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Sodium in PDB 3hw8: Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site

Enzymatic activity of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site, PDB code: 3hw8 was solved by M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.32 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.249, 68.386, 137.108, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 23.3

Other elements in 3hw8:

The structure of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site (pdb code 3hw8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site, PDB code: 3hw8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3hw8

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Sodium binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na577

b:25.9
occ:1.00
 OD1 A:ASP429 2.1 25.0 1.0
OD1 A:ASP427 2.2 30.1 1.0
O1A A:D3T581 2.5 19.3 1.0
O C:HOH17 2.5 22.2 1.0
OD2 A:ASP490 2.7 36.5 1.0
CG A:ASP427 3.1 28.1 1.0
CG A:ASP429 3.2 25.3 1.0
OD2 A:ASP427 3.4 24.8 1.0
CB A:ASP490 3.4 27.0 1.0
PA A:D3T581 3.5 23.1 1.0
CG A:ASP490 3.5 33.6 1.0
O5' A:D3T581 3.6 23.6 1.0
MG A:MG576 3.6 24.5 1.0
OD2 A:ASP429 3.6 24.7 1.0
C5' A:D3T581 3.9 23.1 1.0
O A:HOH93 3.9 33.4 1.0
O2A A:D3T581 4.1 25.9 1.0
C3' C:DT6 4.1 20.6 1.0
C5' C:DT6 4.5 21.6 1.0
CB A:ASP429 4.5 22.3 1.0
C4' C:DT6 4.5 21.8 1.0
CB A:ASP427 4.5 26.3 1.0
OD1 A:ASP490 4.6 36.0 1.0
O3G A:D3T581 4.8 21.6 1.0
O3A A:D3T581 4.8 21.5 1.0
OP1 C:DT6 4.8 21.4 1.0
CA A:ASP490 4.9 25.2 1.0

Sodium binding site 2 out of 4 in 3hw8

Go back to Sodium Binding Sites List in 3hw8
Sodium binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na578

b:22.2
occ:1.00
 O A:ILE341 2.4 17.8 1.0
OP1 C:DA5 2.4 16.9 1.0
O A:HOH14 2.4 23.3 1.0
O A:SER339 2.4 21.2 1.0
O A:ALA344 2.5 20.9 1.0
O C:HOH40 2.5 29.6 1.0
C A:ILE341 3.4 19.9 1.0
O C:HOH82 3.4 39.9 1.0
C A:SER339 3.4 22.1 1.0
P C:DA5 3.5 19.9 1.0
C A:ALA344 3.5 19.8 1.0
N A:ALA344 3.7 17.2 1.0
OP2 C:DA5 3.7 17.4 1.0
O A:HOH181 3.8 46.8 1.0
N A:GLY343 3.9 18.0 1.0
CA A:TRP342 3.9 20.2 1.0
N A:ILE341 3.9 19.0 1.0
N A:TRP342 4.0 19.2 1.0
C A:ASN340 4.2 19.9 1.0
CA A:ALA344 4.2 19.1 1.0
C A:TRP342 4.3 19.6 1.0
CA A:SER339 4.3 22.0 1.0
N A:ASN340 4.3 21.2 1.0
O3' C:DT4 4.3 17.7 1.0
CA A:ILE341 4.4 18.9 1.0
CA A:ASN340 4.4 23.5 1.0
N A:GLY345 4.6 19.1 1.0
C A:GLY343 4.6 18.8 1.0
CB A:ALA344 4.7 17.8 1.0
O A:ASN340 4.7 22.4 1.0
O5' C:DA5 4.8 19.7 1.0
CA A:GLY343 4.8 19.5 1.0
O A:HOH60 4.9 49.2 1.0
CA A:GLY345 4.9 18.6 1.0
O C:HOH179 4.9 54.9 1.0
CB A:SER339 4.9 21.4 1.0

Sodium binding site 3 out of 4 in 3hw8

Go back to Sodium Binding Sites List in 3hw8
Sodium binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na579

b:39.8
occ:1.00
 O B:HOH62 2.4 40.5 1.0
O B:HOH168 2.4 44.7 1.0
O A:SER463 2.4 27.7 1.0
O A:HOH48 2.5 30.1 1.0
O A:HOH136 2.5 49.3 1.0
O B:HOH78 2.7 38.2 1.0
C A:SER463 3.6 28.2 1.0
O B:HOH216 3.6 50.1 1.0
OP1 B:DT11 4.0 23.7 1.0
N A:GLU465 4.3 33.0 1.0
OE2 A:GLU466 4.3 58.1 1.0
N A:GLN464 4.4 28.2 1.0
CA A:GLN464 4.4 31.1 1.0
CA A:SER463 4.5 27.7 1.0
OE1 A:GLU466 4.5 60.1 1.0
OP2 B:DT11 4.6 27.8 1.0
CB A:SER463 4.6 28.1 1.0
N A:SER463 4.7 26.0 1.0
P B:DT11 4.8 25.4 1.0
OE2 A:GLU465 4.8 38.0 1.0
CD A:GLU466 4.9 56.9 1.0
C A:GLN464 4.9 32.5 1.0

Sodium binding site 4 out of 4 in 3hw8

Go back to Sodium Binding Sites List in 3hw8
Sodium binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na580

b:51.2
occ:1.00
 O A:ILE302 2.3 52.6 1.0
O A:HOH648 2.3 47.7 1.0
O A:CYS300 2.4 59.2 1.0
O A:ILE305 2.5 53.5 1.0
O A:HOH90 2.6 38.0 1.0
C A:ILE302 3.0 52.9 1.0
OP1 D:DC3 3.4 40.9 1.0
C A:CYS300 3.4 59.1 1.0
C A:ILE305 3.6 53.0 1.0
N A:PRO303 3.6 51.8 1.0
N A:ILE302 3.7 55.0 1.0
CA A:PRO303 3.7 51.0 1.0
OP2 D:DC3 3.7 41.0 1.0
N A:ILE305 3.8 49.6 1.0
CA A:ILE302 3.9 54.0 1.0
C A:SER301 4.0 55.7 1.0
P D:DC3 4.0 42.8 1.0
N A:GLY304 4.1 48.7 1.0
CA A:ILE305 4.1 51.8 1.0
CA A:CYS300 4.2 60.8 1.0
C A:PRO303 4.3 50.0 1.0
N A:SER301 4.3 58.0 1.0
O A:ALA299 4.3 63.4 1.0
O A:SER301 4.4 54.8 1.0
CB A:ILE305 4.5 51.8 1.0
CA A:SER301 4.5 56.4 1.0
N A:GLY306 4.6 54.0 1.0
CD A:PRO303 4.9 52.1 1.0
CA A:GLY306 4.9 56.3 1.0
CB A:ILE302 4.9 54.3 1.0
C A:GLY304 4.9 48.9 1.0
CB A:PRO303 5.0 51.5 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel. Scrunching Durning Dna Repair Synthesis To Be Published.
Page generated: Sun Aug 17 15:22:42 2025

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