Sodium 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:
Sodium Binding Sites:
The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium 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 Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 7m0d
Go back to
Sodium Binding Sites List in 7m0d
Sodium binding site 1 out
of 5 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 Sodium with other atoms in the Na 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:Na702
b:15.2
occ:1.00
|
OD1
|
A:ASP429
|
2.2
|
14.6
|
1.0
|
OD2
|
A:ASP427
|
2.3
|
17.5
|
1.0
|
OD2
|
A:ASP490
|
2.4
|
13.8
|
1.0
|
O1A
|
A:DUP701
|
2.4
|
11.2
|
1.0
|
CG
|
A:ASP427
|
3.0
|
17.8
|
1.0
|
OD1
|
A:ASP427
|
3.1
|
14.0
|
1.0
|
CG
|
A:ASP490
|
3.2
|
15.3
|
1.0
|
CG
|
A:ASP429
|
3.3
|
14.4
|
1.0
|
PA
|
A:DUP701
|
3.4
|
12.5
|
1.0
|
MG
|
A:MG703
|
3.5
|
12.5
|
1.0
|
O3'
|
F:DC6
|
3.5
|
13.2
|
1.0
|
OD2
|
A:ASP429
|
3.6
|
11.2
|
1.0
|
C3'
|
F:DC6
|
3.7
|
12.2
|
1.0
|
N
|
A:TRS709
|
3.8
|
28.6
|
0.6
|
O5'
|
A:DUP701
|
3.8
|
11.8
|
1.0
|
O2A
|
A:DUP701
|
3.9
|
13.6
|
1.0
|
CB
|
A:ASP490
|
3.9
|
10.8
|
1.0
|
C5'
|
A:DUP701
|
4.0
|
11.2
|
1.0
|
OD1
|
A:ASP490
|
4.1
|
15.1
|
1.0
|
O2
|
A:TRS709
|
4.2
|
14.6
|
0.6
|
O
|
A:HOH907
|
4.3
|
15.4
|
0.4
|
CB
|
A:ASP427
|
4.4
|
12.4
|
1.0
|
CB
|
A:ASP429
|
4.6
|
12.5
|
1.0
|
O1G
|
A:DUP701
|
4.6
|
11.8
|
1.0
|
NH2
|
A:ARG488
|
4.7
|
13.0
|
1.0
|
C4'
|
F:DC6
|
4.7
|
13.5
|
1.0
|
C2'
|
F:DC6
|
4.8
|
12.4
|
1.0
|
C2
|
A:TRS709
|
4.8
|
19.1
|
0.6
|
O
|
A:VAL428
|
4.8
|
12.0
|
1.0
|
C5'
|
F:DC6
|
4.9
|
12.1
|
1.0
|
CE1
|
A:PHE506
|
4.9
|
11.3
|
1.0
|
N3A
|
A:DUP701
|
4.9
|
10.1
|
1.0
|
C
|
A:TRS709
|
4.9
|
25.4
|
0.6
|
O2B
|
A:DUP701
|
4.9
|
12.4
|
1.0
|
|
Sodium binding site 2 out
of 5 in 7m0d
Go back to
Sodium Binding Sites List in 7m0d
Sodium binding site 2 out
of 5 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 Sodium with other atoms in the Na 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:Na704
b:10.3
occ:1.00
|
O2
|
F:EDO101
|
2.3
|
19.9
|
1.0
|
O
|
A:SER339
|
2.4
|
13.3
|
1.0
|
O
|
A:ALA344
|
2.5
|
13.6
|
1.0
|
OP1
|
F:DG5
|
2.5
|
15.3
|
1.0
|
O
|
A:ILE341
|
2.6
|
12.9
|
1.0
|
O
|
F:HOH406
|
2.7
|
17.0
|
1.0
|
C2
|
F:EDO101
|
3.2
|
22.9
|
1.0
|
C
|
A:SER339
|
3.4
|
13.1
|
1.0
|
P
|
F:DG5
|
3.5
|
12.5
|
1.0
|
C
|
A:ALA344
|
3.5
|
12.9
|
1.0
|
C
|
A:ILE341
|
3.5
|
11.0
|
1.0
|
K
|
A:K706
|
3.6
|
18.6
|
0.8
|
OP2
|
F:DG5
|
3.7
|
13.9
|
1.0
|
N
|
A:ALA344
|
3.9
|
10.2
|
1.0
|
N
|
A:GLY343
|
4.0
|
11.1
|
1.0
|
CA
|
A:SER339
|
4.1
|
13.9
|
1.0
|
CA
|
A:TRP342
|
4.1
|
12.5
|
1.0
|
N
|
A:TRP342
|
4.2
|
10.9
|
1.0
|
N
|
A:ILE341
|
4.2
|
10.2
|
1.0
|
CA
|
A:ALA344
|
4.2
|
9.9
|
1.0
|
C
|
A:ASN340
|
4.3
|
15.2
|
1.0
|
O1
|
A:EDO714
|
4.4
|
27.9
|
1.0
|
O1
|
F:EDO101
|
4.4
|
28.3
|
1.0
|
C1
|
F:EDO101
|
4.4
|
31.8
|
1.0
|
C
|
A:TRP342
|
4.4
|
10.4
|
1.0
|
N
|
A:ASN340
|
4.4
|
12.3
|
1.0
|
N
|
A:GLY345
|
4.4
|
14.1
|
1.0
|
CA
|
A:ILE341
|
4.5
|
8.6
|
1.0
|
O3'
|
F:DT4
|
4.5
|
11.3
|
1.0
|
CB
|
A:SER339
|
4.6
|
13.0
|
1.0
|
CA
|
A:ASN340
|
4.6
|
14.8
|
1.0
|
O5'
|
F:DG5
|
4.6
|
13.8
|
1.0
|
CA
|
A:GLY345
|
4.7
|
13.0
|
1.0
|
C
|
A:GLY343
|
4.8
|
13.2
|
1.0
|
CB
|
A:ALA344
|
4.8
|
10.9
|
1.0
|
O
|
A:ASN340
|
4.8
|
12.4
|
1.0
|
CA
|
A:GLY343
|
5.0
|
14.4
|
1.0
|
|
Sodium binding site 3 out
of 5 in 7m0d
Go back to
Sodium Binding Sites List in 7m0d
Sodium binding site 3 out
of 5 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 Sodium with other atoms in the Na 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
|
B:Na702
b:14.1
occ:1.00
|
OD1
|
B:ASP429
|
2.2
|
12.4
|
1.0
|
OD2
|
B:ASP427
|
2.3
|
17.6
|
1.0
|
O2A
|
B:DUP701
|
2.4
|
11.3
|
1.0
|
OD2
|
B:ASP490
|
2.4
|
13.8
|
1.0
|
CG
|
B:ASP427
|
3.0
|
14.7
|
1.0
|
OD1
|
B:ASP427
|
3.0
|
12.5
|
1.0
|
CG
|
B:ASP429
|
3.2
|
15.8
|
1.0
|
CG
|
B:ASP490
|
3.2
|
13.8
|
1.0
|
O3'
|
J:DC6
|
3.4
|
12.8
|
1.0
|
PA
|
B:DUP701
|
3.4
|
12.2
|
1.0
|
MG
|
B:MG703
|
3.4
|
12.5
|
1.0
|
OD2
|
B:ASP429
|
3.6
|
12.7
|
1.0
|
N
|
J:TRS101
|
3.7
|
22.6
|
0.7
|
C3'
|
J:DC6
|
3.7
|
13.0
|
1.0
|
O5'
|
B:DUP701
|
3.8
|
10.9
|
1.0
|
O1A
|
B:DUP701
|
3.9
|
11.5
|
1.0
|
CB
|
B:ASP490
|
3.9
|
11.6
|
1.0
|
C5'
|
B:DUP701
|
4.0
|
8.8
|
1.0
|
OD1
|
B:ASP490
|
4.1
|
14.6
|
1.0
|
O
|
B:HOH1002
|
4.2
|
17.7
|
0.3
|
O1
|
J:TRS101
|
4.3
|
19.6
|
0.7
|
CB
|
B:ASP427
|
4.4
|
10.4
|
1.0
|
CB
|
B:ASP429
|
4.6
|
11.1
|
1.0
|
O1G
|
B:DUP701
|
4.7
|
11.9
|
1.0
|
C4'
|
J:DC6
|
4.7
|
9.7
|
1.0
|
C2'
|
J:DC6
|
4.8
|
11.4
|
1.0
|
C
|
J:TRS101
|
4.8
|
18.0
|
0.7
|
NH2
|
B:ARG488
|
4.8
|
11.3
|
1.0
|
C1
|
J:TRS101
|
4.8
|
20.1
|
0.7
|
N3A
|
B:DUP701
|
4.9
|
10.8
|
1.0
|
C5'
|
J:DC6
|
4.9
|
11.8
|
1.0
|
O
|
B:VAL428
|
4.9
|
12.6
|
1.0
|
CE1
|
B:PHE506
|
4.9
|
12.6
|
1.0
|
O1B
|
B:DUP701
|
4.9
|
10.9
|
1.0
|
O5'
|
J:DC6
|
5.0
|
12.6
|
1.0
|
|
Sodium binding site 4 out
of 5 in 7m0d
Go back to
Sodium Binding Sites List in 7m0d
Sodium binding site 4 out
of 5 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 Sodium with other atoms in the Na 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:Na704
b:10.2
occ:1.00
|
O1
|
J:EDO102
|
2.4
|
22.2
|
1.0
|
O
|
B:SER339
|
2.4
|
13.3
|
1.0
|
O
|
B:ALA344
|
2.5
|
13.1
|
1.0
|
OP1
|
J:DG5
|
2.5
|
14.4
|
1.0
|
O
|
B:ILE341
|
2.6
|
12.3
|
1.0
|
O
|
J:HOH202
|
2.6
|
18.8
|
1.0
|
C1
|
J:EDO102
|
3.4
|
22.9
|
1.0
|
C
|
B:SER339
|
3.5
|
15.2
|
1.0
|
C
|
B:ALA344
|
3.5
|
13.2
|
1.0
|
P
|
J:DG5
|
3.6
|
13.0
|
1.0
|
C
|
B:ILE341
|
3.6
|
10.7
|
1.0
|
K
|
B:K706
|
3.6
|
22.0
|
0.8
|
OP2
|
J:DG5
|
3.7
|
12.4
|
1.0
|
N
|
B:ALA344
|
3.9
|
11.4
|
1.0
|
C2
|
J:EDO102
|
4.0
|
23.4
|
1.0
|
CA
|
B:SER339
|
4.1
|
13.5
|
1.0
|
N
|
B:GLY343
|
4.1
|
13.3
|
1.0
|
CA
|
B:TRP342
|
4.1
|
12.5
|
1.0
|
N
|
B:TRP342
|
4.2
|
12.7
|
1.0
|
N
|
B:ILE341
|
4.3
|
9.6
|
1.0
|
CA
|
B:ALA344
|
4.3
|
10.7
|
1.0
|
O2
|
J:EDO102
|
4.3
|
27.8
|
1.0
|
C
|
B:ASN340
|
4.4
|
14.8
|
1.0
|
N
|
B:GLY345
|
4.4
|
13.3
|
1.0
|
N
|
B:ASN340
|
4.5
|
12.7
|
1.0
|
C
|
B:TRP342
|
4.5
|
12.4
|
1.0
|
O1
|
B:FMT713
|
4.5
|
29.9
|
1.0
|
CB
|
B:SER339
|
4.5
|
14.9
|
1.0
|
O3'
|
J:DT4
|
4.5
|
11.5
|
1.0
|
CA
|
B:ILE341
|
4.6
|
9.7
|
1.0
|
CA
|
B:ASN340
|
4.6
|
15.7
|
1.0
|
CA
|
B:GLY345
|
4.7
|
13.7
|
1.0
|
O5'
|
J:DG5
|
4.7
|
13.2
|
1.0
|
C
|
B:GLY343
|
4.8
|
12.1
|
1.0
|
CB
|
B:ALA344
|
4.9
|
10.2
|
1.0
|
O
|
B:ASN340
|
4.9
|
15.2
|
1.0
|
CA
|
B:GLY343
|
5.0
|
14.8
|
1.0
|
|
Sodium binding site 5 out
of 5 in 7m0d
Go back to
Sodium Binding Sites List in 7m0d
Sodium binding site 5 out
of 5 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 Sodium with other atoms in the Na 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
|
K:Na101
b:29.2
occ:1.00
|
O
|
K:HOH215
|
2.8
|
35.2
|
1.0
|
O6
|
L:DG1
|
2.9
|
18.0
|
1.0
|
O6
|
K:DG3
|
2.9
|
25.8
|
1.0
|
O
|
L:HOH106
|
3.0
|
41.6
|
1.0
|
O
|
L:HOH114
|
3.2
|
39.6
|
1.0
|
O
|
K:HOH209
|
3.4
|
45.2
|
1.0
|
N4
|
L:DC2
|
3.7
|
22.4
|
1.0
|
C6
|
L:DG1
|
3.9
|
18.0
|
1.0
|
N4
|
K:DC4
|
4.0
|
17.6
|
1.0
|
C6
|
K:DG3
|
4.1
|
21.9
|
1.0
|
O
|
L:HOH112
|
4.3
|
41.1
|
1.0
|
N7
|
K:DG2
|
4.5
|
38.9
|
1.0
|
N7
|
L:DG1
|
4.6
|
19.6
|
1.0
|
C5
|
L:DG1
|
4.6
|
20.4
|
1.0
|
N7
|
K:DG3
|
4.7
|
27.9
|
1.0
|
O
|
K:HOH214
|
4.7
|
28.6
|
1.0
|
O6
|
K:DG2
|
4.7
|
31.2
|
1.0
|
C5
|
K:DG3
|
4.8
|
22.6
|
1.0
|
C4
|
L:DC2
|
5.0
|
25.1
|
1.0
|
C5
|
K:DG2
|
5.0
|
33.6
|
1.0
|
N1
|
L:DG1
|
5.0
|
14.2
|
1.0
|
O
|
B:HOH1006
|
5.0
|
35.9
|
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 17:47:35 2024
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