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Sodium in PDB 3c5g: Structure of A Ternary Complex of the R517K Pol Lambda Mutant

Enzymatic activity of Structure of A Ternary Complex of the R517K Pol Lambda Mutant

All present enzymatic activity of Structure of A Ternary Complex of the R517K Pol Lambda Mutant:
2.7.7.7;

Protein crystallography data

The structure of Structure of A Ternary Complex of the R517K Pol Lambda Mutant, PDB code: 3c5g was solved by M.Garcia-Diaz, K.Bebenek, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.335, 150.819, 85.822, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.6

Other elements in 3c5g:

The structure of Structure of A Ternary Complex of the R517K Pol Lambda Mutant also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant (pdb code 3c5g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant, PDB code: 3c5g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3c5g

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Sodium binding site 1 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:21.4
occ:1.00
 OD1 A:ASP429 2.2 17.1 1.0
O P:HOH671 2.3 33.9 1.0
OD1 A:ASP427 2.4 18.1 1.0
OD2 A:ASP490 2.5 18.7 1.0
O1A A:D3T576 2.6 14.9 1.0
CG A:ASP427 3.1 16.3 1.0
OD2 A:ASP427 3.2 16.5 1.0
CG A:ASP429 3.3 18.8 1.0
CG A:ASP490 3.4 18.1 1.0
MG A:MG602 3.5 14.9 1.0
PA A:D3T576 3.5 17.2 1.0
OD2 A:ASP429 3.7 15.1 1.0
O5' A:D3T576 3.8 18.9 1.0
O A:HOH1047 3.8 41.3 1.0
C5' A:D3T576 3.9 15.8 1.0
O2A A:D3T576 3.9 20.5 1.0
CB A:ASP490 4.1 15.2 1.0
OD1 A:ASP490 4.1 15.2 1.0
C3' P:2DT6 4.2 14.3 1.0
O A:HOH1126 4.4 27.9 1.0
C5' P:2DT6 4.5 15.7 1.0
CB A:ASP427 4.6 14.0 1.0
CB A:ASP429 4.6 17.1 1.0
NH2 A:ARG488 4.6 10.9 1.0
O A:HOH812 4.7 13.8 1.0
C4' P:2DT6 4.7 16.9 1.0
O A:HOH939 4.7 28.3 1.0
O3G A:D3T576 4.7 16.0 1.0
OP1 P:2DT6 4.7 14.2 1.0
O3A A:D3T576 4.9 17.7 1.0
O1B A:D3T576 4.9 11.3 1.0
O5' P:2DT6 4.9 16.1 1.0

Sodium binding site 2 out of 8 in 3c5g

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Sodium binding site 2 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:22.2
occ:1.00
 O A:ALA344 2.3 16.9 1.0
O A:ILE341 2.4 14.9 1.0
O A:SER339 2.5 16.3 1.0
O P:HOH311 2.5 21.4 1.0
OP1 P:DA5 2.5 19.5 1.0
O P:HOH170 2.6 25.1 1.0
C A:ILE341 3.3 17.3 1.0
C A:SER339 3.4 17.0 1.0
C A:ALA344 3.4 16.6 1.0
P P:DA5 3.5 17.8 1.0
N A:ALA344 3.7 14.4 1.0
OP2 P:DA5 3.7 18.4 1.0
CA A:TRP342 4.0 16.8 1.0
N A:GLY343 4.0 17.7 1.0
N A:ILE341 4.0 16.7 1.0
N A:TRP342 4.0 16.9 1.0
O P:HOH633 4.1 37.3 1.0
CA A:SER339 4.1 17.9 1.0
CA A:ALA344 4.1 14.6 1.0
O A:HOH841 4.1 34.5 1.0
C A:ASN340 4.2 17.4 1.0
C A:TRP342 4.3 17.3 1.0
CA A:ILE341 4.3 17.6 1.0
N A:ASN340 4.4 16.4 1.0
O3' P:DT4 4.4 17.2 1.0
N A:GLY345 4.5 15.8 1.0
CB A:ALA344 4.5 13.8 1.0
CA A:ASN340 4.6 16.2 1.0
CB A:SER339 4.6 18.6 1.0
C A:GLY343 4.7 15.4 1.0
O A:ASN340 4.7 16.0 1.0
CA A:GLY345 4.7 17.0 1.0
O5' P:DA5 4.8 16.5 1.0
CA A:GLY343 4.9 16.0 1.0
O A:PHE338 5.0 17.6 1.0

Sodium binding site 3 out of 8 in 3c5g

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Sodium binding site 3 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:28.1
occ:1.00
 O A:ILE302 2.6 30.3 1.0
OP1 D:DC3 2.7 30.5 1.0
O A:ILE305 2.8 28.6 1.0
O A:CYS300 2.9 28.5 1.0
C A:ILE302 3.3 29.8 1.0
CA A:PRO303 3.6 30.9 1.0
N A:PRO303 3.7 29.9 1.0
C A:ILE305 3.8 27.4 1.0
P D:DC3 3.9 27.1 1.0
N A:ILE305 3.9 29.3 1.0
N A:GLY304 3.9 29.2 1.0
C A:CYS300 4.0 29.1 1.0
OP2 D:DC3 4.1 29.7 1.0
C A:PRO303 4.2 30.0 1.0
N A:ILE302 4.2 29.3 1.0
O D:HOH738 4.3 45.4 1.0
CA A:ILE302 4.3 29.7 1.0
CA A:ILE305 4.3 27.8 1.0
C A:SER301 4.4 29.8 1.0
CA A:CYS300 4.7 28.9 1.0
O3' D:DC2 4.7 26.9 1.0
CB A:ILE305 4.7 27.3 1.0
O A:SER301 4.8 31.7 1.0
N A:GLY306 4.8 27.1 1.0
CD A:PRO303 4.8 31.0 1.0
CB A:PRO303 4.9 30.7 1.0
N A:SER301 4.9 28.7 1.0
C A:GLY304 4.9 28.3 1.0
CA A:SER301 5.0 29.6 1.0

Sodium binding site 4 out of 8 in 3c5g

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Sodium binding site 4 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na807

b:38.7
occ:1.00
 O A:HOH934 2.7 46.4 1.0
O A:HOH866 2.9 23.1 1.0
O4' P:DT4 3.0 20.8 1.0
N2 P:DG3 3.1 21.7 1.0
O P:HOH342 3.1 28.3 1.0
C4' P:DT4 3.3 20.4 1.0
N3 P:DG3 3.4 22.1 1.0
O P:HOH825 3.5 46.0 1.0
O A:HOH873 3.6 25.5 1.0
C1' P:DT4 3.6 19.8 1.0
C2 P:DG3 3.7 20.9 1.0
OE1 A:GLN372 3.7 18.0 1.0
O T:HOH56 3.8 20.1 1.0
O T:HOH622 3.9 41.1 1.0
C5' P:DT4 4.0 18.8 1.0
O P:HOH88 4.1 18.0 1.0
O2 P:DT4 4.3 19.3 1.0
N1 P:DT4 4.4 20.9 1.0
O A:GLY343 4.6 15.3 1.0
C3' P:DT4 4.6 20.4 1.0
C2 P:DT4 4.7 19.1 1.0
C4 P:DG3 4.7 23.3 1.0
CD A:GLN372 4.8 18.2 1.0
C2' P:DT4 4.8 17.5 1.0
N1 P:DG3 5.0 21.2 1.0

Sodium binding site 5 out of 8 in 3c5g

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Sodium binding site 5 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:18.3
occ:1.00
 O Q:HOH7 2.3 18.2 1.0
O B:ALA344 2.4 16.9 1.0
O B:SER339 2.5 20.6 1.0
OP1 Q:DA5 2.5 20.1 1.0
O Q:HOH12 2.6 33.0 1.0
O B:ILE341 2.6 16.6 1.0
C B:SER339 3.5 20.6 1.0
C B:ILE341 3.5 15.9 1.0
P Q:DA5 3.5 18.6 1.0
C B:ALA344 3.6 18.1 1.0
OP2 Q:DA5 3.6 21.6 1.0
N B:ALA344 3.8 15.7 1.0
CA B:TRP342 4.0 15.9 1.0
N B:GLY343 4.0 15.9 1.0
N B:ILE341 4.1 15.9 1.0
N B:TRP342 4.1 16.1 1.0
CA B:SER339 4.1 20.4 1.0
O Q:HOH19 4.2 30.4 1.0
O B:HOH950 4.2 43.5 1.0
C B:ASN340 4.2 18.9 1.0
CA B:ALA344 4.2 17.1 1.0
N B:ASN340 4.4 19.2 1.0
C B:TRP342 4.4 15.3 1.0
O3' Q:DT4 4.4 19.9 1.0
CA B:ILE341 4.4 16.6 1.0
O B:HOH1043 4.5 39.6 1.0
CA B:ASN340 4.6 18.1 1.0
O B:HOH1035 4.6 51.6 1.0
N B:GLY345 4.6 17.9 1.0
CB B:SER339 4.7 20.4 1.0
O B:ASN340 4.7 17.8 1.0
CB B:ALA344 4.7 17.4 1.0
O5' Q:DA5 4.7 17.9 1.0
C B:GLY343 4.8 17.0 1.0
CA B:GLY345 4.9 18.2 1.0

Sodium binding site 6 out of 8 in 3c5g

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Sodium binding site 6 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:22.0
occ:1.00
 OD1 B:ASP429 2.1 19.6 1.0
OD2 B:ASP490 2.4 20.3 1.0
O Q:HOH16 2.4 29.5 1.0
OD1 B:ASP427 2.4 18.1 1.0
O1A B:D3T577 2.6 12.8 1.0
CG B:ASP429 3.2 21.3 1.0
CG B:ASP427 3.2 16.6 1.0
CG B:ASP490 3.3 20.2 1.0
OD2 B:ASP427 3.4 16.2 1.0
O B:HOH997 3.5 36.7 1.0
OD2 B:ASP429 3.6 18.1 1.0
PA B:D3T577 3.6 18.9 1.0
MG B:MG601 3.6 16.2 1.0
O5' B:D3T577 3.8 18.1 1.0
C5' B:D3T577 4.0 14.5 1.0
CB B:ASP490 4.0 15.4 1.0
O2A B:D3T577 4.0 16.7 1.0
C3' Q:2DT6 4.2 16.8 1.0
OD1 B:ASP490 4.2 19.8 1.0
C5' Q:2DT6 4.4 17.8 1.0
O B:HOH855 4.5 31.1 1.0
O B:HOH815 4.5 21.3 1.0
CB B:ASP429 4.5 19.7 1.0
CB B:ASP427 4.6 14.1 1.0
C4' Q:2DT6 4.6 18.5 1.0
NH2 B:ARG488 4.7 11.7 1.0
OP1 Q:2DT6 4.7 14.2 1.0
O3G B:D3T577 4.8 17.0 1.0
O B:VAL428 5.0 16.0 1.0
O3A B:D3T577 5.0 17.6 1.0

Sodium binding site 7 out of 8 in 3c5g

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Sodium binding site 7 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na806

b:30.6
occ:1.00
 O B:ILE302 2.5 25.2 1.0
O B:ILE305 2.6 20.9 1.0
OP1 E:DC3 2.8 25.5 1.0
O B:CYS300 2.8 25.3 1.0
C B:ILE302 3.3 24.2 1.0
C B:ILE305 3.6 24.0 1.0
C B:CYS300 3.7 25.9 1.0
N B:ILE305 3.8 25.6 1.0
P E:DC3 3.9 27.1 1.0
CA B:PRO303 3.9 23.3 1.0
N B:PRO303 3.9 24.0 1.0
N B:ILE302 4.0 27.4 1.0
OP2 E:DC3 4.1 29.3 1.0
N B:GLY304 4.1 21.5 1.0
CA B:ILE305 4.2 24.5 1.0
C B:SER301 4.2 27.6 1.0
CA B:ILE302 4.3 26.6 1.0
C B:PRO303 4.3 22.3 1.0
CA B:CYS300 4.4 25.2 1.0
N B:SER301 4.5 26.4 1.0
O B:SER301 4.6 27.7 1.0
CB B:ILE305 4.6 25.6 1.0
O3' E:DC2 4.7 27.6 1.0
N B:GLY306 4.7 24.1 1.0
CA B:SER301 4.7 26.5 1.0
O B:ALA299 4.7 23.0 1.0
C B:GLY304 4.9 24.8 1.0
CA B:GLY306 5.0 25.5 1.0

Sodium binding site 8 out of 8 in 3c5g

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Sodium binding site 8 out of 8 in the Structure of A Ternary Complex of the R517K Pol Lambda Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of A Ternary Complex of the R517K Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na808

b:36.8
occ:1.00
 O B:HOH1076 2.4 42.6 1.0
O B:HOH947 2.4 34.3 1.0
OE1 B:GLN400 2.6 30.0 1.0
OE1 B:GLU396 2.6 33.8 1.0
O B:HOH949 2.7 32.3 1.0
O B:CYS412 3.0 21.6 1.0
CD B:GLU396 3.3 28.7 1.0
OE2 B:GLU396 3.6 29.6 1.0
CD B:GLN400 3.8 25.7 1.0
NE2 B:GLN397 3.9 31.1 1.0
C B:CYS412 4.2 21.4 1.0
NE2 B:GLN400 4.3 25.4 1.0
CG B:GLU396 4.5 27.4 1.0
O B:HOH1024 4.6 40.5 1.0
CA B:VAL413 4.7 17.7 1.0
O B:HOH891 4.8 24.9 1.0
N B:VAL413 4.9 19.0 1.0
CG B:GLN400 5.0 25.4 1.0

Reference:

K.Bebenek, M.Garcia-Diaz, M.C.Foley, L.C.Pedersen, T.Schlick, T.A.Kunkel. Substrate-Induced Dna Strand Misalignment During Catalytic Cycling By Dna Polymerase Lambda. Embo Rep. V. 9 459 2008.
ISSN: ISSN 1469-221X
PubMed: 18369368
DOI: 10.1038/EMBOR.2008.33
Page generated: Sun Aug 17 12:55:39 2025

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