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Sodium in PDB 3c5f: Structure of A Binary Complex of the R517A Pol Lambda Mutant

Enzymatic activity of Structure of A Binary Complex of the R517A Pol Lambda Mutant

All present enzymatic activity of Structure of A Binary Complex of the R517A Pol Lambda Mutant:
2.7.7.7;

Protein crystallography data

The structure of Structure of A Binary Complex of the R517A Pol Lambda Mutant, PDB code: 3c5f 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 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.237, 151.884, 85.635, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Binary Complex of the R517A Pol Lambda Mutant (pdb code 3c5f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of A Binary Complex of the R517A Pol Lambda Mutant, PDB code: 3c5f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3c5f

Go back to Sodium Binding Sites List in 3c5f
Sodium binding site 1 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na800

b:39.8
occ:0.50
 O A:ILE305 2.4 31.2 0.5
O A:HOH991 2.4 43.2 0.5
O A:CYS300 2.6 30.1 0.5
O A:ILE302 2.7 31.0 0.5
OP1 D:DC3 2.8 45.9 0.5
C A:ILE305 3.4 30.6 0.5
C A:ILE302 3.5 32.3 0.5
OP2 D:DC3 3.6 46.0 0.5
P D:DC3 3.7 44.6 0.5
N A:ILE305 3.7 29.8 0.5
C A:CYS300 3.8 29.5 0.5
CA A:PRO303 3.9 33.9 0.5
N A:GLY304 4.0 30.4 0.5
CA A:ILE305 4.1 29.8 0.5
N A:PRO303 4.1 33.2 0.5
N A:ILE302 4.4 31.8 0.5
C A:PRO303 4.4 32.5 0.5
C A:SER301 4.4 32.1 0.5
N A:GLY306 4.4 31.8 0.5
CA A:CYS300 4.5 28.3 0.5
O A:SER301 4.6 35.4 0.5
O3' D:DC2 4.6 42.1 0.5
CA A:ILE302 4.6 31.6 0.5
CA A:GLY306 4.6 33.6 0.5
CB A:ILE305 4.6 29.1 0.5
C A:GLY304 4.7 30.6 0.5
N A:SER301 4.8 29.1 0.5
CA A:SER301 4.9 31.0 0.5
CA A:GLY304 5.0 29.8 0.5
O A:ALA299 5.0 29.3 0.5
O5' D:DC3 5.0 46.2 0.5

Sodium binding site 2 out of 6 in 3c5f

Go back to Sodium Binding Sites List in 3c5f
Sodium binding site 2 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:32.2
occ:0.50
 O A:ALA344 2.3 22.4 0.5
OP1 P:DA5 2.4 22.1 0.5
O P:HOH35 2.5 16.7 0.5
O A:SER339 2.6 23.9 0.5
O A:ILE341 2.7 22.3 0.5
O P:HOH179 2.7 31.6 0.5
C A:ALA344 3.3 23.6 0.5
P P:DA5 3.4 23.1 0.5
C A:SER339 3.4 22.6 0.5
C A:ILE341 3.5 21.6 0.5
OP2 P:DA5 3.5 21.9 0.5
N A:ALA344 3.6 21.4 0.5
O A:HOH826 3.7 26.2 0.5
N A:GLY343 3.9 22.6 0.5
CA A:ALA344 4.0 23.1 0.5
CA A:TRP342 4.0 21.5 0.5
CA A:SER339 4.0 23.2 0.5
N A:TRP342 4.1 20.5 0.5
N A:ILE341 4.1 20.8 0.5
C A:TRP342 4.3 22.8 0.5
C A:ASN340 4.3 23.0 0.5
O3' P:DT4 4.3 25.5 0.5
N A:GLY345 4.4 24.5 0.5
CA A:ILE341 4.4 20.9 0.5
N A:ASN340 4.4 22.4 0.5
CB A:ALA344 4.5 20.8 0.5
CB A:SER339 4.5 22.1 0.5
O P:HOH298 4.5 27.2 0.5
C A:GLY343 4.6 22.4 0.5
O5' P:DA5 4.6 21.7 0.5
CA A:GLY345 4.6 23.5 0.5
CA A:ASN340 4.7 22.1 0.5
O A:HOH946 4.7 36.4 0.5
O A:ASN340 4.8 22.1 0.5
CA A:GLY343 4.9 22.1 0.5
O A:PHE338 5.0 25.5 0.5

Sodium binding site 3 out of 6 in 3c5f

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Sodium binding site 3 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:32.2
occ:0.50
 O A:HIS530 2.7 21.6 0.5
O A:HOH1052 2.8 22.2 0.5
O A:HOH840 2.9 32.8 0.5
O A:SER497 3.0 22.3 0.5
O A:HOH819 3.0 17.8 0.5
CB A:ALA531 3.2 22.9 0.5
CA A:ALA531 3.5 23.8 0.5
O A:HOH883 3.5 30.8 0.5
CA A:GLU498 3.7 22.7 0.5
C A:HIS530 3.8 23.2 0.5
C A:SER497 3.9 23.5 0.5
OG1 A:THR553 4.0 17.0 0.5
N A:ALA531 4.1 23.7 0.5
N A:GLU498 4.2 23.6 0.5
SG A:CYS501 4.2 19.8 0.5
O A:HOH914 4.2 24.3 0.5
CG A:GLU498 4.3 23.4 0.5
CB A:GLU498 4.3 21.9 0.5
CG1 A:VAL550 4.6 23.2 0.5
O A:HOH954 4.6 36.0 0.5
C A:GLU498 4.6 22.3 0.5
C A:ALA531 4.7 24.4 0.5
CB A:CYS501 4.7 17.5 0.5
N A:LEU532 4.8 24.0 0.5
O A:GLU498 4.8 23.7 0.5
O A:HOH822 4.9 19.5 0.5

Sodium binding site 4 out of 6 in 3c5f

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Sodium binding site 4 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:26.1
occ:0.50
 O B:HOH844 2.3 25.9 0.5
O B:ALA344 2.3 26.0 0.5
OP1 Q:DA5 2.3 25.6 0.5
O Q:HOH1066 2.4 28.5 0.5
O B:SER339 2.5 21.2 0.5
O B:ILE341 2.6 20.2 0.5
P Q:DA5 3.4 21.9 0.5
C B:SER339 3.4 22.5 0.5
C B:ALA344 3.4 26.5 0.5
O B:HOH814 3.5 29.2 0.5
C B:ILE341 3.5 21.2 0.5
OP2 Q:DA5 3.6 25.9 0.5
N B:ALA344 3.8 23.9 0.5
N B:GLY343 4.0 25.3 0.5
CA B:TRP342 4.0 22.5 0.5
CA B:SER339 4.0 23.1 0.5
N B:ILE341 4.1 22.7 0.5
N B:TRP342 4.1 21.1 0.5
CA B:ALA344 4.2 24.7 0.5
O B:HOH930 4.2 35.5 0.5
C B:TRP342 4.3 23.7 0.5
O3' Q:DT4 4.4 27.4 0.5
C B:ASN340 4.4 23.9 0.5
N B:ASN340 4.4 23.5 0.5
N B:GLY345 4.4 27.4 0.5
CB B:SER339 4.5 23.2 0.5
CA B:ILE341 4.5 21.4 0.5
O5' Q:DA5 4.5 23.9 0.5
CA B:GLY345 4.6 27.5 0.5
CA B:ASN340 4.7 23.9 0.5
C B:GLY343 4.7 25.2 0.5
CB B:ALA344 4.7 22.5 0.5
O B:HOH839 4.7 41.1 0.5
CA B:GLY343 4.9 25.0 0.5
O B:ASN340 4.9 23.9 0.5

Sodium binding site 5 out of 6 in 3c5f

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Sodium binding site 5 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:30.0
occ:0.50
 O B:HIS530 2.8 22.3 0.5
O B:HOH808 2.9 15.9 0.5
O B:HOH840 2.9 20.1 0.5
CB B:ALA531 3.0 21.9 0.5
O B:SER497 3.1 22.3 0.5
O B:HOH816 3.2 21.8 0.5
CA B:ALA531 3.4 22.8 0.5
O B:HOH834 3.5 30.4 0.5
C B:HIS530 3.8 23.0 0.5
CA B:GLU498 3.8 22.7 0.5
C B:SER497 4.0 21.9 0.5
N B:ALA531 4.1 23.1 0.5
OG1 B:THR553 4.1 21.4 0.5
O B:HOH975 4.2 33.0 0.5
CG1 B:VAL550 4.3 25.9 0.5
N B:GLU498 4.3 21.6 0.5
SG B:CYS501 4.4 18.1 0.5
CB B:GLU498 4.4 24.8 0.5
CG B:GLU498 4.4 24.1 0.5
C B:ALA531 4.7 23.5 0.5
N B:LEU532 4.7 23.2 0.5
C B:GLU498 4.8 22.4 0.5
CB B:CYS501 4.9 16.4 0.5

Sodium binding site 6 out of 6 in 3c5f

Go back to Sodium Binding Sites List in 3c5f
Sodium binding site 6 out of 6 in the Structure of A Binary Complex of the R517A 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 Binary Complex of the R517A Pol Lambda Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na805

b:50.6
occ:0.50
 O B:ILE305 2.4 30.5 0.5
O B:CYS300 2.6 34.2 0.5
O B:ILE302 2.7 33.7 0.5
OP1 E:DC3 3.0 48.6 0.5
OP2 E:DC3 3.4 46.1 0.5
C B:ILE305 3.4 31.6 0.5
C B:ILE302 3.5 34.4 0.5
C B:CYS300 3.5 32.1 0.5
P E:DC3 3.7 48.1 0.5
N B:ILE305 3.9 32.3 0.5
N B:ILE302 4.0 35.1 0.5
CA B:ILE305 4.1 31.1 0.5
C B:SER301 4.1 34.7 0.5
CA B:CYS300 4.2 32.0 0.5
N B:PRO303 4.2 34.5 0.5
CA B:PRO303 4.3 35.0 0.5
CA B:ILE302 4.3 34.1 0.5
N B:SER301 4.4 33.8 0.5
N B:GLY306 4.4 31.2 0.5
N B:GLY304 4.5 35.0 0.5
O B:SER301 4.5 34.3 0.5
CB B:ILE305 4.6 30.5 0.5
O B:ALA299 4.6 26.1 0.5
CA B:SER301 4.6 33.7 0.5
CA B:GLY306 4.7 30.9 0.5
O3' E:DC2 4.7 45.3 0.5
C B:PRO303 4.7 35.0 0.5
O5' E:DC3 4.9 47.5 0.5

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 12:55:32 2025

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