Sodium in PDB 7m07: Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Enzymatic activity of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
All present enzymatic activity of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp:
2.7.7.7;
Protein crystallography data
The structure of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m07
was solved by
A.M.Kaminski,
K.Bebenek,
L.C.Pedersen,
T.A.Kunkel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.36 /
1.57
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.003,
59.665,
139.649,
90,
90,
90
|
R / Rfree (%)
|
17.1 /
18.8
|
Other elements in 7m07:
The structure of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
(pdb code 7m07). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m07:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 7m07
Go back to
Sodium Binding Sites List in 7m07
Sodium binding site 1 out
of 5 in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na704
b:11.4
occ:1.00
|
O
|
A:SER339
|
2.3
|
13.1
|
1.0
|
O
|
A:HOH1052
|
2.3
|
22.4
|
1.0
|
O
|
A:ALA344
|
2.4
|
12.9
|
1.0
|
OP1
|
P:DA5
|
2.4
|
14.1
|
1.0
|
O
|
A:ILE341
|
2.5
|
11.8
|
1.0
|
O
|
P:HOH103
|
2.7
|
19.8
|
1.0
|
C
|
A:SER339
|
3.4
|
11.4
|
1.0
|
C
|
A:ILE341
|
3.4
|
11.3
|
1.0
|
C
|
A:ALA344
|
3.5
|
12.8
|
1.0
|
P
|
P:DA5
|
3.5
|
12.3
|
1.0
|
O
|
A:HOH992
|
3.6
|
24.3
|
1.0
|
OP2
|
P:DA5
|
3.7
|
13.3
|
1.0
|
O
|
P:HOH126
|
3.7
|
21.1
|
0.5
|
N
|
A:ALA344
|
3.8
|
12.5
|
1.0
|
CA
|
A:TRP342
|
4.0
|
11.6
|
1.0
|
N
|
A:GLY343
|
4.0
|
11.8
|
1.0
|
N
|
A:ILE341
|
4.1
|
10.5
|
1.0
|
N
|
A:TRP342
|
4.1
|
11.7
|
1.0
|
CA
|
A:SER339
|
4.1
|
11.0
|
1.0
|
CA
|
A:ALA344
|
4.2
|
11.7
|
1.0
|
C
|
A:ASN340
|
4.2
|
12.2
|
1.0
|
N
|
A:ASN340
|
4.3
|
11.1
|
1.0
|
C
|
A:TRP342
|
4.4
|
12.4
|
1.0
|
CA
|
A:ASN340
|
4.4
|
10.6
|
1.0
|
CA
|
A:ILE341
|
4.4
|
10.7
|
1.0
|
O3'
|
P:DT4
|
4.4
|
12.7
|
1.0
|
O
|
P:HOH126
|
4.4
|
27.9
|
0.5
|
N
|
A:GLY345
|
4.5
|
11.0
|
1.0
|
O5'
|
P:DA5
|
4.7
|
10.8
|
1.0
|
CB
|
A:ALA344
|
4.7
|
11.3
|
1.0
|
O
|
A:HOH1001
|
4.7
|
30.3
|
1.0
|
CB
|
A:SER339
|
4.7
|
20.3
|
1.0
|
CA
|
A:GLY345
|
4.7
|
11.8
|
1.0
|
C
|
A:GLY343
|
4.8
|
13.5
|
1.0
|
O
|
A:ASN340
|
4.8
|
13.6
|
1.0
|
O
|
A:HOH886
|
4.8
|
40.4
|
1.0
|
CA
|
A:GLY343
|
4.9
|
13.4
|
1.0
|
|
Sodium binding site 2 out
of 5 in 7m07
Go back to
Sodium Binding Sites List in 7m07
Sodium binding site 2 out
of 5 in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na705
b:30.1
occ:1.00
|
O
|
A:CYS300
|
2.5
|
44.4
|
1.0
|
O
|
A:ILE305
|
2.7
|
37.7
|
1.0
|
O
|
A:ILE302
|
2.7
|
39.1
|
1.0
|
O
|
A:HOH1030
|
2.8
|
40.1
|
1.0
|
OP1
|
D:DC3
|
2.9
|
34.5
|
1.0
|
O
|
D:HOH104
|
3.5
|
33.9
|
1.0
|
C
|
A:ILE302
|
3.6
|
45.1
|
1.0
|
C
|
A:CYS300
|
3.7
|
43.0
|
1.0
|
OP2
|
D:DC3
|
3.7
|
41.3
|
1.0
|
C
|
A:ILE305
|
3.8
|
33.5
|
1.0
|
P
|
D:DC3
|
3.8
|
33.4
|
1.0
|
CA
|
A:PRO303
|
4.1
|
41.6
|
1.0
|
N
|
A:ILE305
|
4.1
|
33.0
|
1.0
|
N
|
A:ILE302
|
4.2
|
43.9
|
1.0
|
N
|
A:PRO303
|
4.2
|
41.5
|
1.0
|
C
|
A:SER301
|
4.3
|
51.5
|
1.0
|
CA
|
A:CYS300
|
4.4
|
48.4
|
1.0
|
N
|
A:GLY304
|
4.4
|
31.9
|
1.0
|
CA
|
A:ILE305
|
4.5
|
32.8
|
1.0
|
CA
|
A:ILE302
|
4.6
|
41.9
|
1.0
|
O
|
A:SER301
|
4.6
|
44.8
|
1.0
|
N
|
A:SER301
|
4.6
|
49.0
|
1.0
|
C
|
A:PRO303
|
4.7
|
39.2
|
1.0
|
N
|
A:GLY306
|
4.7
|
35.1
|
1.0
|
CA
|
A:SER301
|
4.7
|
50.7
|
1.0
|
O3'
|
D:DC2
|
4.7
|
30.5
|
1.0
|
CA
|
A:GLY306
|
4.9
|
36.2
|
1.0
|
O
|
A:ALA299
|
4.9
|
49.1
|
1.0
|
CB
|
A:ILE305
|
5.0
|
38.8
|
1.0
|
O
|
D:HOH103
|
5.0
|
36.8
|
1.0
|
|
Sodium binding site 3 out
of 5 in 7m07
Go back to
Sodium Binding Sites List in 7m07
Sodium binding site 3 out
of 5 in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na706
b:34.4
occ:1.00
|
O
|
A:THR250
|
2.5
|
67.1
|
1.0
|
O
|
A:GLN247
|
2.6
|
53.5
|
1.0
|
O
|
A:LYS287
|
2.8
|
45.1
|
1.0
|
O
|
A:PHE289
|
2.9
|
42.0
|
1.0
|
O
|
A:SER288
|
3.1
|
45.9
|
1.0
|
C
|
A:SER288
|
3.3
|
49.5
|
1.0
|
CA
|
A:SER288
|
3.6
|
44.4
|
1.0
|
O
|
A:HOH870
|
3.6
|
39.8
|
1.0
|
C
|
A:THR250
|
3.7
|
72.8
|
1.0
|
C
|
A:GLN247
|
3.8
|
57.7
|
1.0
|
C
|
A:PHE289
|
3.8
|
55.7
|
1.0
|
C
|
A:LYS287
|
3.9
|
42.1
|
1.0
|
N
|
A:PHE289
|
4.0
|
39.1
|
1.0
|
CD2
|
A:HIS252
|
4.1
|
63.0
|
1.0
|
N
|
A:SER288
|
4.2
|
40.2
|
1.0
|
NE2
|
A:HIS252
|
4.5
|
63.8
|
1.0
|
N
|
A:ASN251
|
4.6
|
53.2
|
1.0
|
CA
|
A:PHE289
|
4.6
|
40.4
|
1.0
|
CA
|
A:THR250
|
4.6
|
90.8
|
1.0
|
CA
|
A:ASN251
|
4.6
|
49.0
|
1.0
|
CA
|
A:GLN247
|
4.7
|
51.8
|
1.0
|
CB
|
A:THR250
|
4.7
|
85.4
|
1.0
|
N
|
A:HIS290
|
4.7
|
53.2
|
1.0
|
CA
|
A:LYS248
|
4.7
|
62.5
|
1.0
|
N
|
A:THR250
|
4.7
|
82.7
|
1.0
|
CA
|
A:HIS290
|
4.7
|
63.2
|
1.0
|
N
|
A:LYS248
|
4.7
|
55.3
|
1.0
|
N
|
A:HIS252
|
4.8
|
42.3
|
1.0
|
CB
|
A:SER288
|
4.9
|
50.6
|
1.0
|
CB
|
A:GLN247
|
4.9
|
44.1
|
1.0
|
|
Sodium binding site 4 out
of 5 in 7m07
Go back to
Sodium Binding Sites List in 7m07
Sodium binding site 4 out
of 5 in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na708
b:36.2
occ:0.92
|
O
|
A:SER463
|
2.4
|
16.8
|
1.0
|
O
|
A:HOH1094
|
2.6
|
35.5
|
1.0
|
O
|
A:HOH1023
|
2.6
|
33.7
|
1.0
|
O
|
A:HOH1116
|
2.6
|
38.7
|
1.0
|
O
|
T:HOH216
|
3.0
|
37.7
|
1.0
|
O
|
T:HOH208
|
3.0
|
27.3
|
1.0
|
C
|
A:SER463
|
3.6
|
17.2
|
1.0
|
O
|
T:HOH246
|
3.7
|
42.6
|
1.0
|
OP1
|
T:DT10
|
3.9
|
17.6
|
1.0
|
O
|
T:HOH253
|
4.5
|
45.1
|
1.0
|
CA
|
A:SER463
|
4.5
|
13.3
|
1.0
|
OP2
|
T:DT10
|
4.5
|
17.2
|
1.0
|
N
|
A:GLN464
|
4.5
|
14.1
|
0.7
|
N
|
A:GLN464
|
4.5
|
14.2
|
0.3
|
CB
|
A:SER463
|
4.5
|
16.7
|
1.0
|
N
|
A:GLU465
|
4.6
|
18.6
|
1.0
|
CA
|
A:GLN464
|
4.6
|
16.0
|
0.7
|
CA
|
A:GLN464
|
4.6
|
16.1
|
0.3
|
N
|
A:SER463
|
4.7
|
14.0
|
1.0
|
P
|
T:DT10
|
4.8
|
17.3
|
1.0
|
OE2
|
A:GLU465
|
4.9
|
21.3
|
1.0
|
|
Sodium binding site 5 out
of 5 in 7m07
Go back to
Sodium Binding Sites List in 7m07
Sodium binding site 5 out
of 5 in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Na101
b:44.8
occ:1.00
|
OP2
|
T:DC4
|
2.7
|
34.3
|
1.0
|
O
|
A:HOH1103
|
2.8
|
44.9
|
1.0
|
O
|
T:HOH254
|
2.9
|
37.4
|
1.0
|
O5'
|
T:DC4
|
3.0
|
36.7
|
1.0
|
C2'
|
T:DG3
|
3.3
|
26.6
|
1.0
|
P
|
T:DC4
|
3.4
|
40.3
|
1.0
|
O
|
T:HOH220
|
3.7
|
31.7
|
1.0
|
C3'
|
T:DG3
|
3.8
|
26.6
|
1.0
|
C2'
|
T:DC4
|
3.8
|
30.2
|
1.0
|
C6
|
T:DC4
|
3.9
|
20.0
|
1.0
|
O
|
T:HOH233
|
3.9
|
31.8
|
1.0
|
C3'
|
T:DC4
|
4.0
|
29.4
|
1.0
|
O3'
|
T:DG3
|
4.1
|
33.8
|
1.0
|
CH2
|
A:TRP274
|
4.1
|
30.6
|
1.0
|
C5'
|
T:DC4
|
4.2
|
28.6
|
1.0
|
CZ2
|
A:TRP274
|
4.3
|
28.4
|
1.0
|
O4'
|
T:DC4
|
4.4
|
23.7
|
1.0
|
C4'
|
T:DC4
|
4.5
|
24.5
|
1.0
|
C1'
|
T:DC4
|
4.6
|
31.8
|
1.0
|
C5
|
T:DC4
|
4.6
|
19.5
|
1.0
|
N1
|
T:DC4
|
4.7
|
22.9
|
1.0
|
C1'
|
T:DG3
|
4.8
|
26.0
|
1.0
|
OP1
|
T:DC4
|
4.8
|
38.4
|
1.0
|
|
Reference:
A.M.Kaminski,
K.Bebenek,
T.A.Kunkel,
L.C.Pedersen.
Comprehensive Structural Survey of Dna Double-Strand Break Synapsis By Dna Polymerase Lambda To Be Published.
Page generated: Tue Oct 8 17:46:06 2024
|