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Sodium in PDB 7m45: Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec, PDB code: 7m45 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 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.018, 62.547, 140.01, 90, 90, 90
R / Rfree (%) 20.5 / 24.2

Other elements in 7m45:

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec 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+ Reaction State Ternary Complex, 120 Sec (pdb code 7m45). 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+ Reaction State Ternary Complex, 120 Sec, PDB code: 7m45:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7m45

Go back to Sodium Binding Sites List in 7m45
Sodium binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec


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+ Reaction State Ternary Complex, 120 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:21.0
occ:1.00
 O A:ALA344 2.3 20.1 1.0
O A:SER339 2.3 19.9 0.4
OP1 P:DA5 2.4 21.8 1.0
O A:ILE341 2.4 22.3 1.0
O A:SER339 2.5 19.5 0.6
O P:HOH128 2.5 28.3 1.0
O P:HOH111 2.6 26.1 1.0
C A:ILE341 3.3 21.7 1.0
C A:ALA344 3.4 20.5 1.0
C A:SER339 3.4 21.9 0.4
P P:DA5 3.4 31.1 1.0
C A:SER339 3.4 22.4 0.6
OP2 P:DA5 3.6 18.3 1.0
O A:HOH800 3.8 38.4 1.0
N A:ALA344 3.8 17.9 1.0
CA A:TRP342 3.9 19.7 1.0
N A:GLY343 4.0 24.2 1.0
N A:TRP342 4.0 20.8 1.0
N A:ILE341 4.1 17.7 1.0
CA A:ALA344 4.1 23.8 1.0
CA A:SER339 4.1 20.0 0.6
CA A:SER339 4.2 21.0 0.4
C A:ASN340 4.3 19.8 1.0
C A:TRP342 4.3 22.4 1.0
N A:ASN340 4.3 19.0 1.0
O3' P:DT4 4.4 24.6 1.0
CA A:ILE341 4.4 17.5 1.0
CA A:ASN340 4.4 20.2 1.0
N A:GLY345 4.4 18.4 1.0
O P:HOH126 4.5 24.3 0.5
CB A:ALA344 4.6 23.1 1.0
O P:HOH126 4.6 22.2 0.5
O5' P:DA5 4.6 18.1 1.0
CB A:SER339 4.7 23.4 0.6
CA A:GLY345 4.7 20.0 1.0
C A:GLY343 4.7 22.3 1.0
O A:ASN340 4.8 23.1 1.0
CA A:GLY343 4.9 22.2 1.0
CB A:SER339 4.9 22.9 0.4
O A:HOH830 5.0 45.4 1.0

Sodium binding site 2 out of 4 in 7m45

Go back to Sodium Binding Sites List in 7m45
Sodium binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec


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+ Reaction State Ternary Complex, 120 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:53.3
occ:1.00
 O D:HOH102 2.2 50.2 1.0
O A:ILE302 2.3 64.0 1.0
O A:CYS300 2.6 82.8 1.0
O A:ILE305 2.9 59.8 1.0
C A:ILE302 3.1 66.3 1.0
OP1 D:DC3 3.1 55.4 1.0
C A:CYS300 3.6 84.5 1.0
N A:PRO303 3.6 70.8 1.0
CA A:PRO303 3.6 66.2 1.0
N A:ILE305 3.9 50.3 1.0
C A:ILE305 3.9 55.6 1.0
N A:ILE302 3.9 67.9 1.0
OP2 D:DC3 4.0 55.1 1.0
C A:SER301 4.0 68.8 1.0
P D:DC3 4.0 53.6 1.0
N A:GLY304 4.1 49.6 1.0
O A:SER301 4.1 68.2 1.0
CA A:ILE302 4.2 66.3 1.0
C A:PRO303 4.2 63.0 1.0
CA A:CYS300 4.3 85.2 1.0
CA A:ILE305 4.4 53.1 1.0
N A:SER301 4.5 78.0 1.0
CB A:ILE305 4.6 56.7 1.0
CA A:SER301 4.7 75.4 1.0
O A:ALA299 4.8 68.6 1.0
CD A:PRO303 4.8 72.1 1.0
C A:GLY304 4.9 53.4 1.0
CB A:PRO303 5.0 65.9 1.0

Sodium binding site 3 out of 4 in 7m45

Go back to Sodium Binding Sites List in 7m45
Sodium binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec


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+ Reaction State Ternary Complex, 120 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:30.5
occ:1.00
 OD1 A:ASP429 2.1 28.4 1.0
OD2 A:ASP427 2.2 35.1 0.4
OD2 A:ASP490 2.3 24.5 1.0
OP1 P:DT7 2.4 22.7 0.6
O A:HOH818 2.4 26.2 0.6
O A:HOH775 2.5 28.1 0.6
O3' P:DC6 2.6 30.7 0.6
O3' P:DC6 2.6 29.2 0.4
O1A A:TTP602 2.7 23.3 0.4
CG A:ASP427 3.0 34.2 0.4
P P:DT7 3.1 26.5 0.6
OD1 A:ASP427 3.1 32.8 0.6
CG A:ASP490 3.1 26.2 1.0
OD1 A:ASP427 3.2 33.7 0.4
CG A:ASP429 3.2 32.9 1.0
CG A:ASP427 3.5 34.4 0.6
MG A:MG603 3.5 25.8 1.0
OD2 A:ASP429 3.6 30.2 1.0
C3' P:DC6 3.7 27.4 0.4
PA A:TTP602 3.7 27.4 0.4
CB A:ASP490 3.8 21.0 1.0
C3' P:DC6 3.8 26.8 0.6
OD2 A:ASP427 3.9 34.4 0.6
O5' A:TTP602 3.9 26.2 0.4
OD1 A:ASP490 4.0 26.9 1.0
C4' P:DC6 4.1 26.1 0.6
O2A A:TTP602 4.1 27.2 0.4
OP2 P:DT7 4.2 27.2 0.6
O5' P:DT7 4.2 25.0 0.6
CB A:ASP427 4.3 31.0 0.6
C5' A:TTP602 4.3 26.6 0.4
C5' P:DC6 4.3 23.9 0.6
C5' P:DC6 4.3 24.3 0.4
CB A:ASP427 4.3 30.7 0.4
C4' P:DC6 4.3 26.4 0.4
C5' P:DT7 4.4 27.1 0.6
CB A:ASP429 4.5 28.6 1.0
O2G A:TTP602 4.5 39.8 0.4
NH2 A:ARG488 4.6 26.9 1.0
O A:VAL428 4.7 23.3 1.0
O5' P:DC6 4.8 22.4 0.4
O5' P:DC6 4.8 21.2 0.6
C2' P:DC6 4.9 26.6 0.6
CA A:ASP429 4.9 23.5 1.0
CE1 A:PHE506 5.0 28.5 1.0
OP1 P:DC6 5.0 21.2 0.4
O1B A:TTP602 5.0 32.3 0.4
N A:ASP490 5.0 21.4 1.0

Sodium binding site 4 out of 4 in 7m45

Go back to Sodium Binding Sites List in 7m45
Sodium binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec


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+ Reaction State Ternary Complex, 120 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:72.7
occ:0.97
 NE2 A:GLN366 2.4 58.5 1.0
O A:HOH848 3.0 75.0 1.0
O A:HOH811 3.0 61.8 1.0
O A:HOH829 3.2 50.0 1.0
O A:HOH705 3.4 68.3 1.0
CD A:GLN366 3.5 55.6 1.0
OE1 A:GLN366 3.8 55.7 1.0
CG A:GLN366 4.8 49.1 1.0
CE1 A:PHE357 4.9 42.0 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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