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Magnesium in PDB 3hw8: Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site

Enzymatic activity of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site, PDB code: 3hw8 was solved by M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.32 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.249, 68.386, 137.108, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 23.3

Other elements in 3hw8:

The structure of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site (pdb code 3hw8). 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 Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site, PDB code: 3hw8:

Magnesium binding site 1 out of 1 in 3hw8

Go back to Magnesium Binding Sites List in 3hw8
Magnesium binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Lambda of A Two Nucleotide Gapped Dna Substrate with A C in the Scrunch Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg576

b:24.5
occ:1.00
OD2 A:ASP427 2.0 24.8 1.0
O A:HOH582 2.1 25.9 1.0
O1B A:D3T581 2.1 21.6 1.0
OD2 A:ASP429 2.1 24.7 1.0
O1A A:D3T581 2.1 19.3 1.0
O3G A:D3T581 2.2 21.6 1.0
CG A:ASP429 3.1 25.3 1.0
PB A:D3T581 3.1 24.2 1.0
CG A:ASP427 3.1 28.1 1.0
PG A:D3T581 3.3 25.6 1.0
PA A:D3T581 3.3 23.1 1.0
OD1 A:ASP429 3.4 25.0 1.0
O3A A:D3T581 3.5 21.5 1.0
O3B A:D3T581 3.5 25.1 1.0
NA A:NA577 3.6 25.9 1.0
OD1 A:ASP427 3.6 30.1 1.0
O1G A:D3T581 3.8 25.5 1.0
O A:HOH93 4.0 33.4 1.0
O A:ASP427 4.0 23.9 1.0
O A:HOH32 4.1 25.1 1.0
OG A:SER417 4.1 26.5 1.0
N A:ASP427 4.2 24.5 1.0
C5' A:D3T581 4.2 23.1 1.0
C A:ASP427 4.2 24.4 1.0
O5' A:D3T581 4.2 23.6 1.0
N A:SER417 4.3 26.4 1.0
CB A:ASP427 4.4 26.3 1.0
CB A:ASP429 4.4 22.3 1.0
O2A A:D3T581 4.5 25.9 1.0
O2B A:D3T581 4.5 22.1 1.0
O2G A:D3T581 4.5 27.1 1.0
CA A:GLY416 4.5 27.4 1.0
CA A:ASP427 4.5 25.0 1.0
N A:ASP429 4.7 25.2 1.0
N A:VAL428 4.8 24.4 1.0
O C:HOH17 4.9 22.2 1.0
CB A:SER417 4.9 27.7 1.0
C A:GLY416 5.0 27.6 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel. Scrunching Durning Dna Repair Synthesis To Be Published.
Page generated: Mon Dec 14 08:14:54 2020

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