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Sodium in PDB 7m48: Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 Min

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 Min, PDB code: 7m48 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) 35.90 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.168, 62.653, 139.912, 90, 90, 90
R / Rfree (%) 18.4 / 22

Other elements in 7m48:

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 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, 960 Min (pdb code 7m48). 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, 960 Min, PDB code: 7m48:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7m48

Go back to Sodium Binding Sites List in 7m48
Sodium binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:29.6
occ:1.00
 OD1 A:ASP429 2.2 26.7 1.0
OD2 A:ASP490 2.3 25.1 1.0
O A:HOH816 2.4 30.5 1.0
OP1 P:DT7 2.5 24.3 1.0
O A:HOH773 2.6 33.2 1.0
O3' P:DC6 2.8 22.4 1.0
CG A:ASP490 3.1 28.5 1.0
OD1 A:ASP427 3.2 30.6 1.0
P P:DT7 3.2 23.8 1.0
CG A:ASP429 3.3 29.8 1.0
CG A:ASP427 3.5 37.2 1.0
MG A:MG605 3.6 27.1 1.0
OD2 A:ASP429 3.7 30.6 1.0
CB A:ASP490 3.8 24.9 1.0
OD1 A:ASP490 3.8 30.4 1.0
OD2 A:ASP427 4.0 37.4 1.0
C3' P:DC6 4.0 22.1 1.0
C4' P:DC6 4.2 18.9 1.0
CB A:ASP427 4.2 29.8 1.0
C5' P:DC6 4.3 20.7 1.0
NH2 A:ARG488 4.3 23.0 1.0
OP2 P:DT7 4.3 18.6 1.0
O5' P:DT7 4.4 24.9 1.0
O A:VAL428 4.5 23.6 1.0
C5' P:DT7 4.6 27.3 1.0
CB A:ASP429 4.6 29.7 1.0
O A:HOH812 4.6 29.4 1.0
N A:ASP490 4.9 21.5 1.0
O5' P:DC6 4.9 21.5 1.0
C A:VAL428 4.9 25.4 1.0
CA A:ASP490 4.9 24.5 1.0
CA A:ASP429 5.0 25.4 1.0

Sodium binding site 2 out of 4 in 7m48

Go back to Sodium Binding Sites List in 7m48
Sodium binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:21.9
occ:1.00
 O A:SER339 2.2 21.9 0.3
O A:ALA344 2.3 18.3 1.0
OP1 P:DA5 2.4 19.7 1.0
O A:ILE341 2.4 22.3 1.0
O A:SER339 2.4 21.1 0.7
O A:HOH723 2.5 26.5 1.0
O P:HOH105 2.6 25.6 1.0
C A:ILE341 3.4 20.7 1.0
C A:ALA344 3.4 19.1 1.0
C A:SER339 3.4 22.1 0.3
P P:DA5 3.4 22.5 1.0
C A:SER339 3.4 22.7 0.7
OP2 P:DA5 3.6 20.0 1.0
O A:HOH763 3.7 37.3 1.0
N A:ALA344 3.7 18.1 1.0
N A:GLY343 3.9 21.1 1.0
CA A:TRP342 4.0 20.7 1.0
N A:TRP342 4.0 18.2 1.0
N A:ILE341 4.1 18.6 1.0
CA A:SER339 4.1 19.0 0.7
CA A:ALA344 4.1 21.5 1.0
CA A:SER339 4.2 21.2 0.3
C A:ASN340 4.3 19.1 1.0
C A:TRP342 4.3 22.3 1.0
N A:ASN340 4.3 19.0 1.0
O3' P:DT4 4.4 20.4 1.0
CA A:ILE341 4.4 19.5 1.0
N A:GLY345 4.4 21.1 1.0
CA A:ASN340 4.4 22.6 1.0
O5' P:DA5 4.6 17.5 1.0
CB A:ALA344 4.6 24.0 1.0
CA A:GLY345 4.7 21.7 1.0
O P:HOH128 4.7 44.4 1.0
CB A:SER339 4.7 25.4 0.7
C A:GLY343 4.7 20.8 1.0
O1 A:EDO607 4.8 44.1 1.0
O A:HOH855 4.8 54.4 1.0
CA A:GLY343 4.9 22.1 1.0
O A:ASN340 4.9 21.2 1.0
CB A:SER339 5.0 23.8 0.3
O A:PHE338 5.0 19.4 1.0

Sodium binding site 3 out of 4 in 7m48

Go back to Sodium Binding Sites List in 7m48
Sodium binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:59.3
occ:1.00
 O A:ILE302 2.5 73.8 1.0
OP1 D:DC3 2.9 54.6 1.0
O A:ILE305 2.9 60.9 1.0
O A:CYS300 3.0 94.9 1.0
C A:ILE302 3.4 73.9 1.0
OP2 D:DC3 3.7 50.7 1.0
P D:DC3 3.7 52.8 1.0
C A:ILE305 3.9 57.5 1.0
CA A:PRO303 4.0 71.7 1.0
N A:ILE305 4.0 49.9 1.0
C A:CYS300 4.0 94.6 1.0
N A:PRO303 4.0 75.6 1.0
N A:GLY304 4.2 55.6 1.0
N A:ILE302 4.2 71.2 1.0
C A:SER301 4.3 71.8 1.0
O A:SER301 4.3 70.9 1.0
CA A:ILE305 4.4 54.2 1.0
CA A:ILE302 4.4 72.3 1.0
C A:PRO303 4.5 68.0 1.0
CA A:CYS300 4.7 92.2 1.0
CB A:ILE305 4.7 54.2 1.0
O3' D:DC2 4.8 45.4 1.0
O5' D:DC3 4.9 46.9 1.0
N A:SER301 4.9 80.8 1.0

Sodium binding site 4 out of 4 in 7m48

Go back to Sodium Binding Sites List in 7m48
Sodium binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:63.4
occ:1.00
 NE2 A:GLN366 2.4 58.0 1.0
O A:HOH845 3.1 73.7 1.0
O A:HOH843 3.2 52.7 1.0
CD A:GLN366 3.4 56.0 1.0
OE1 A:GLN366 3.7 55.8 1.0
CG A:GLN366 4.8 49.6 1.0
CE2 A:PHE357 4.8 46.9 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 17:50:57 2024

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