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Sodium in PDB 7m46: Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min, PDB code: 7m46 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) 23.62 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.263, 62.808, 139.452, 90, 90, 90
R / Rfree (%) 18.6 / 21.7

Other elements in 7m46:

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 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, 5 Min (pdb code 7m46). 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, 5 Min, PDB code: 7m46:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7m46

Go back to Sodium Binding Sites List in 7m46
Sodium binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 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, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:24.6
occ:1.00
 O A:SER339 2.3 25.2 0.4
O A:ALA344 2.3 22.2 1.0
OP1 P:DA5 2.4 23.9 1.0
O A:SER339 2.4 24.9 0.6
O A:HOH726 2.4 30.9 1.0
O A:ILE341 2.4 25.1 1.0
O P:HOH109 2.7 30.4 1.0
C A:ILE341 3.4 22.8 1.0
C A:SER339 3.4 26.8 0.6
C A:SER339 3.4 26.8 0.4
P P:DA5 3.4 25.0 1.0
C A:ALA344 3.5 22.6 1.0
OP2 P:DA5 3.6 24.6 1.0
O A:HOH801 3.8 45.5 1.0
N A:ALA344 3.8 21.8 1.0
N A:GLY343 3.9 22.7 1.0
CA A:TRP342 4.0 22.1 1.0
N A:TRP342 4.0 22.6 1.0
N A:ILE341 4.1 21.9 1.0
CA A:SER339 4.1 24.6 0.6
CA A:ALA344 4.2 24.4 1.0
C A:ASN340 4.2 23.5 1.0
CA A:SER339 4.3 24.7 0.4
O P:HOH122 4.3 29.2 0.5
C A:TRP342 4.3 22.4 1.0
N A:ASN340 4.3 21.6 1.0
O3' P:DT4 4.3 24.7 1.0
CA A:ILE341 4.4 21.1 1.0
CA A:ASN340 4.4 23.9 1.0
N A:GLY345 4.5 23.5 1.0
O P:HOH122 4.6 32.3 0.5
O5' P:DA5 4.6 22.2 1.0
CB A:ALA344 4.7 25.2 1.0
CB A:SER339 4.7 27.0 0.6
CA A:GLY345 4.7 24.3 1.0
C A:GLY343 4.7 22.9 1.0
O1 A:EDO609 4.7 35.6 0.8
O A:ASN340 4.8 26.2 1.0
CA A:GLY343 4.9 24.4 1.0
CB A:SER339 5.0 26.2 0.4

Sodium binding site 2 out of 4 in 7m46

Go back to Sodium Binding Sites List in 7m46
Sodium binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 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, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:31.6
occ:1.00
 OD1 A:ASP429 2.1 27.1 1.0
OD2 A:ASP490 2.4 30.2 1.0
OP1 P:DT7 2.4 28.9 1.0
O A:HOH824 2.5 41.1 1.0
O A:HOH767 2.5 44.4 1.0
O3' P:DC6 2.7 30.3 1.0
OD1 A:ASP427 3.0 28.4 1.0
CG A:ASP490 3.1 27.3 1.0
P P:DT7 3.2 30.5 1.0
CG A:ASP429 3.2 31.4 1.0
CG A:ASP427 3.5 43.0 1.0
MG A:MG601 3.5 28.0 1.0
OD2 A:ASP429 3.7 29.6 1.0
CB A:ASP490 3.8 25.6 1.0
OD1 A:ASP490 3.9 25.8 1.0
OD2 A:ASP427 3.9 43.3 1.0
C3' P:DC6 3.9 26.7 1.0
C4' P:DC6 4.2 25.2 1.0
OP2 P:DT7 4.2 25.7 1.0
C5' P:DC6 4.2 24.9 1.0
CB A:ASP427 4.3 29.9 1.0
O5' P:DT7 4.4 27.5 1.0
NH2 A:ARG488 4.4 27.7 1.0
CB A:ASP429 4.5 29.0 1.0
C5' P:DT7 4.5 28.6 1.0
O A:VAL428 4.6 25.4 1.0
O A:HOH828 4.7 32.2 1.0
O22 A:PPV610 4.9 34.0 0.8
O5' P:DC6 4.9 26.5 1.0
CA A:ASP429 4.9 24.4 1.0
CE1 A:PHE506 5.0 29.9 1.0
C A:VAL428 5.0 24.3 1.0
N A:ASP490 5.0 24.5 1.0
CA A:ASP490 5.0 25.9 1.0

Sodium binding site 3 out of 4 in 7m46

Go back to Sodium Binding Sites List in 7m46
Sodium binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 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, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:62.8
occ:1.00
 O D:HOH103 2.2 60.0 1.0
O A:ILE302 2.2 61.1 1.0
O A:CYS300 2.9 75.6 1.0
C A:ILE302 2.9 71.6 1.0
OP1 D:DC3 3.0 51.5 1.0
O A:ILE305 3.2 61.6 1.0
CA A:PRO303 3.3 64.0 1.0
N A:PRO303 3.3 70.0 1.0
N A:ILE302 3.8 72.3 1.0
C A:CYS300 3.9 81.7 1.0
P D:DC3 3.9 53.3 1.0
N A:GLY304 4.0 55.8 1.0
OP2 D:DC3 4.0 57.0 1.0
CA A:ILE302 4.0 69.8 1.0
C A:SER301 4.0 73.1 1.0
N A:ILE305 4.0 51.4 1.0
C A:PRO303 4.0 59.9 1.0
C A:ILE305 4.1 59.0 1.0
O A:SER301 4.2 73.1 1.0
CB A:PRO303 4.5 66.7 1.0
CA A:ILE305 4.5 59.5 1.0
CA A:SER301 4.6 74.5 1.0
N A:SER301 4.7 73.4 1.0
CD A:PRO303 4.7 75.6 1.0
CA A:CYS300 4.8 79.5 1.0
CB A:ILE305 4.8 56.4 1.0
O A:ALA299 4.9 68.9 1.0
O3' D:DC2 4.9 45.1 1.0
C A:GLY304 5.0 49.9 1.0

Sodium binding site 4 out of 4 in 7m46

Go back to Sodium Binding Sites List in 7m46
Sodium binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 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, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:78.4
occ:1.00
 O A:HOH848 2.3 53.7 1.0
OE1 A:GLN366 3.2 59.0 1.0
O A:HOH705 3.6 46.4 1.0
OD1 A:ASP362 3.9 32.6 1.0
CD A:GLN366 4.0 63.6 1.0
NE2 A:GLN366 4.0 64.7 1.0
O A:HOH706 4.1 57.7 1.0
CG A:ASP362 4.5 34.5 1.0
OD2 A:ASP362 4.8 30.8 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 17:49:49 2024

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