Sodium in PDB 7m47: Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min:
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min, PDB code: 7m47
was solved by
J.A.Jamsen,
S.H.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.84 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.049,
62.462,
140.059,
90,
90,
90
|
R / Rfree (%)
|
18 /
20.8
|
Other elements in 7m47:
The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
(pdb code 7m47). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min, PDB code: 7m47:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7m47
Go back to
Sodium Binding Sites List in 7m47
Sodium binding site 1 out
of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na602
b:24.1
occ:1.00
|
OD1
|
A:ASP429
|
2.2
|
24.2
|
1.0
|
O
|
A:HOH851
|
2.4
|
27.5
|
1.0
|
OP1
|
P:DT7
|
2.4
|
23.4
|
1.0
|
OD2
|
A:ASP490
|
2.4
|
23.0
|
1.0
|
O
|
A:HOH847
|
2.6
|
24.3
|
1.0
|
O3'
|
P:DC6
|
2.8
|
20.3
|
1.0
|
OD1
|
A:ASP427
|
3.1
|
24.8
|
1.0
|
CG
|
A:ASP490
|
3.1
|
19.8
|
1.0
|
P
|
P:DT7
|
3.2
|
20.2
|
1.0
|
CG
|
A:ASP429
|
3.3
|
28.1
|
1.0
|
CG
|
A:ASP427
|
3.5
|
28.1
|
1.0
|
MG
|
A:MG606
|
3.6
|
20.2
|
1.0
|
OD2
|
A:ASP429
|
3.7
|
22.9
|
1.0
|
OD1
|
A:ASP490
|
3.8
|
21.6
|
1.0
|
CB
|
A:ASP490
|
3.9
|
18.9
|
1.0
|
C3'
|
P:DC6
|
4.0
|
18.3
|
1.0
|
OD2
|
A:ASP427
|
4.1
|
30.2
|
1.0
|
C5'
|
P:DC6
|
4.1
|
19.3
|
1.0
|
C4'
|
P:DC6
|
4.2
|
19.2
|
1.0
|
OP2
|
P:DT7
|
4.2
|
18.6
|
1.0
|
CB
|
A:ASP427
|
4.3
|
25.6
|
1.0
|
NH2
|
A:ARG488
|
4.3
|
21.9
|
1.0
|
O5'
|
P:DT7
|
4.4
|
20.7
|
1.0
|
C5'
|
P:DT7
|
4.5
|
20.8
|
1.0
|
O22
|
A:PPV607
|
4.6
|
28.0
|
1.0
|
CB
|
A:ASP429
|
4.6
|
23.2
|
1.0
|
O
|
A:VAL428
|
4.6
|
21.9
|
1.0
|
O
|
A:HOH794
|
4.7
|
28.1
|
1.0
|
O5'
|
P:DC6
|
4.9
|
20.5
|
1.0
|
C
|
A:VAL428
|
5.0
|
20.6
|
1.0
|
CA
|
A:ASP429
|
5.0
|
19.7
|
1.0
|
N
|
A:ASP490
|
5.0
|
18.5
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7m47
Go back to
Sodium Binding Sites List in 7m47
Sodium binding site 2 out
of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:19.2
occ:1.00
|
O
|
A:HOH822
|
2.3
|
27.7
|
1.0
|
O
|
A:ALA344
|
2.3
|
18.6
|
1.0
|
O
|
A:SER339
|
2.4
|
20.1
|
1.0
|
OP1
|
P:DA5
|
2.4
|
19.8
|
1.0
|
O
|
A:ILE341
|
2.5
|
20.6
|
1.0
|
O
|
P:HOH110
|
2.7
|
26.2
|
1.0
|
C
|
A:ILE341
|
3.4
|
18.8
|
1.0
|
C
|
A:SER339
|
3.4
|
19.7
|
1.0
|
C
|
A:ALA344
|
3.5
|
19.6
|
1.0
|
P
|
P:DA5
|
3.5
|
20.3
|
1.0
|
O
|
A:HOH807
|
3.6
|
33.1
|
1.0
|
OP2
|
P:DA5
|
3.7
|
20.7
|
1.0
|
N
|
A:ALA344
|
3.7
|
18.6
|
1.0
|
N
|
A:GLY343
|
3.9
|
20.3
|
1.0
|
CA
|
A:TRP342
|
3.9
|
19.5
|
1.0
|
N
|
A:TRP342
|
4.0
|
18.2
|
1.0
|
O
|
P:HOH128
|
4.0
|
50.4
|
1.0
|
N
|
A:ILE341
|
4.1
|
15.4
|
1.0
|
CA
|
A:ALA344
|
4.1
|
20.1
|
1.0
|
CA
|
A:SER339
|
4.1
|
19.0
|
1.0
|
C
|
A:ASN340
|
4.2
|
18.8
|
1.0
|
C
|
A:TRP342
|
4.3
|
18.8
|
1.0
|
N
|
A:ASN340
|
4.3
|
17.9
|
1.0
|
O3'
|
P:DT4
|
4.3
|
17.9
|
1.0
|
CA
|
A:ASN340
|
4.4
|
18.6
|
1.0
|
CA
|
A:ILE341
|
4.4
|
15.3
|
1.0
|
N
|
A:GLY345
|
4.5
|
17.7
|
1.0
|
CB
|
A:ALA344
|
4.7
|
21.2
|
1.0
|
O
|
P:HOH133
|
4.7
|
41.8
|
1.0
|
C
|
A:GLY343
|
4.7
|
17.7
|
1.0
|
O5'
|
P:DA5
|
4.7
|
17.5
|
1.0
|
CA
|
A:GLY345
|
4.7
|
18.1
|
1.0
|
O
|
A:ASN340
|
4.7
|
19.7
|
1.0
|
O2
|
A:EDO608
|
4.8
|
34.0
|
1.0
|
CB
|
A:SER339
|
4.8
|
27.5
|
1.0
|
O
|
A:HOH882
|
4.8
|
37.9
|
1.0
|
CA
|
A:GLY343
|
4.9
|
20.4
|
1.0
|
O
|
A:HOH709
|
4.9
|
47.8
|
1.0
|
O
|
A:PHE338
|
5.0
|
19.1
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7m47
Go back to
Sodium Binding Sites List in 7m47
Sodium binding site 3 out
of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:60.0
occ:1.00
|
O
|
A:ILE302
|
2.6
|
61.5
|
1.0
|
O
|
A:CYS300
|
2.6
|
81.4
|
1.0
|
O
|
A:ILE305
|
2.7
|
53.0
|
1.0
|
OP1
|
D:DC3
|
3.0
|
46.7
|
1.0
|
C
|
A:ILE302
|
3.5
|
71.7
|
1.0
|
C
|
A:CYS300
|
3.7
|
85.9
|
1.0
|
OP2
|
D:DC3
|
3.7
|
64.7
|
1.0
|
C
|
A:ILE305
|
3.8
|
61.8
|
1.0
|
P
|
D:DC3
|
3.8
|
46.7
|
1.0
|
N
|
A:ILE305
|
4.0
|
53.5
|
1.0
|
CA
|
A:PRO303
|
4.1
|
58.3
|
1.0
|
N
|
A:PRO303
|
4.2
|
71.8
|
1.0
|
N
|
A:ILE302
|
4.2
|
68.4
|
1.0
|
CA
|
A:CYS300
|
4.2
|
82.3
|
1.0
|
N
|
A:GLY304
|
4.3
|
58.4
|
1.0
|
CA
|
A:ILE305
|
4.4
|
51.2
|
1.0
|
C
|
A:SER301
|
4.4
|
66.5
|
1.0
|
CA
|
A:ILE302
|
4.5
|
63.5
|
1.0
|
C
|
A:PRO303
|
4.6
|
54.7
|
1.0
|
O
|
A:SER301
|
4.7
|
62.9
|
1.0
|
CB
|
A:ILE305
|
4.7
|
51.2
|
1.0
|
N
|
A:SER301
|
4.8
|
67.2
|
1.0
|
O3'
|
D:DC2
|
4.8
|
37.8
|
1.0
|
N
|
A:GLY306
|
4.8
|
51.0
|
1.0
|
CB
|
A:CYS300
|
4.9
|
83.5
|
1.0
|
O
|
A:ALA299
|
4.9
|
74.6
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7m47
Go back to
Sodium Binding Sites List in 7m47
Sodium binding site 4 out
of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:43.9
occ:0.97
|
NE2
|
A:GLN366
|
2.2
|
51.5
|
1.0
|
O
|
A:HOH894
|
2.3
|
64.3
|
1.0
|
O
|
A:HOH868
|
2.6
|
68.4
|
1.0
|
O
|
A:HOH859
|
3.1
|
60.7
|
1.0
|
O
|
A:HOH775
|
3.3
|
55.2
|
1.0
|
CD
|
A:GLN366
|
3.3
|
56.9
|
1.0
|
OE1
|
A:GLN366
|
3.7
|
64.4
|
1.0
|
CG
|
A:GLN366
|
4.6
|
34.9
|
1.0
|
|
Reference:
J.A.Jamsen,
D.D.Shock,
S.H.Wilson.
Watching Right and Wrong Nucleotide Insertion Captures Hidden Polymerase Fidelity Checkpoints. Nat Commun V. 13 3193 2022.
ISSN: ESSN 2041-1723
PubMed: 35680862
DOI: 10.1038/S41467-022-30141-W
Page generated: Tue Oct 8 17:50:22 2024
|