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Sodium in PDB 7m43: Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex

Enzymatic activity of Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 7m43 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) 24.02 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.988, 62.653, 140.386, 90, 90, 90
R / Rfree (%) 19.3 / 23.1

Other elements in 7m43:

The structure of Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex (pdb code 7m43). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 7m43:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7m43

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Sodium binding site 1 out of 5 in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex


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 CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:39.2
occ:1.00
 OD2 A:ASP427 2.4 47.1 1.0
OD1 A:ASP429 2.4 32.4 1.0
OD2 A:ASP490 2.6 30.7 1.0
O1A A:TTP606 2.7 30.6 1.0
OD1 A:ASP427 2.9 42.5 1.0
CG A:ASP427 2.9 43.0 1.0
CG A:ASP490 3.4 31.4 1.0
CG A:ASP429 3.5 36.1 1.0
O3' P:DC6 3.6 30.2 1.0
C3' P:DC6 3.6 27.3 1.0
PA A:TTP606 3.7 30.8 1.0
OD2 A:ASP429 3.8 30.8 1.0
O5' A:TTP606 3.8 29.5 1.0
CA A:CA601 3.9 36.3 1.0
OD1 A:ASP490 4.1 28.6 1.0
C5' A:TTP606 4.1 28.1 1.0
CB A:ASP490 4.2 21.6 1.0
O2A A:TTP606 4.2 30.9 1.0
O A:HOH771 4.2 33.6 1.0
CB A:ASP427 4.3 43.1 1.0
NH2 A:ARG488 4.5 32.3 1.0
C5' P:DC6 4.5 28.2 1.0
C4' P:DC6 4.5 26.6 1.0
O5' P:DC6 4.7 24.7 1.0
C2' P:DC6 4.8 29.6 1.0
OP1 P:DC6 4.8 20.9 1.0
CB A:ASP429 4.8 29.1 1.0
O A:VAL428 4.9 22.8 1.0

Sodium binding site 2 out of 5 in 7m43

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Sodium binding site 2 out of 5 in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex


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 CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:19.4
occ:1.00
 O A:ALA344 2.2 19.9 1.0
O A:SER339 2.3 20.4 1.0
OP1 P:DA5 2.4 20.5 1.0
O A:HOH711 2.4 32.6 1.0
O A:ILE341 2.5 19.7 1.0
O P:HOH104 2.6 25.6 1.0
C A:ALA344 3.4 22.2 1.0
C A:SER339 3.4 20.3 1.0
P P:DA5 3.4 21.1 1.0
C A:ILE341 3.4 22.4 1.0
OP2 P:DA5 3.6 19.7 1.0
O A:HOH796 3.6 28.4 1.0
N A:ALA344 3.7 19.7 1.0
N A:GLY343 4.0 17.5 1.0
O P:HOH126 4.0 38.7 1.0
CA A:TRP342 4.0 17.6 1.0
CA A:SER339 4.1 18.7 1.0
N A:TRP342 4.1 20.3 1.0
CA A:ALA344 4.1 18.1 1.0
N A:ILE341 4.1 18.2 1.0
C A:ASN340 4.3 19.4 1.0
C A:TRP342 4.3 20.6 1.0
O3' P:DT4 4.3 19.2 1.0
N A:ASN340 4.4 22.4 1.0
N A:GLY345 4.4 18.6 1.0
CA A:ILE341 4.5 18.1 1.0
CA A:ASN340 4.5 18.4 1.0
CB A:SER339 4.5 29.2 1.0
O2 A:EDO607 4.5 45.8 0.8
CB A:ALA344 4.6 24.5 1.0
O5' P:DA5 4.6 19.8 1.0
O A:HOH855 4.7 36.3 1.0
CA A:GLY345 4.7 20.6 1.0
C A:GLY343 4.7 19.3 1.0
CA A:GLY343 4.9 18.8 1.0
O A:ASN340 4.9 19.8 1.0

Sodium binding site 3 out of 5 in 7m43

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Sodium binding site 3 out of 5 in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex


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 CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:64.2
occ:1.00
 O A:ILE302 2.2 59.9 1.0
O A:HOH785 2.2 44.6 1.0
OP1 D:DC3 2.8 62.8 1.0
C A:ILE302 3.0 76.5 1.0
O A:CYS300 3.2 85.4 1.0
O A:ILE305 3.3 62.1 1.0
CA A:PRO303 3.4 79.2 1.0
N A:PRO303 3.5 77.6 1.0
N A:ILE302 4.0 79.3 1.0
P D:DC3 4.0 63.4 1.0
N A:GLY304 4.0 51.5 1.0
CA A:ILE302 4.1 88.0 1.0
C A:SER301 4.1 60.2 1.0
C A:PRO303 4.2 56.1 1.0
C A:CYS300 4.2 67.6 1.0
O A:SER301 4.2 81.7 1.0
N A:ILE305 4.2 60.7 1.0
OP2 D:DC3 4.2 55.1 1.0
C A:ILE305 4.3 50.8 1.0
CB A:PRO303 4.6 60.5 1.0
CD A:PRO303 4.7 73.2 1.0
CA A:ILE305 4.8 50.5 1.0
CA A:SER301 4.8 69.0 1.0
N A:SER301 4.9 58.6 1.0
CG A:PRO303 4.9 63.6 1.0

Sodium binding site 4 out of 5 in 7m43

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Sodium binding site 4 out of 5 in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex


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 CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:53.1
occ:1.00
 NE2 A:GLN366 2.4 51.0 1.0
CD A:GLN366 3.4 55.9 1.0
O A:HOH827 3.4 32.1 0.5
OE1 A:GLN366 3.6 55.1 1.0
O A:HOH827 3.8 40.1 0.5
CG A:GLN366 4.8 62.0 1.0

Sodium binding site 5 out of 5 in 7m43

Go back to Sodium Binding Sites List in 7m43
Sodium binding site 5 out of 5 in the Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:57.2
occ:1.00
 O P:HOH120 2.4 35.2 1.0
O2 T:DT10 2.6 22.0 1.0
O T:HOH231 2.6 55.3 1.0
O A:HOH839 3.2 33.0 1.0
O A:HOH844 3.5 45.2 1.0
O4' T:DG11 3.7 26.9 1.0
C2 T:DT10 3.8 23.3 1.0
C1' T:DT10 4.1 28.6 1.0
O P:HOH119 4.1 37.0 1.0
N2 P:DG3 4.4 19.1 1.0
N1 T:DT10 4.4 24.2 1.0
C2 P:DA2 4.5 23.1 1.0
C4' T:DG11 4.5 26.5 1.0
N3 T:DG11 4.5 23.4 1.0
O P:HOH103 4.6 30.1 1.0
C5' T:DG11 4.7 23.9 1.0
C1' T:DG11 4.8 23.3 1.0
N3 P:DG3 4.8 19.1 1.0
N3 T:DT10 4.8 21.9 1.0
C4 T:DG11 4.9 18.2 1.0
C2 P:DG3 4.9 19.7 1.0
O4' T:DT10 4.9 20.7 1.0
C2' T:DT10 4.9 22.4 1.0
N9 T:DG11 5.0 22.7 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 17:49:05 2024

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