Magnesium in PDB 6w2m: Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da

Enzymatic activity of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da

All present enzymatic activity of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da:
2.7.7.7;

Protein crystallography data

The structure of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da, PDB code: 6w2m was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.93 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.751, 80.462, 55.612, 90.00, 107.75, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 6w2m:

The structure of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da (pdb code 6w2m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da, PDB code: 6w2m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6w2m

Go back to Magnesium Binding Sites List in 6w2m
Magnesium binding site 1 out of 2 in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:10.8
occ:1.00
 OD1 A:ASP192 2.0 8.3 1.0
OD2 A:ASP256 2.1 9.2 1.0
OD2 A:ASP190 2.1 10.8 1.0
O A:HOH537 2.1 10.9 1.0
O A:HOH638 2.2 8.1 1.0
O1A A:SFV407 2.4 9.2 1.0
CG A:ASP190 3.1 9.4 1.0
CG A:ASP192 3.1 10.3 1.0
CG A:ASP256 3.2 10.4 1.0
OD1 A:ASP190 3.4 9.8 1.0
PA A:SFV407 3.4 12.6 1.0
OD2 A:ASP192 3.5 7.6 1.0
MG A:MG402 3.6 9.9 1.0
O2A A:SFV407 3.7 11.3 1.0
O5' A:SFV407 3.8 12.1 1.0
CB A:ASP256 3.8 10.3 1.0
O A:HOH672 4.1 17.3 1.0
C5' A:SFV407 4.2 11.4 1.0
OD1 A:ASP256 4.2 10.6 1.0
CB A:ASP192 4.3 9.9 1.0
O A:HOH773 4.3 17.9 1.0
CB A:ASP190 4.4 9.7 1.0
OP1 P:DA10 4.5 15.5 1.0
O3G A:SFV407 4.6 11.7 1.0
O A:HOH680 4.8 11.9 1.0
O3A A:SFV407 4.9 11.6 1.0
CA A:ASP192 5.0 13.0 1.0
NH2 A:ARG254 5.0 15.0 1.0

Magnesium binding site 2 out of 2 in 6w2m

Go back to Magnesium Binding Sites List in 6w2m
Magnesium binding site 2 out of 2 in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:9.9
occ:1.00
 OD1 A:ASP190 2.0 9.8 1.0
O1A A:SFV407 2.1 9.2 1.0
O3G A:SFV407 2.1 11.7 1.0
O2B A:SFV407 2.1 10.4 1.0
OD2 A:ASP192 2.1 7.6 1.0
O A:HOH595 2.3 10.6 1.0
CG A:ASP190 3.0 9.4 1.0
CG A:ASP192 3.0 10.3 1.0
PB A:SFV407 3.2 11.1 1.0
PA A:SFV407 3.2 12.6 1.0
PG A:SFV407 3.3 15.2 1.0
OD1 A:ASP192 3.4 8.3 1.0
OD2 A:ASP190 3.5 10.8 1.0
O3A A:SFV407 3.5 11.6 1.0
MG A:MG401 3.6 10.8 1.0
O2G A:SFV407 3.7 11.9 1.0
C3B A:SFV407 3.9 13.4 1.0
O A:ASP190 4.1 11.9 1.0
C5' A:SFV407 4.2 11.4 1.0
O2A A:SFV407 4.3 11.3 1.0
O5' A:SFV407 4.3 12.1 1.0
CB A:ASP190 4.3 9.7 1.0
C A:ASP190 4.4 10.1 1.0
O A:HOH656 4.4 10.9 1.0
N A:ASP190 4.4 6.9 1.0
CB A:ASP192 4.4 9.9 1.0
O A:HOH694 4.4 13.2 1.0
O1B A:SFV407 4.5 12.7 1.0
O1G A:SFV407 4.5 14.6 1.0
CA A:GLY179 4.5 10.8 1.0
N A:SER180 4.6 10.8 1.0
CA A:ASP190 4.6 9.9 1.0
O A:HOH537 4.6 10.9 1.0
OG A:SER180 4.7 14.9 1.0
N A:ASP192 4.8 10.6 1.0
O P:HOH114 5.0 22.0 1.0
N A:MET191 5.0 9.1 1.0

Reference:

V.K.Batra, S.H.Wilson. Structure of A Dna Polymerase Abortive Complex with the 8OG:Da Base Pair at the Primer Terminus. Commun Biol V. 3 348 2020.
ISSN: ESSN 2399-3642
PubMed: 32620932
DOI: 10.1038/S42003-020-1080-4
Page generated: Tue Dec 15 01:31:33 2020

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