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Sodium in PDB 3pml: Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T

Enzymatic activity of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T

All present enzymatic activity of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T, PDB code: 3pml was solved by K.Bebenek, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.02 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.038, 191.570, 59.084, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 27.1

Other elements in 3pml:

The structure of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T (pdb code 3pml). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T, PDB code: 3pml:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3pml

Go back to Sodium Binding Sites List in 3pml
Sodium binding site 1 out of 3 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:35.5
occ:1.00
 O A:SER339 2.4 35.1 1.0
O H:HOH29 2.5 23.0 1.0
OP1 H:DA5 2.5 28.7 1.0
O A:ALA344 2.7 30.7 1.0
O A:ILE341 2.8 24.0 1.0
C A:SER339 3.4 34.1 1.0
O H:HOH19 3.4 44.8 1.0
C A:ILE341 3.5 27.5 1.0
P H:DA5 3.6 32.2 1.0
OP2 H:DA5 3.7 29.1 1.0
O A:HOH61 3.8 36.4 1.0
C A:ALA344 3.8 32.3 1.0
C A:ASN340 4.0 33.8 1.0
CA A:TRP342 4.1 28.5 1.0
N A:ILE341 4.1 30.9 1.0
N A:TRP342 4.1 26.8 1.0
N A:ALA344 4.2 29.8 1.0
CA A:SER339 4.2 34.9 1.0
N A:ASN340 4.2 33.7 1.0
N A:GLY343 4.3 30.2 1.0
O A:ASN340 4.3 34.3 1.0
CA A:ASN340 4.3 34.1 1.0
CA A:ILE341 4.5 29.9 1.0
CA A:ALA344 4.5 31.0 1.0
C A:TRP342 4.5 30.3 1.0
O3' H:DT4 4.6 30.7 1.0
O5' H:DA5 4.7 29.9 1.0
CB A:SER339 4.7 31.9 1.0
N A:GLY345 4.8 31.0 1.0
CB A:ALA344 4.9 31.0 1.0
O H:HOH78 4.9 39.9 1.0
CA A:GLY345 4.9 32.4 1.0

Sodium binding site 2 out of 3 in 3pml

Go back to Sodium Binding Sites List in 3pml
Sodium binding site 2 out of 3 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:73.7
occ:1.00
 O B:HOH15 2.2 47.1 1.0
O B:SER339 2.3 54.4 1.0
OP1 F:DA5 2.5 43.4 1.0
O B:ALA344 2.8 46.2 1.0
O B:ILE341 3.1 41.8 1.0
C B:SER339 3.4 53.0 1.0
P F:DA5 3.4 44.1 1.0
OP2 F:DA5 3.5 45.0 1.0
O B:HOH111 3.6 51.9 1.0
C B:ALA344 3.9 47.1 1.0
C B:ILE341 3.9 43.0 1.0
CA B:SER339 4.1 53.0 1.0
N B:ILE341 4.3 47.1 1.0
N B:ALA344 4.3 44.7 1.0
CA B:TRP342 4.3 45.4 1.0
N B:GLY343 4.3 45.5 1.0
O5' F:DA5 4.4 45.2 1.0
N B:ASN340 4.4 52.4 1.0
C B:ASN340 4.4 50.8 1.0
N B:TRP342 4.4 44.2 1.0
CB B:SER339 4.5 51.9 1.0
CA B:ASN340 4.6 52.4 1.0
CA B:ALA344 4.6 46.5 1.0
O3' F:DT4 4.7 45.3 1.0
CA B:ILE341 4.8 45.3 1.0
C B:TRP342 4.8 45.9 1.0
N B:GLY345 4.8 47.9 1.0
CA B:GLY345 4.9 49.3 1.0
O B:ASN340 4.9 52.0 1.0

Sodium binding site 3 out of 3 in 3pml

Go back to Sodium Binding Sites List in 3pml
Sodium binding site 3 out of 3 in the Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Polymerase Lambda Variant with A Dgtp Analog Opposite A Templating T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7

b:49.0
occ:1.00
 O B:HOH135 2.1 33.8 1.0
O B:CYS300 2.3 42.3 1.0
O B:ILE305 2.7 39.8 1.0
OP1 G:DC3 2.8 47.4 1.0
O B:ILE302 2.8 32.2 1.0
C B:CYS300 3.5 40.5 1.0
C B:ILE302 3.5 36.1 1.0
P G:DC3 3.8 49.6 1.0
C B:ILE305 3.9 40.5 1.0
OP2 G:DC3 3.9 49.4 1.0
N B:ILE302 4.0 35.3 1.0
C B:SER301 4.0 36.9 1.0
N B:PRO303 4.0 37.9 1.0
CA B:PRO303 4.1 38.4 1.0
O B:SER301 4.3 36.9 1.0
CA B:CYS300 4.3 41.3 1.0
N B:ILE305 4.4 40.3 1.0
CA B:ILE302 4.4 35.1 1.0
N B:SER301 4.4 39.0 1.0
CA B:SER301 4.5 38.1 1.0
N B:GLY304 4.6 38.0 1.0
CA B:ILE305 4.6 40.0 1.0
C B:PRO303 4.8 38.9 1.0
O3' G:DC2 4.8 48.4 1.0
O B:ALA299 4.9 45.8 1.0
N B:GLY306 4.9 41.3 1.0
O5' G:DC3 5.0 50.9 1.0

Reference:

K.Bebenek, L.C.Pedersen, T.A.Kunkel. Replication Infidelity Via A Mismatch with Watson-Crick Geometry. Proc.Natl.Acad.Sci.Usa V. 108 1862 2011.
ISSN: ISSN 0027-8424
PubMed: 21233421
DOI: 10.1073/PNAS.1012825108
Page generated: Mon Oct 7 12:20:44 2024

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