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Magnesium in PDB 3g6x: Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position

Enzymatic activity of Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position

All present enzymatic activity of Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position, PDB code: 3g6x was solved by D.T.Nair, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.08
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.114, 98.114, 202.823, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position (pdb code 3g6x). 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 Iota:Dna:Dgtp with An Abasic Site at the Templating Position, PDB code: 3g6x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3g6x

Go back to Magnesium Binding Sites List in 3g6x
Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position


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 Iota:Dna:Dgtp with An Abasic Site at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg871

b:2.8
occ:1.00
O1A A:DGT875 2.1 13.4 1.0
OD1 A:ASP126 2.2 28.4 1.0
O A:LEU35 2.4 17.5 1.0
O2B A:DGT875 2.4 8.9 1.0
OD2 A:ASP34 2.4 21.1 1.0
O1G A:DGT875 2.5 14.5 1.0
CG A:ASP126 2.9 23.6 1.0
OD2 A:ASP126 3.0 25.2 1.0
PB A:DGT875 3.4 16.0 1.0
PA A:DGT875 3.5 16.2 1.0
C A:LEU35 3.5 16.5 1.0
CG A:ASP34 3.6 20.5 1.0
PG A:DGT875 3.7 14.8 1.0
N A:LEU35 3.8 15.3 1.0
O3A A:DGT875 3.8 13.3 1.0
MG A:MG872 3.8 59.7 1.0
O A:HOH429 3.9 22.8 1.0
O3B A:DGT875 4.0 18.2 1.0
C5' A:DGT875 4.2 17.7 1.0
OD1 A:ASP34 4.2 17.9 1.0
C A:ASP34 4.2 17.3 1.0
CA A:LEU35 4.2 17.4 1.0
O3G A:DGT875 4.3 13.5 1.0
O5' A:DGT875 4.4 18.8 1.0
CB A:ASP126 4.4 19.4 1.0
O A:HOH478 4.4 29.0 1.0
N A:ASP36 4.6 16.0 1.0
O2A A:DGT875 4.7 16.1 1.0
O A:ASP126 4.7 16.8 1.0
CA A:ASP34 4.7 16.3 1.0
O A:ASP34 4.7 16.9 1.0
CB A:ASP34 4.7 16.9 1.0
N A:CYS37 4.7 13.8 1.0
O1B A:DGT875 4.8 17.6 1.0
CB A:LEU35 4.9 16.8 1.0
CA A:ASP36 4.9 16.1 1.0
N A:PHE38 4.9 14.8 1.0
CB A:PHE38 4.9 13.6 1.0
C A:ASP36 4.9 16.2 1.0
O2G A:DGT875 4.9 13.6 1.0

Magnesium binding site 2 out of 2 in 3g6x

Go back to Magnesium Binding Sites List in 3g6x
Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Iota:Dna:Dgtp with An Abasic Site at the Templating Position


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 Iota:Dna:Dgtp with An Abasic Site at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg872

b:59.7
occ:1.00
OE2 A:GLU127 2.3 21.3 1.0
O A:HOH478 2.7 29.0 1.0
OD1 A:ASP34 2.8 17.9 1.0
O1A A:DGT875 2.8 13.4 1.0
CD A:GLU127 3.3 20.4 1.0
OD2 A:ASP34 3.3 21.1 1.0
CG A:ASP34 3.4 20.5 1.0
O2A A:DGT875 3.5 16.1 1.0
PA A:DGT875 3.5 16.2 1.0
C3' P:DOC873 3.7 17.6 1.0
CG A:GLU127 3.8 14.2 1.0
MG A:MG871 3.8 2.8 1.0
O1G A:DGT875 4.1 14.5 1.0
OD2 A:ASP126 4.3 25.2 1.0
OE1 A:GLU127 4.3 18.9 1.0
NZ A:LYS207 4.6 31.5 1.0
C4' P:DOC873 4.7 18.3 1.0
O3A A:DGT875 4.7 13.3 1.0
O5' A:DGT875 4.7 18.8 1.0
C5' P:DOC873 4.7 17.9 1.0
CB A:ASP34 4.8 16.9 1.0
C2' P:DOC873 4.9 21.0 1.0
O A:HOH433 5.0 19.4 1.0

Reference:

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Dna Synthesis Across An Abasic Lesion By Human Dna Polymerase Iota. Structure V. 17 530 2009.
ISSN: ISSN 0969-2126
PubMed: 19368886
DOI: 10.1016/J.STR.2009.02.015
Page generated: Mon Dec 14 08:10:22 2020

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