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Magnesium in PDB 2bcs: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp

Enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp

All present enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp, PDB code: 2bcs was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, 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) 26.90 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.968, 62.542, 140.817, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.1

Other elements in 2bcs:

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp (pdb code 2bcs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp, PDB code: 2bcs:

Magnesium binding site 1 out of 1 in 2bcs

Go back to Magnesium Binding Sites List in 2bcs
Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg900

b:33.9
occ:1.00
 OD1 A:ASP427 2.2 35.3 1.0
O12 A:PPV901 2.3 35.9 1.0
OD2 A:ASP429 2.4 26.8 1.0
O A:HOH1006 2.5 42.2 1.0
OP1 P:DG7 2.7 23.9 1.0
O31 A:PPV901 2.9 44.6 1.0
O22 A:PPV901 2.9 40.5 1.0
P2 A:PPV901 3.0 34.6 1.0
CG A:ASP427 3.2 33.4 1.0
CG A:ASP429 3.3 30.2 1.0
OD1 A:ASP429 3.5 26.3 1.0
OD2 A:ASP427 3.6 33.5 1.0
P1 A:PPV901 3.7 48.0 1.0
OPP A:PPV901 3.7 42.1 1.0
O11 A:PPV901 3.9 43.4 1.0
P P:DG7 3.9 25.3 1.0
O A:ASP427 4.0 35.7 1.0
C5' P:DG7 4.2 26.2 1.0
O5' P:DG7 4.2 26.0 1.0
OG A:SER417 4.3 29.6 1.0
N A:ASP427 4.3 32.7 1.0
C A:ASP427 4.3 34.1 1.0
O P:HOH35 4.4 48.9 1.0
N A:SER417 4.4 32.1 1.0
CA A:GLY416 4.4 31.5 1.0
CB A:ASP427 4.5 31.1 1.0
O A:HOH909 4.5 26.4 1.0
O32 A:PPV901 4.5 38.7 1.0
OP2 P:DG7 4.6 27.8 1.0
CB A:ASP429 4.6 30.8 1.0
CA A:ASP427 4.7 33.3 1.0
N A:ASP429 4.9 32.3 1.0
C A:GLY416 4.9 32.4 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Structural Analysis of Strand Misalignment During Dna Synthesis By A Human Dna Polymerase Cell(Cambridge,Mass.) V. 124 331 2006.
ISSN: ISSN 0092-8674
PubMed: 16439207
DOI: 10.1016/J.CELL.2005.10.039
Page generated: Tue Aug 13 21:50:03 2024

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