Sodium in PDB 3isc: Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
Enzymatic activity of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
All present enzymatic activity of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna:
2.7.7.7;
Protein crystallography data
The structure of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna, PDB code: 3isc
was solved by
W.A.Beard,
D.D.Shock,
V.K.Batra,
L.C.Pedersen,
S.H.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.81 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.410,
79.300,
54.950,
90.00,
105.80,
90.00
|
R / Rfree (%)
|
18.6 /
22.7
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
(pdb code 3isc). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna, PDB code: 3isc:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 3isc
Go back to
Sodium Binding Sites List in 3isc
Sodium binding site 1 out
of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na401
b:12.4
occ:1.00
|
O
|
A:THR101
|
2.3
|
13.7
|
1.0
|
OP1
|
P:DG9
|
2.4
|
10.0
|
1.0
|
O
|
A:ILE106
|
2.4
|
13.1
|
1.0
|
O
|
A:VAL103
|
2.4
|
12.0
|
1.0
|
O
|
P:HOH11
|
2.5
|
12.9
|
1.0
|
O
|
A:HOH507
|
2.6
|
21.0
|
1.0
|
C
|
A:THR101
|
3.2
|
15.8
|
1.0
|
NA
|
A:NA403
|
3.2
|
28.6
|
1.0
|
C
|
A:VAL103
|
3.4
|
13.1
|
1.0
|
C
|
A:ILE106
|
3.4
|
12.2
|
1.0
|
P
|
P:DG9
|
3.5
|
13.4
|
1.0
|
OP2
|
P:DG9
|
3.7
|
13.8
|
1.0
|
N
|
A:ILE106
|
3.8
|
11.4
|
1.0
|
CA
|
A:THR101
|
3.8
|
14.4
|
1.0
|
CA
|
A:SER104
|
3.9
|
12.9
|
1.0
|
N
|
A:GLY105
|
4.0
|
10.6
|
1.0
|
N
|
A:SER104
|
4.0
|
13.0
|
1.0
|
N
|
A:VAL103
|
4.1
|
13.0
|
1.0
|
CA
|
A:ILE106
|
4.1
|
12.4
|
1.0
|
N
|
A:ARG102
|
4.3
|
16.4
|
1.0
|
C
|
A:ARG102
|
4.3
|
15.4
|
1.0
|
CB
|
A:THR101
|
4.3
|
13.2
|
1.0
|
C
|
A:SER104
|
4.3
|
11.7
|
1.0
|
N
|
A:GLY107
|
4.3
|
12.5
|
1.0
|
CA
|
A:VAL103
|
4.4
|
12.7
|
1.0
|
O3'
|
P:DC8
|
4.5
|
13.5
|
1.0
|
CB
|
A:ILE106
|
4.5
|
13.8
|
1.0
|
CA
|
A:GLY107
|
4.6
|
12.2
|
1.0
|
O5'
|
P:DG9
|
4.6
|
13.7
|
1.0
|
CA
|
A:ARG102
|
4.6
|
15.5
|
1.0
|
C
|
A:GLY105
|
4.6
|
12.1
|
1.0
|
O
|
A:ARG102
|
4.8
|
13.2
|
1.0
|
O
|
A:HOH655
|
4.9
|
30.4
|
1.0
|
O
|
A:LEU100
|
4.9
|
14.2
|
1.0
|
CA
|
A:GLY105
|
5.0
|
10.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 3isc
Go back to
Sodium Binding Sites List in 3isc
Sodium binding site 2 out
of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:24.8
occ:1.00
|
O
|
A:VAL65
|
2.2
|
23.9
|
1.0
|
O
|
D:HOH280
|
2.4
|
23.1
|
1.0
|
O
|
A:LYS60
|
2.5
|
28.4
|
1.0
|
OP1
|
D:DC3
|
2.5
|
23.6
|
1.0
|
O
|
A:LEU62
|
2.6
|
25.3
|
1.0
|
O
|
A:HOH687
|
2.7
|
30.0
|
1.0
|
C
|
A:VAL65
|
3.3
|
20.5
|
1.0
|
C
|
A:LYS60
|
3.5
|
28.6
|
1.0
|
C
|
A:LEU62
|
3.6
|
26.6
|
1.0
|
P
|
D:DC3
|
3.6
|
20.4
|
1.0
|
N
|
A:VAL65
|
3.7
|
20.6
|
1.0
|
OP2
|
D:DC3
|
3.8
|
16.2
|
1.0
|
O
|
D:HOH279
|
3.9
|
38.6
|
1.0
|
CA
|
A:VAL65
|
4.0
|
20.1
|
1.0
|
N
|
A:GLY64
|
4.1
|
23.4
|
1.0
|
CA
|
A:LYS60
|
4.2
|
26.2
|
1.0
|
N
|
A:LEU62
|
4.2
|
28.3
|
1.0
|
CA
|
A:PRO63
|
4.2
|
25.3
|
1.0
|
N
|
A:PRO63
|
4.3
|
26.0
|
1.0
|
CB
|
A:VAL65
|
4.3
|
20.6
|
1.0
|
CG
|
A:LYS60
|
4.3
|
29.1
|
1.0
|
C
|
A:LYS61
|
4.3
|
30.0
|
1.0
|
N
|
A:GLY66
|
4.3
|
19.6
|
1.0
|
O3'
|
D:DT2
|
4.5
|
21.0
|
1.0
|
N
|
A:LYS61
|
4.5
|
29.4
|
1.0
|
C
|
A:PRO63
|
4.5
|
23.1
|
1.0
|
CA
|
A:LEU62
|
4.5
|
27.2
|
1.0
|
CA
|
A:GLY66
|
4.6
|
17.9
|
1.0
|
C
|
A:GLY64
|
4.7
|
21.0
|
1.0
|
O
|
A:LYS61
|
4.7
|
30.9
|
1.0
|
CA
|
A:LYS61
|
4.7
|
30.1
|
1.0
|
O5'
|
D:DC3
|
4.9
|
20.9
|
1.0
|
CB
|
A:LYS60
|
4.9
|
26.7
|
1.0
|
O
|
A:ALA59
|
4.9
|
22.9
|
1.0
|
CA
|
A:GLY64
|
5.0
|
20.7
|
1.0
|
|
Sodium binding site 3 out
of 4 in 3isc
Go back to
Sodium Binding Sites List in 3isc
Sodium binding site 3 out
of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:28.6
occ:1.00
|
O
|
A:HOH399
|
2.4
|
17.9
|
1.0
|
O
|
A:HOH638
|
2.5
|
43.1
|
1.0
|
O
|
P:HOH11
|
2.5
|
12.9
|
1.0
|
O
|
A:THR101
|
2.6
|
13.7
|
1.0
|
O
|
A:HOH507
|
2.7
|
21.0
|
1.0
|
O
|
A:HOH627
|
2.8
|
30.4
|
1.0
|
NA
|
A:NA401
|
3.2
|
12.4
|
1.0
|
C
|
A:THR101
|
3.6
|
15.8
|
1.0
|
O
|
A:HOH655
|
4.2
|
30.4
|
1.0
|
CA
|
A:ARG102
|
4.2
|
15.5
|
1.0
|
N
|
A:ARG102
|
4.3
|
16.4
|
1.0
|
NZ
|
A:LYS27
|
4.3
|
24.4
|
1.0
|
OG1
|
A:THR101
|
4.4
|
13.3
|
1.0
|
CB
|
A:THR101
|
4.4
|
13.2
|
1.0
|
CA
|
A:THR101
|
4.6
|
14.4
|
1.0
|
C
|
A:ARG102
|
4.7
|
15.4
|
1.0
|
O
|
A:HOH675
|
4.7
|
32.7
|
1.0
|
OP1
|
P:DG9
|
4.7
|
10.0
|
1.0
|
O
|
P:HOH130
|
4.8
|
22.8
|
1.0
|
O
|
A:HOH689
|
4.8
|
27.3
|
1.0
|
OP2
|
P:DG9
|
4.8
|
13.8
|
1.0
|
O
|
A:HOH548
|
4.9
|
23.1
|
1.0
|
O
|
A:ARG102
|
5.0
|
13.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 3isc
Go back to
Sodium Binding Sites List in 3isc
Sodium binding site 4 out
of 4 in the Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Binary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf) in the Gapped Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:20.6
occ:1.00
|
OG
|
A:SER171
|
2.2
|
13.6
|
1.0
|
O
|
A:HOH586
|
2.3
|
30.8
|
1.0
|
O
|
A:HOH497
|
2.5
|
18.3
|
1.0
|
O
|
A:HOH557
|
2.5
|
19.7
|
1.0
|
O
|
A:HOH486
|
2.7
|
21.8
|
1.0
|
CB
|
A:SER171
|
3.4
|
13.9
|
1.0
|
N
|
A:SER171
|
3.9
|
13.7
|
1.0
|
O
|
A:HOH504
|
4.1
|
17.4
|
1.0
|
CA
|
A:SER171
|
4.2
|
14.7
|
1.0
|
O
|
A:HOH397
|
4.3
|
34.6
|
1.0
|
O
|
A:HOH692
|
4.6
|
35.9
|
1.0
|
OD1
|
A:ASP170
|
4.6
|
15.5
|
1.0
|
C
|
A:SER171
|
4.9
|
15.5
|
1.0
|
N
|
A:GLU172
|
4.9
|
13.1
|
1.0
|
C
|
A:ASP170
|
5.0
|
14.9
|
1.0
|
|
Reference:
W.A.Beard,
D.D.Shock,
V.K.Batra,
L.C.Pedersen,
S.H.Wilson.
Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843
Page generated: Mon Oct 7 11:02:05 2024
|