Magnesium in PDB 6e3w: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6e3w was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.588, 79.594, 55.718, 90.00, 107.54, 90.00
R / Rfree (%) 19.3 / 24.5

Other elements in 6e3w:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 6e3w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6e3w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6e3w

Go back to Magnesium Binding Sites List in 6e3w
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.8
occ:1.00
 OD1 A:ASP190 2.0 14.0 1.0
O2A A:XG4405 2.0 11.1 1.0
OD2 A:ASP192 2.0 13.2 1.0
O2G A:XG4405 2.1 12.2 1.0
O2B A:XG4405 2.1 11.3 1.0
O A:HOH530 2.2 11.5 1.0
CG A:ASP190 3.0 14.7 1.0
CG A:ASP192 3.1 14.6 1.0
PB A:XG4405 3.1 12.3 1.0
PA A:XG4405 3.2 12.7 1.0
PG A:XG4405 3.3 13.7 1.0
MG A:MG402 3.3 22.0 1.0
OD2 A:ASP190 3.5 18.1 1.0
OD1 A:ASP192 3.5 18.2 1.0
O3B A:XG4405 3.7 12.7 1.0
N3A A:XG4405 3.7 11.5 1.0
O A:ASP190 4.0 16.7 1.0
C5' A:XG4405 4.1 12.7 1.0
O A:HOH593 4.2 14.1 1.0
O1G A:XG4405 4.2 12.0 1.0
C A:ASP190 4.2 13.7 1.0
O5' A:XG4405 4.3 12.7 1.0
N A:ASP190 4.3 13.6 1.0
CB A:ASP190 4.3 14.4 1.0
OG A:SER180 4.3 17.8 1.0
O3G A:XG4405 4.4 14.9 1.0
CB A:ASP192 4.4 14.3 1.0
O1A A:XG4405 4.4 11.7 1.0
N A:SER180 4.5 18.2 1.0
CA A:ASP190 4.5 12.7 1.0
CA A:GLY179 4.6 14.9 1.0
O1B A:XG4405 4.6 11.1 1.0
O A:HOH589 4.8 29.0 1.0
N A:ASP192 4.8 13.7 1.0
O A:HOH585 4.8 22.6 1.0
N A:MET191 4.8 11.9 1.0
C A:MET191 4.9 13.7 1.0

Magnesium binding site 2 out of 2 in 6e3w

Go back to Magnesium Binding Sites List in 6e3w
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:22.0
occ:1.00
 OD1 A:ASP192 2.2 18.2 1.0
OD2 A:ASP190 2.3 18.1 1.0
O A:HOH585 2.4 22.6 1.0
O2A A:XG4405 2.4 11.1 1.0
CG A:ASP190 2.7 14.7 1.0
OD1 A:ASP190 2.8 14.0 1.0
OD2 A:ASP256 2.9 26.3 1.0
CG A:ASP192 3.1 14.6 1.0
MG A:MG401 3.3 13.8 1.0
OD2 A:ASP192 3.3 13.2 1.0
PA A:XG4405 3.5 12.7 1.0
CG A:ASP256 3.9 20.8 1.0
O1A A:XG4405 4.0 11.7 1.0
CB A:ASP190 4.0 14.4 1.0
O5' A:XG4405 4.1 12.7 1.0
C5' A:XG4405 4.2 12.7 1.0
O3' P:DA10 4.3 37.5 1.0
C3' P:DA10 4.4 28.3 1.0
O A:MET191 4.5 15.9 1.0
CB A:ASP192 4.5 14.3 1.0
CB A:ASP256 4.5 18.0 1.0
O2G A:XG4405 4.6 12.2 1.0
OD1 A:ASP256 4.7 20.2 1.0
OP1 P:DA10 4.8 21.6 1.0
C A:MET191 4.8 13.7 1.0
C5' P:DA10 4.9 33.1 1.0
O2B A:XG4405 4.9 11.3 1.0
O5' P:DA10 4.9 32.0 1.0
NH2 A:ARG254 5.0 20.2 1.0
CA A:ASP192 5.0 14.1 1.0

Reference:

M.C.Koag, H.Jung, S.Lee. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-Oxoadenine By Human Dna Polymerases. J. Am. Chem. Soc. V. 141 4584 2019.
ISSN: ESSN 1520-5126
PubMed: 30817143
DOI: 10.1021/JACS.8B08551
Page generated: Mon Dec 14 22:37:54 2020

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