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Magnesium in PDB 3rjf: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp):
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.17 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.550, 79.810, 55.690, 90.00, 107.88, 90.00
R / Rfree (%) 19.3 / 25.6

Other elements in 3rjf:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) (pdb code 3rjf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3rjf

Go back to Magnesium Binding Sites List in 3rjf
Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)


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 Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:17.1
occ:1.00
OD1 A:ASP190 1.9 15.1 1.0
O2B A:F2A338 1.9 13.2 1.0
O3G A:F2A338 2.0 21.4 1.0
O A:HOH472 2.1 25.6 1.0
O1A A:F2A338 2.2 17.8 1.0
OD2 A:ASP192 2.2 25.4 1.0
PB A:F2A338 2.9 18.7 1.0
CG A:ASP190 3.0 20.4 1.0
PG A:F2A338 3.1 24.9 1.0
CG A:ASP192 3.3 27.0 1.0
PA A:F2A338 3.3 21.4 1.0
O3B A:F2A338 3.3 25.6 1.0
C3A A:F2A338 3.3 20.6 1.0
OD2 A:ASP190 3.5 16.8 1.0
O2G A:F2A338 3.5 22.2 1.0
MG A:MG340 3.6 18.3 1.0
OD1 A:ASP192 3.7 27.2 1.0
O A:ASP190 3.9 20.9 1.0
C5' A:F2A338 4.0 21.4 1.0
O A:HOH378 4.0 22.6 1.0
O5' A:F2A338 4.1 21.7 1.0
OG A:SER180 4.2 20.4 1.0
O1G A:F2A338 4.3 24.2 1.0
CB A:ASP190 4.3 18.3 1.0
C A:ASP190 4.3 21.6 1.0
N A:ASP190 4.3 19.9 1.0
O1B A:F2A338 4.3 21.4 1.0
N A:SER180 4.4 20.8 1.0
O A:HOH350 4.4 14.2 1.0
CA A:GLY179 4.5 19.6 1.0
O2A A:F2A338 4.5 22.4 1.0
CA A:ASP190 4.6 20.8 1.0
CB A:ASP192 4.6 25.5 1.0
O A:HOH470 4.7 20.2 1.0
N A:ASP192 5.0 23.6 1.0

Magnesium binding site 2 out of 2 in 3rjf

Go back to Magnesium Binding Sites List in 3rjf
Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:18.3
occ:1.00
O3' P:DA10 2.0 25.1 1.0
OD1 A:ASP192 2.0 27.2 1.0
OD2 A:ASP190 2.0 16.8 1.0
O1A A:F2A338 2.1 17.8 1.0
OD2 A:ASP256 2.2 30.6 1.0
O A:HOH470 2.2 20.2 1.0
CG A:ASP192 3.0 27.0 1.0
PA A:F2A338 3.0 21.4 1.0
CG A:ASP190 3.1 20.4 1.0
C3' P:DA10 3.3 27.6 1.0
OD2 A:ASP192 3.3 25.4 1.0
CG A:ASP256 3.3 31.5 1.0
O5' A:F2A338 3.4 21.7 1.0
OD1 A:ASP190 3.4 15.1 1.0
O2A A:F2A338 3.5 22.4 1.0
MG A:MG339 3.6 17.1 1.0
C5' A:F2A338 3.9 21.4 1.0
CB A:ASP256 3.9 29.5 1.0
C4' P:DA10 4.0 25.2 1.0
C5' P:DA10 4.2 26.9 1.0
O A:HOH378 4.3 22.6 1.0
OD1 A:ASP256 4.3 35.5 1.0
CB A:ASP192 4.3 25.5 1.0
CB A:ASP190 4.4 18.3 1.0
C2' P:DA10 4.4 26.0 1.0
OP1 P:DA10 4.5 29.8 1.0
O5' P:DA10 4.6 27.6 1.0
C3A A:F2A338 4.6 20.6 1.0
O3G A:F2A338 4.7 21.4 1.0
O2B A:F2A338 4.7 13.2 1.0
O A:MET191 4.8 24.6 1.0
O P:HOH216 4.9 41.9 1.0
CA A:ASP192 4.9 23.9 1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108
Page generated: Mon Dec 14 08:44:58 2020

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