Potassium in PDB 7m0d: Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
All present enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp:
2.7.7.7;
Protein crystallography data
The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp, PDB code: 7m0d
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)
|
41.78 /
1.80
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.442,
151.989,
86.473,
90,
90,
90
|
R / Rfree (%)
|
16.4 /
18.9
|
Other elements in 7m0d:
The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
(pdb code 7m0d). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp, PDB code: 7m0d:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 1 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K705
b:20.6
occ:1.00
|
O
|
A:ILE305
|
2.6
|
18.2
|
1.0
|
O
|
A:ILE302
|
2.7
|
17.3
|
1.0
|
O
|
A:CYS300
|
2.7
|
19.9
|
1.0
|
O
|
A:HOH1106
|
2.7
|
31.7
|
1.0
|
O
|
H:HOH104
|
2.8
|
35.5
|
1.0
|
OP1
|
H:DC3
|
2.9
|
25.2
|
1.0
|
C
|
A:ILE302
|
3.5
|
18.4
|
1.0
|
C
|
A:ILE305
|
3.7
|
20.0
|
1.0
|
OP2
|
H:DC3
|
3.7
|
28.2
|
1.0
|
C
|
A:CYS300
|
3.7
|
18.9
|
1.0
|
P
|
H:DC3
|
3.8
|
23.0
|
1.0
|
O
|
H:HOH102
|
3.8
|
35.1
|
1.0
|
N
|
A:ILE305
|
4.0
|
15.9
|
1.0
|
N
|
A:ILE302
|
4.1
|
17.1
|
1.0
|
CA
|
A:PRO303
|
4.1
|
18.9
|
1.0
|
N
|
A:PRO303
|
4.1
|
18.3
|
1.0
|
C
|
A:SER301
|
4.3
|
23.5
|
1.0
|
N
|
A:GLY304
|
4.3
|
17.2
|
1.0
|
CA
|
A:ILE305
|
4.4
|
14.7
|
1.0
|
O
|
A:HOH1108
|
4.4
|
51.9
|
1.0
|
CA
|
A:CYS300
|
4.4
|
16.8
|
1.0
|
CA
|
A:ILE302
|
4.5
|
14.7
|
1.0
|
C
|
A:PRO303
|
4.6
|
18.5
|
1.0
|
O
|
A:SER301
|
4.6
|
19.6
|
1.0
|
N
|
A:SER301
|
4.6
|
17.7
|
1.0
|
O3'
|
H:DC2
|
4.7
|
17.7
|
1.0
|
N
|
A:GLY306
|
4.7
|
16.5
|
1.0
|
CA
|
A:SER301
|
4.7
|
17.9
|
1.0
|
O
|
A:ALA299
|
4.8
|
14.8
|
1.0
|
CB
|
A:ILE305
|
4.8
|
13.6
|
1.0
|
CA
|
A:GLY306
|
4.9
|
16.8
|
1.0
|
|
Potassium binding site 2 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 2 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K706
b:18.6
occ:0.84
|
O1
|
F:EDO101
|
2.7
|
28.3
|
1.0
|
O
|
A:SER339
|
2.8
|
13.3
|
1.0
|
O
|
F:HOH406
|
2.8
|
17.0
|
1.0
|
O
|
A:HOH983
|
2.8
|
27.4
|
1.0
|
O2
|
F:EDO101
|
3.0
|
19.9
|
1.0
|
O
|
A:HOH939
|
3.2
|
18.0
|
1.0
|
NA
|
A:NA704
|
3.6
|
10.3
|
1.0
|
C1
|
F:EDO101
|
3.7
|
31.8
|
1.0
|
C
|
A:SER339
|
3.7
|
13.1
|
1.0
|
C2
|
F:EDO101
|
3.8
|
22.9
|
1.0
|
CA
|
A:ASN340
|
4.3
|
14.8
|
1.0
|
OD1
|
A:ASN340
|
4.4
|
15.5
|
1.0
|
N
|
A:ASN340
|
4.4
|
12.3
|
1.0
|
CB
|
A:SER339
|
4.6
|
13.0
|
1.0
|
OG
|
A:SER339
|
4.6
|
17.7
|
1.0
|
O
|
A:HOH1222
|
4.7
|
33.4
|
1.0
|
CA
|
A:SER339
|
4.7
|
13.9
|
1.0
|
O2
|
A:EDO714
|
4.9
|
39.3
|
1.0
|
O1
|
A:EDO714
|
4.9
|
27.9
|
1.0
|
|
Potassium binding site 3 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 3 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K707
b:17.1
occ:1.00
|
O
|
A:THR250
|
2.6
|
19.3
|
1.0
|
O
|
A:GLN247
|
2.6
|
18.2
|
1.0
|
O
|
A:LYS287
|
2.7
|
14.9
|
1.0
|
O
|
A:HOH1133
|
2.7
|
26.7
|
1.0
|
O
|
A:PHE289
|
2.8
|
15.1
|
1.0
|
O
|
A:HOH909
|
3.2
|
14.6
|
1.0
|
O
|
A:SER288
|
3.2
|
16.0
|
1.0
|
C
|
A:SER288
|
3.5
|
20.8
|
1.0
|
C
|
A:PHE289
|
3.7
|
15.6
|
1.0
|
C
|
A:THR250
|
3.8
|
15.4
|
1.0
|
C
|
A:LYS287
|
3.8
|
14.6
|
1.0
|
C
|
A:GLN247
|
3.8
|
16.1
|
1.0
|
N
|
A:PHE289
|
3.9
|
13.7
|
1.0
|
CD2
|
A:HIS252
|
4.0
|
18.6
|
1.0
|
CA
|
A:SER288
|
4.0
|
14.8
|
1.0
|
O
|
A:HOH1096
|
4.0
|
29.0
|
1.0
|
N
|
A:SER288
|
4.3
|
15.4
|
1.0
|
CA
|
A:LYS248
|
4.5
|
14.4
|
1.0
|
CA
|
A:PHE289
|
4.5
|
17.6
|
1.0
|
NE2
|
A:HIS252
|
4.6
|
20.3
|
1.0
|
CA
|
A:ASN251
|
4.6
|
15.4
|
1.0
|
N
|
A:LYS248
|
4.6
|
13.3
|
1.0
|
N
|
A:ASN251
|
4.6
|
16.9
|
1.0
|
N
|
A:HIS290
|
4.6
|
17.0
|
1.0
|
N
|
A:HIS252
|
4.7
|
13.8
|
1.0
|
CA
|
A:HIS290
|
4.7
|
17.3
|
1.0
|
O
|
A:HOH1206
|
4.7
|
32.7
|
1.0
|
CA
|
A:THR250
|
4.7
|
20.3
|
1.0
|
N
|
A:THR250
|
4.7
|
19.3
|
1.0
|
C
|
A:LYS248
|
4.8
|
14.5
|
1.0
|
O
|
A:HOH925
|
4.8
|
27.4
|
1.0
|
CA
|
A:GLN247
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH884
|
4.9
|
30.2
|
1.0
|
CG
|
A:HIS252
|
4.9
|
22.0
|
1.0
|
CB
|
A:THR250
|
5.0
|
30.5
|
1.0
|
|
Potassium binding site 4 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 4 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K705
b:20.4
occ:1.00
|
O
|
B:ILE305
|
2.6
|
17.3
|
1.0
|
O
|
B:CYS300
|
2.7
|
17.5
|
1.0
|
O
|
L:HOH105
|
2.7
|
37.5
|
1.0
|
O
|
B:HOH1107
|
2.7
|
27.6
|
1.0
|
O
|
B:ILE302
|
2.8
|
15.7
|
1.0
|
OP1
|
L:DC3
|
2.9
|
22.6
|
1.0
|
OP2
|
L:DC3
|
3.5
|
24.5
|
1.0
|
C
|
B:ILE302
|
3.6
|
14.3
|
1.0
|
P
|
L:DC3
|
3.6
|
20.2
|
1.0
|
C
|
B:CYS300
|
3.7
|
16.3
|
1.0
|
C
|
B:ILE305
|
3.7
|
18.9
|
1.0
|
O
|
L:HOH116
|
3.9
|
21.7
|
0.5
|
N
|
B:ILE305
|
4.1
|
16.8
|
1.0
|
N
|
B:ILE302
|
4.1
|
17.4
|
1.0
|
CA
|
B:PRO303
|
4.1
|
15.5
|
1.0
|
N
|
B:PRO303
|
4.1
|
15.4
|
1.0
|
C
|
B:SER301
|
4.3
|
19.0
|
1.0
|
N
|
B:GLY304
|
4.3
|
17.9
|
1.0
|
CA
|
B:CYS300
|
4.4
|
16.1
|
1.0
|
CA
|
B:ILE305
|
4.4
|
13.3
|
1.0
|
CA
|
B:ILE302
|
4.5
|
14.2
|
1.0
|
O3'
|
L:DC2
|
4.6
|
19.2
|
1.0
|
N
|
B:SER301
|
4.6
|
16.3
|
1.0
|
C
|
B:PRO303
|
4.6
|
17.4
|
1.0
|
O
|
B:SER301
|
4.6
|
18.6
|
1.0
|
CA
|
B:SER301
|
4.7
|
17.6
|
1.0
|
N
|
B:GLY306
|
4.7
|
15.3
|
1.0
|
O
|
B:ALA299
|
4.8
|
15.9
|
1.0
|
CB
|
B:ILE305
|
4.9
|
16.1
|
1.0
|
CA
|
B:GLY306
|
5.0
|
20.2
|
1.0
|
O5'
|
L:DC3
|
5.0
|
21.4
|
1.0
|
|
Potassium binding site 5 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 5 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K706
b:22.0
occ:0.79
|
O
|
B:SER339
|
2.7
|
13.3
|
1.0
|
O
|
B:HOH1042
|
2.8
|
31.6
|
1.0
|
O2
|
J:EDO102
|
2.8
|
27.8
|
1.0
|
O
|
J:HOH202
|
2.9
|
18.8
|
1.0
|
O1
|
J:EDO102
|
3.1
|
22.2
|
1.0
|
O
|
B:HOH876
|
3.2
|
20.0
|
1.0
|
NA
|
B:NA704
|
3.6
|
10.2
|
1.0
|
C
|
B:SER339
|
3.7
|
15.2
|
1.0
|
C2
|
J:EDO102
|
3.8
|
23.4
|
1.0
|
O
|
B:HOH1176
|
4.0
|
48.7
|
1.0
|
C1
|
J:EDO102
|
4.0
|
22.9
|
1.0
|
CA
|
B:ASN340
|
4.4
|
15.7
|
1.0
|
OD1
|
B:ASN340
|
4.4
|
18.2
|
1.0
|
N
|
B:ASN340
|
4.4
|
12.7
|
1.0
|
CB
|
B:SER339
|
4.5
|
14.9
|
1.0
|
OG
|
B:SER339
|
4.5
|
17.1
|
1.0
|
O
|
B:HOH1224
|
4.6
|
35.3
|
1.0
|
CA
|
B:SER339
|
4.7
|
13.5
|
1.0
|
O1
|
B:FMT713
|
4.9
|
29.9
|
1.0
|
|
Potassium binding site 6 out
of 6 in 7m0d
Go back to
Potassium Binding Sites List in 7m0d
Potassium binding site 6 out
of 6 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K707
b:16.8
occ:1.00
|
O
|
B:GLN247
|
2.6
|
15.1
|
1.0
|
O
|
B:THR250
|
2.6
|
18.6
|
1.0
|
O
|
B:HOH1124
|
2.7
|
23.3
|
1.0
|
O
|
B:LYS287
|
2.7
|
15.5
|
1.0
|
O
|
B:PHE289
|
2.8
|
14.4
|
1.0
|
O
|
B:SER288
|
3.2
|
17.8
|
1.0
|
O
|
B:HOH873
|
3.2
|
14.1
|
1.0
|
C
|
B:SER288
|
3.4
|
16.9
|
1.0
|
C
|
B:PHE289
|
3.7
|
17.0
|
1.0
|
C
|
B:THR250
|
3.8
|
16.0
|
1.0
|
C
|
B:GLN247
|
3.8
|
21.8
|
1.0
|
C
|
B:LYS287
|
3.8
|
16.9
|
1.0
|
N
|
B:PHE289
|
4.0
|
14.9
|
1.0
|
CA
|
B:SER288
|
4.0
|
15.8
|
1.0
|
CD2
|
B:HIS252
|
4.1
|
20.3
|
1.0
|
O
|
B:HOH1066
|
4.1
|
22.8
|
1.0
|
N
|
B:SER288
|
4.4
|
13.4
|
1.0
|
CA
|
B:PHE289
|
4.5
|
15.0
|
1.0
|
CA
|
B:LYS248
|
4.5
|
14.3
|
1.0
|
N
|
B:HIS290
|
4.5
|
14.7
|
1.0
|
CA
|
B:HIS290
|
4.5
|
15.2
|
1.0
|
O
|
B:HOH1217
|
4.5
|
30.8
|
1.0
|
CA
|
B:ASN251
|
4.6
|
16.2
|
1.0
|
N
|
B:ASN251
|
4.6
|
18.4
|
1.0
|
N
|
B:LYS248
|
4.6
|
17.1
|
1.0
|
NE2
|
B:HIS252
|
4.7
|
20.3
|
1.0
|
N
|
B:HIS252
|
4.7
|
14.7
|
1.0
|
CA
|
B:THR250
|
4.8
|
21.0
|
1.0
|
O
|
B:HOH939
|
4.8
|
17.8
|
0.7
|
N
|
B:THR250
|
4.8
|
17.2
|
1.0
|
CA
|
B:GLN247
|
4.8
|
15.6
|
1.0
|
O
|
B:HOH948
|
4.8
|
25.2
|
1.0
|
C
|
B:LYS248
|
4.9
|
19.0
|
1.0
|
CB
|
B:THR250
|
5.0
|
25.6
|
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: Mon Aug 12 19:24:03 2024
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