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Sodium in PDB 2gws: Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

Enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus, PDB code: 2gws was solved by M.Garcia-Diaz, A.J.Picher, K.Bebenek, L.C.Pedersen, T.A.Kunkel, L.Blanco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 192.374, 98.268, 104.960, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.3

Other elements in 2gws:

The structure of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Arsenic (As) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus (pdb code 2gws). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus, PDB code: 2gws:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2gws

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Sodium binding site 1 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


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 Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na944

b:43.1
occ:1.00
O T:HOH635 2.1 44.3 1.0
O T:HOH636 2.2 39.1 1.0
O T:HOH633 2.2 38.6 1.0
O D:HOH634 2.3 44.9 1.0
O T:HOH631 2.3 29.7 1.0
O T:HOH632 2.7 35.9 1.0
O6 D:DG1 3.9 34.8 1.0
O6 T:DG3 4.0 24.9 1.0
N4 D:DC2 4.2 24.2 1.0
N7 T:DG2 4.5 35.0 1.0
O6 T:DG2 4.5 28.4 1.0
O T:HOH124 4.7 28.1 1.0
C6 D:DG1 4.9 30.0 1.0

Sodium binding site 2 out of 8 in 2gws

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Sodium binding site 2 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


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 Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na945

b:39.4
occ:1.00
O T:HOH507 2.2 46.4 1.0
O T:HOH568 2.4 49.3 1.0
O6 P:DG6 2.5 27.1 1.0
O P:HOH282 2.5 37.0 1.0
O6 T:DG6 2.7 26.2 1.0
O6 P:DG5 2.8 17.6 1.0
C6 P:DG6 3.5 25.8 1.0
C6 P:DG5 3.6 18.5 1.0
C6 T:DG6 3.7 22.2 1.0
N1 P:DG6 3.8 25.1 1.0
O T:HOH434 3.9 32.4 1.0
N1 T:DG6 4.0 22.6 1.0
N7 P:DG5 4.1 19.8 1.0
C5 P:DG5 4.1 19.5 1.0
O T:HOH455 4.1 33.5 1.0
O P:HOH506 4.2 45.6 1.0
N4 T:DC7 4.2 21.7 1.0
N1 P:DG5 4.6 15.3 1.0
C5 P:DG6 4.8 23.3 1.0
O P:HOH144 4.9 43.5 1.0
C5 T:DG6 5.0 23.8 1.0

Sodium binding site 3 out of 8 in 2gws

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Sodium binding site 3 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


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 Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Na948

b:53.3
occ:1.00
O Q:HOH805 2.4 47.5 1.0
O N:HOH2834 2.5 40.7 1.0
O N:HOH2835 2.5 52.0 1.0
O Q:HOH416 3.1 37.2 1.0
O6 Q:DG1 3.8 29.4 1.0
N4 Q:DC2 4.0 29.2 1.0
O6 N:DG3 4.1 27.8 1.0
O6 N:DG2 4.6 38.1 1.0
O N:HOH2811 4.6 41.7 1.0
C6 Q:DG1 4.6 26.7 1.0
N7 Q:DG1 4.7 30.3 1.0
O Q:HOH435 4.7 38.8 1.0

Sodium binding site 4 out of 8 in 2gws

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Sodium binding site 4 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na940

b:25.5
occ:1.00
O A:SER339 2.3 28.7 1.0
O P:HOH423 2.4 27.8 1.0
OP1 P:DG5 2.4 19.0 1.0
O A:ALA344 2.5 25.9 1.0
O A:ILE341 2.7 26.1 1.0
O A:HOH959 2.8 33.4 1.0
C A:SER339 3.4 30.1 1.0
O A:HOH1074 3.4 43.6 1.0
C A:ALA344 3.5 23.8 1.0
P P:DG5 3.5 23.9 1.0
C A:ILE341 3.7 28.4 1.0
OP2 P:DG5 3.7 20.7 1.0
N A:ALA344 3.8 24.4 1.0
CA A:SER339 4.0 32.0 1.0
N A:GLY343 4.2 25.5 1.0
N A:ILE341 4.2 26.6 1.0
CA A:ALA344 4.2 24.7 1.0
CA A:TRP342 4.4 26.8 1.0
N A:TRP342 4.4 27.7 1.0
CB A:SER339 4.4 29.9 1.0
N A:GLY345 4.4 25.2 1.0
N A:ASN340 4.4 28.2 1.0
C A:ASN340 4.4 27.9 1.0
O3' P:DC4 4.5 21.6 1.0
CA A:ILE341 4.6 27.2 1.0
CA A:GLY345 4.6 24.7 1.0
C A:TRP342 4.6 26.4 1.0
O5' P:DG5 4.7 21.7 1.0
CA A:ASN340 4.7 27.9 1.0
CB A:ALA344 4.8 22.8 1.0
C A:GLY343 4.8 25.0 1.0
O P:HOH273 4.9 35.0 1.0
O A:ASN340 5.0 29.1 1.0

Sodium binding site 5 out of 8 in 2gws

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Sodium binding site 5 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na941

b:44.8
occ:1.00
O E:SER339 2.3 54.6 1.0
OP1 G:DG5 2.4 48.6 1.0
O E:ILE341 2.5 51.1 1.0
O E:ALA344 2.5 41.1 1.0
O E:HOH2821 3.0 47.6 1.0
O G:HOH262 3.0 36.2 1.0
C E:SER339 3.3 55.1 1.0
C E:ILE341 3.3 52.7 1.0
C E:ALA344 3.4 42.9 1.0
N E:ALA344 3.6 45.1 1.0
P G:DG5 3.6 48.4 1.0
N E:ILE341 3.9 52.9 1.0
N E:GLY343 3.9 49.1 1.0
CA E:SER339 3.9 55.6 1.0
OP2 G:DG5 3.9 46.6 1.0
N E:TRP342 4.0 51.4 1.0
CA E:ALA344 4.0 44.1 1.0
CA E:TRP342 4.0 51.5 1.0
C E:ASN340 4.1 54.5 1.0
N E:ASN340 4.2 54.5 1.0
CA E:ILE341 4.2 52.6 1.0
C E:TRP342 4.3 50.7 1.0
CB E:ALA344 4.4 43.0 1.0
N E:GLY345 4.4 43.1 1.0
CA E:ASN340 4.5 54.4 1.0
CB E:SER339 4.5 54.5 1.0
C E:GLY343 4.6 46.3 1.0
O3' G:DC4 4.6 47.0 1.0
O E:ASN340 4.7 56.2 1.0
O5' G:DG5 4.7 46.8 1.0
CA E:GLY345 4.8 43.9 1.0
CA E:GLY343 4.8 47.0 1.0
O E:PHE338 4.9 54.2 1.0

Sodium binding site 6 out of 8 in 2gws

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Sodium binding site 6 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na942

b:41.2
occ:1.00
O I:SER339 2.2 42.5 1.0
O I:ILE341 2.4 39.5 1.0
OP1 K:DG5 2.5 38.1 1.0
O I:ALA344 2.5 39.5 1.0
O K:HOH648 2.6 36.9 1.0
O I:HOH989 3.3 50.4 1.0
C I:SER339 3.3 43.2 1.0
C I:ILE341 3.3 39.1 1.0
C I:ALA344 3.6 40.2 1.0
P K:DG5 3.7 38.0 1.0
N I:ALA344 3.9 38.7 1.0
N I:ILE341 3.9 38.9 1.0
CA I:SER339 4.0 45.3 1.0
OP2 K:DG5 4.0 38.2 1.0
CA I:TRP342 4.0 39.1 1.0
N I:TRP342 4.0 38.9 1.0
N I:GLY343 4.0 38.2 1.0
C I:ASN340 4.2 40.3 1.0
CA I:ALA344 4.3 39.9 1.0
CA I:ILE341 4.3 38.3 1.0
N I:ASN340 4.3 40.4 1.0
C I:TRP342 4.4 39.7 1.0
CA I:ASN340 4.5 40.6 1.0
CB I:ALA344 4.7 39.9 1.0
O I:ASN340 4.7 42.1 1.0
N I:GLY345 4.7 41.1 1.0
CB I:SER339 4.7 46.2 1.0
O5' K:DG5 4.7 38.1 1.0
O3' K:DC4 4.8 38.4 1.0
O I:PHE338 4.8 43.1 1.0
C I:GLY343 4.8 39.5 1.0
CA I:GLY345 4.9 40.0 1.0

Sodium binding site 7 out of 8 in 2gws

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Sodium binding site 7 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na943

b:25.0
occ:1.00
OP1 R:DG5 2.3 17.9 1.0
O M:SER339 2.4 23.3 1.0
O M:ALA344 2.4 24.3 1.0
O R:HOH33 2.4 20.3 1.0
O M:ILE341 2.6 22.0 1.0
O M:HOH1033 2.7 29.1 1.0
C M:ALA344 3.4 22.9 1.0
C M:SER339 3.5 24.6 1.0
P R:DG5 3.5 21.6 1.0
C M:ILE341 3.5 21.2 1.0
O M:HOH1046 3.6 32.8 1.0
N M:ALA344 3.6 22.0 1.0
OP2 R:DG5 3.8 17.3 1.0
N M:GLY343 3.9 21.3 1.0
CA M:TRP342 4.0 21.3 1.0
CA M:ALA344 4.1 22.6 1.0
N M:TRP342 4.1 20.7 1.0
N M:ILE341 4.1 20.7 1.0
CA M:SER339 4.2 25.3 1.0
O M:HOH1183 4.2 53.1 1.0
C M:TRP342 4.3 21.6 1.0
C M:ASN340 4.3 24.7 1.0
N M:ASN340 4.5 25.0 1.0
N M:GLY345 4.5 23.2 1.0
CA M:ILE341 4.5 21.6 1.0
CB M:ALA344 4.5 21.2 1.0
O3' R:DC4 4.5 20.7 1.0
O5' R:DG5 4.5 14.7 1.0
C M:GLY343 4.6 23.2 1.0
CA M:ASN340 4.6 24.8 1.0
CB M:SER339 4.7 24.1 1.0
CA M:GLY345 4.7 20.0 1.0
CA M:GLY343 4.8 21.7 1.0
O M:ASN340 4.8 27.2 1.0

Sodium binding site 8 out of 8 in 2gws

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Sodium binding site 8 out of 8 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na947

b:43.2
occ:1.00
O M:HOH1033 2.9 29.1 1.0
O M:ASN340 3.6 27.2 1.0
O M:HOH997 4.3 25.5 1.0
O M:HOH1183 4.3 53.1 1.0
C M:ASN340 4.4 24.7 1.0
O M:PHE383 4.6 23.4 1.0
O M:HOH1046 4.8 32.8 1.0
CA M:ASN340 4.8 24.8 1.0
CD2 M:LEU384 4.9 29.9 1.0
N M:TRP342 4.9 20.7 1.0

Reference:

A.J.Picher, M.Garcia-Diaz, K.Bebenek, L.C.Pedersen, T.A.Kunkel, L.Blanco. Promiscuous Mismatch Extension By Human Dna Polymerase Lambda. Nucleic Acids Res. V. 34 3259 2006.
ISSN: ISSN 0305-1048
PubMed: 16807316
DOI: 10.1093/NAR/GKL377
Page generated: Tue Dec 15 05:50:18 2020

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