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Arsenic 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
Chlorine (Cl) 1 atom
Sodium (Na) 8 atoms

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 3 binding sites of Arsenic 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 Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 2gws

Go back to Arsenic Binding Sites List in 2gws
Arsenic binding site 1 out of 3 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 Arsenic with other atoms in the As 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
D:As949

b:0.5
occ:1.00
AS D:CAC949 0.0 0.5 1.0
O2 D:CAC949 1.6 0.1 1.0
O1 D:CAC949 1.7 0.2 1.0
C2 D:CAC949 1.8 0.2 1.0
C1 D:CAC949 2.0 0.9 1.0
O6 D:DG4 3.9 43.2 1.0
N7 D:DG4 4.1 38.7 1.0
O A:HOH1064 4.5 37.0 1.0
C6 D:DG4 4.6 38.5 1.0
C5 D:DG4 4.7 38.7 1.0

Arsenic binding site 2 out of 3 in 2gws

Go back to Arsenic Binding Sites List in 2gws
Arsenic binding site 2 out of 3 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 Arsenic with other atoms in the As 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
H:As950

b:0.6
occ:1.00
AS H:CAC950 0.0 0.6 1.0
O2 H:CAC950 1.6 0.7 1.0
O1 H:CAC950 1.7 0.3 1.0
C2 H:CAC950 1.8 0.5 1.0
C1 H:CAC950 2.0 0.3 1.0
O6 L:DG4 4.5 56.7 1.0
O6 H:DG4 4.6 50.3 1.0
N7 H:DG4 4.7 52.0 1.0
N7 L:DG4 4.7 57.8 1.0
O L:HOH56 4.8 39.7 1.0
C5 L:DC3 4.9 55.8 1.0
O I:HOH953 5.0 36.0 1.0

Arsenic binding site 3 out of 3 in 2gws

Go back to Arsenic Binding Sites List in 2gws
Arsenic binding site 3 out of 3 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 Arsenic with other atoms in the As 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
J:As951

b:0.2
occ:1.00
AS J:CAC951 0.0 0.2 1.0
O2 J:CAC951 1.6 0.1 1.0
O1 J:CAC951 1.7 0.9 1.0
C2 J:CAC951 1.8 0.0 1.0
C1 J:CAC951 2.0 0.8 1.0
N7 J:DG2 3.9 56.6 1.0
O6 J:DG3 4.1 50.8 1.0
O6 J:DG2 4.1 54.5 1.0
O L:HOH610 4.2 41.9 1.0
N4 L:DC2 4.5 51.5 1.0
C5 J:DG2 4.6 55.6 1.0
C6 J:DG2 4.7 54.3 1.0
O6 L:DG1 4.7 48.9 1.0
O J:HOH459 4.8 32.9 1.0
C8 J:DG2 4.9 57.6 1.0
C5 J:DC1 5.0 60.9 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 Oct 27 16:48:50 2020

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