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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:

Magnesium (Mg) 1 atom

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

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