List in 3jpp
Sodium binding site 2 out
of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na341
b:27.0
occ:1.00
|
OP1
|
P:DG9
|
2.3
|
22.6
|
1.0
|
O
|
A:THR101
|
2.3
|
26.1
|
1.0
|
O
|
P:HOH33
|
2.4
|
25.1
|
1.0
|
O
|
A:ILE106
|
2.5
|
20.0
|
1.0
|
O
|
A:HOH524
|
2.6
|
29.6
|
1.0
|
O
|
A:VAL103
|
2.7
|
18.4
|
1.0
|
P
|
P:DG9
|
3.3
|
22.7
|
1.0
|
C
|
A:THR101
|
3.3
|
24.1
|
1.0
|
OP2
|
P:DG9
|
3.4
|
23.3
|
1.0
|
C
|
A:ILE106
|
3.5
|
20.2
|
1.0
|
C
|
A:VAL103
|
3.6
|
19.1
|
1.0
|
N
|
A:ILE106
|
3.8
|
20.5
|
1.0
|
CA
|
A:THR101
|
4.0
|
24.3
|
1.0
|
N
|
A:GLY105
|
4.0
|
19.9
|
1.0
|
O
|
A:HOH525
|
4.0
|
35.1
|
1.0
|
CA
|
A:SER104
|
4.1
|
20.3
|
1.0
|
CA
|
A:ILE106
|
4.2
|
19.8
|
1.0
|
N
|
A:VAL103
|
4.2
|
21.4
|
1.0
|
N
|
A:SER104
|
4.2
|
19.6
|
1.0
|
O3'
|
P:DC8
|
4.3
|
24.0
|
1.0
|
N
|
A:ARG102
|
4.4
|
23.7
|
1.0
|
C
|
A:ARG102
|
4.4
|
22.5
|
1.0
|
C
|
A:SER104
|
4.4
|
19.6
|
1.0
|
N
|
A:GLY107
|
4.5
|
20.5
|
1.0
|
O5'
|
P:DG9
|
4.5
|
25.8
|
1.0
|
CB
|
A:THR101
|
4.6
|
23.9
|
1.0
|
CA
|
A:VAL103
|
4.6
|
20.0
|
1.0
|
CB
|
A:ILE106
|
4.6
|
19.9
|
1.0
|
CA
|
A:ARG102
|
4.6
|
24.8
|
1.0
|
C
|
A:GLY105
|
4.7
|
21.9
|
1.0
|
CA
|
A:GLY107
|
4.7
|
22.7
|
1.0
|
O
|
A:ARG102
|
4.9
|
23.7
|
1.0
|
O
|
A:LEU100
|
4.9
|
21.0
|
1.0
|
CA
|
A:GLY105
|
4.9
|
22.1
|
1.0
|
O
|
P:HOH219
|
5.0
|
34.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 3jpp
Go back to
Sodium Binding Sites List in 3jpp
Sodium binding site 3 out
of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na342
b:38.1
occ:1.00
|
O
|
A:LYS60
|
2.4
|
32.7
|
1.0
|
O
|
A:LEU62
|
2.4
|
36.8
|
1.0
|
O
|
A:HOH481
|
2.5
|
31.6
|
1.0
|
O
|
A:VAL65
|
2.5
|
30.6
|
1.0
|
OP1
|
D:DC3
|
2.6
|
36.2
|
1.0
|
O
|
D:HOH337
|
2.9
|
36.8
|
1.0
|
C
|
A:LEU62
|
3.3
|
36.5
|
1.0
|
C
|
A:LYS60
|
3.4
|
34.0
|
1.0
|
C
|
A:VAL65
|
3.4
|
30.6
|
1.0
|
N
|
A:VAL65
|
3.7
|
30.2
|
1.0
|
P
|
D:DC3
|
3.7
|
35.4
|
1.0
|
CA
|
A:PRO63
|
3.9
|
35.9
|
1.0
|
OP2
|
D:DC3
|
4.0
|
36.3
|
1.0
|
N
|
A:PRO63
|
4.0
|
36.6
|
1.0
|
N
|
A:GLY64
|
4.0
|
33.1
|
1.0
|
CA
|
A:VAL65
|
4.0
|
28.9
|
1.0
|
C
|
A:LYS61
|
4.0
|
37.5
|
1.0
|
CA
|
A:LYS60
|
4.1
|
32.2
|
1.0
|
N
|
A:LEU62
|
4.1
|
36.8
|
1.0
|
O
|
A:LYS61
|
4.2
|
35.9
|
1.0
|
CB
|
A:VAL65
|
4.3
|
26.6
|
1.0
|
C
|
A:PRO63
|
4.3
|
34.6
|
1.0
|
N
|
A:LYS61
|
4.3
|
36.1
|
1.0
|
CG
|
A:LYS60
|
4.3
|
34.6
|
1.0
|
CA
|
A:LEU62
|
4.4
|
36.4
|
1.0
|
N
|
A:GLY66
|
4.5
|
30.4
|
1.0
|
CA
|
A:LYS61
|
4.6
|
37.4
|
1.0
|
O3'
|
D:DT2
|
4.6
|
37.3
|
1.0
|
C
|
A:GLY64
|
4.7
|
31.7
|
1.0
|
O
|
A:ALA59
|
4.7
|
27.8
|
1.0
|
CA
|
A:GLY66
|
4.8
|
30.7
|
1.0
|
CB
|
A:LYS60
|
4.8
|
33.3
|
1.0
|
O5'
|
D:DC3
|
5.0
|
40.5
|
1.0
|
CA
|
A:GLY64
|
5.0
|
32.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 3jpp
Go back to
Sodium Binding Sites List in 3jpp
Sodium binding site 4 out
of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/jp/3jpp-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na347
b:51.9
occ:1.00
|
O
|
A:HOH404
|
1.9
|
33.7
|
1.0
|
O
|
A:HOH578
|
2.0
|
27.9
|
1.0
|
O
|
A:HOH528
|
2.2
|
46.3
|
1.0
|
O
|
A:HOH440
|
2.4
|
39.7
|
1.0
|
O2G
|
A:G1M338
|
3.9
|
28.3
|
0.5
|
O2G
|
A:G1M338
|
4.0
|
21.4
|
0.5
|
O
|
P:HOH196
|
4.0
|
36.0
|
1.0
|
O1G
|
A:G1M338
|
4.2
|
16.1
|
0.5
|
O1G
|
A:G1M338
|
4.3
|
24.7
|
0.5
|
O
|
A:HOH422
|
4.4
|
32.3
|
1.0
|
PG
|
A:G1M338
|
4.6
|
27.3
|
0.5
|
PG
|
A:G1M338
|
4.6
|
19.4
|
0.5
|
C3B2
|
A:G1M338
|
4.7
|
11.0
|
0.5
|
O2A
|
A:G1M338
|
4.7
|
15.2
|
0.5
|
O2A
|
A:G1M338
|
4.7
|
20.9
|
0.5
|
CA
|
A:GLY189
|
4.7
|
18.3
|
1.0
|
C
|
A:GLY189
|
4.8
|
19.5
|
1.0
|
O
|
A:GLY189
|
4.8
|
20.3
|
1.0
|
OD2
|
A:ASP190
|
4.9
|
19.5
|
1.0
|
O
|
P:HOH273
|
4.9
|
35.2
|
1.0
|
|
Reference:
V.K.Batra,
L.C.Pedersen,
W.A.Beard,
S.H.Wilson,
B.A.Kashemirov,
T.G.Upton,
M.F.Goodman,
C.E.Mckenna.
Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Tue Dec 15 06:15:35 2020
|